def read_data(filename,
dpath_pion_mp,
dpath_pion_pp,
dpath_etas_mp,
dpath_etas_pp,
plot='off'):
pion_mp = c51.fold(c51.open_data(filename, dpath_pion_mp))
pion_pp = c51.fold(c51.open_data(filename, dpath_pion_pp))
etas_mp = c51.fold(c51.open_data(filename, dpath_etas_mp))
etas_pp = c51.fold(c51.open_data(filename, dpath_etas_pp))
#pion_mp = c51.open_data(filename, dpath_pion_mp)
#pion_pp = c51.open_data(filename, dpath_pion_pp)
#etas_mp = c51.open_data(filename, dpath_etas_mp)
#etas_pp = c51.open_data(filename, dpath_etas_pp)
pion = pion_mp / pion_pp
etas = etas_mp / etas_pp
pion_gv = c51.make_gvars(pion)
etas_gv = c51.make_gvars(etas)
pion_gv = gv.gvar(np.array([pion_gv[i].mean for i in range(len(pion_gv))]),
np.array([pion_gv[j].sdev for j in range(len(pion_gv))]))
etas_gv = gv.gvar(np.array([etas_gv[i].mean for i in range(len(pion_gv))]),
np.array([etas_gv[j].sdev for j in range(len(pion_gv))]))
if plot == 'on':
x = np.arange(len(pion_gv))
c51.scatter_plot(x, pion_gv, title='pion mres')
c51.scatter_plot(x, etas_gv, title='etas mres')
else:
pass
return pion_gv, etas_gv
def read_data(filename, dpath_pion_mp, dpath_pion_pp, dpath_etas_mp, dpath_etas_pp, plot='off'):
pion_mp = c51.fold(c51.open_data(filename, dpath_pion_mp))
pion_pp = c51.fold(c51.open_data(filename, dpath_pion_pp))
etas_mp = c51.fold(c51.open_data(filename, dpath_etas_mp))
etas_pp = c51.fold(c51.open_data(filename, dpath_etas_pp))
#pion_mp = c51.open_data(filename, dpath_pion_mp)
#pion_pp = c51.open_data(filename, dpath_pion_pp)
#etas_mp = c51.open_data(filename, dpath_etas_mp)
#etas_pp = c51.open_data(filename, dpath_etas_pp)
pion = pion_mp/pion_pp
etas = etas_mp/etas_pp
pion_gv = c51.make_gvars(pion)
etas_gv = c51.make_gvars(etas)
pion_gv = gv.gvar(np.array([pion_gv[i].mean for i in range(len(pion_gv))]), np.array([pion_gv[j].sdev for j in range(len(pion_gv))]))
etas_gv = gv.gvar(np.array([etas_gv[i].mean for i in range(len(pion_gv))]), np.array([etas_gv[j].sdev for j in range(len(pion_gv))]))
if plot=='on':
x = np.arange(len(pion_gv))
c51.scatter_plot(x, pion_gv, title='pion mres')
c51.scatter_plot(x, etas_gv, title='etas mres')
else: pass
return pion_gv, etas_gv
def fit_proton(pr, p_avg, T):
# priors
priors = c51.dict_of_tuple_to_gvar(pr.priors['proton'])
# trange
trange = pr.trange['proton']
# make data
# ss + ps
p_data = np.concatenate((p_avg[:, :, 0, 0], p_avg[:, :, 3, 0]), axis=1)
# ss
#p_data = p_avg[:,:,0,0]
# ps
#p_data = p_avg[:,:,3,0]
p_data = c51.make_gvars(p_data)
# fit
grandfit = dict()
for n in range(2, 3):
fitfcn = c51.fit_function(T, nstates=n)
# ss + ps
fit = c51.fitscript_v2(trange, T, p_data, priors,
fitfcn.twopt_fitfcn_ss_ps, pr.print_fit_flag)
# ss
#fit = c51.fitscript_v2(trange, T, p_data, priors, fitfcn.twopt_fitfcn_ss, pr.print_fit_flag)
# ps
#fit = c51.fitscript_v2(trange, T, p_data, priors, fitfcn.twopt_fitfcn_ps, pr.print_fit_flag)
for k in fit.keys():
try:
grandfit[k] = np.concatenate((grandfit[k], fit[k]), axis=0)
except:
grandfit[k] = fit[k]
try:
grandfit['nstates'] = np.concatenate(
(grandfit['nstates'], n * np.ones(len(fit[k]))), axis=0)
except:
grandfit['nstates'] = n * np.ones(len(fit[k]))
return np.array([[0, grandfit]])
def mres_bs(params, meson, draws):
#Read data
mp = c51.open_data(params.data_loc['file_loc'],
params.data_loc['mres_' + meson + '_mp'])
pp = c51.open_data(params.data_loc['file_loc'],
params.data_loc['mres_' + meson + '_pp'])
T = len(pp)
mres_dat = mp / pp
# plot mres
if params.plot_data_flag == 'on':
c51.scatter_plot(np.arange(len(mres_dat[0])), c51.make_gvars(mres_dat),
meson + ' folded mres')
#Read priors
prior = params.priors[meson]
#Read trange
print params.priors
trange = params.trange['mres']
print trange
#Fit
args = ((g, trange, T, mres_dat, prior, draws) for g in range(len(draws)))
pool = multi.Pool()
p = pool.map_async(mres_fit, args)
# sort by bootstrap number
output = np.sort(np.array(p.get()), axis=0)
return output
def fit_proton(pr, p_avg, T):
# priors
priors = c51.dict_of_tuple_to_gvar(pr.priors['proton'])
# trange
trange = pr.trange['proton']
# make data
# ss + ps
p_data = np.concatenate((p_avg[:,:,0,0], p_avg[:,:,3,0]), axis=1)
# ss
#p_data = p_avg[:,:,0,0]
# ps
#p_data = p_avg[:,:,3,0]
p_data = c51.make_gvars(p_data)
# fit
grandfit = dict()
for n in range(2,3):
fitfcn = c51.fit_function(T, nstates=n)
# ss + ps
fit = c51.fitscript_v2(trange, T, p_data, priors, fitfcn.twopt_fitfcn_ss_ps, pr.print_fit_flag)
# ss
#fit = c51.fitscript_v2(trange, T, p_data, priors, fitfcn.twopt_fitfcn_ss, pr.print_fit_flag)
# ps
#fit = c51.fitscript_v2(trange, T, p_data, priors, fitfcn.twopt_fitfcn_ps, pr.print_fit_flag)
for k in fit.keys():
try:
grandfit[k] = np.concatenate((grandfit[k], fit[k]), axis=0)
except:
grandfit[k] = fit[k]
try:
grandfit['nstates'] = np.concatenate((grandfit['nstates'], n*np.ones(len(fit[k]))), axis=0)
except:
grandfit['nstates'] = n*np.ones(len(fit[k]))
return np.array([[0, grandfit]])
def mres_bs(params, meson, draws):
print 'mres', meson
ens = params.ens
ml = params.ml
ms = params.ms
loc = params.data_loc
#Read data
mp = c51.open_data(loc['file_loc'], loc['mres_' + meson + '_mp'])
pp = c51.open_data(loc['file_loc'], loc['mres_' + meson + '_pp'])
T = len(pp[0])
mres_dat = mp / pp
# plot mres
if params.plot_data_flag == 'on':
c51.scatter_plot(np.arange(len(mres_dat[0])), c51.make_gvars(mres_dat),
meson + ' mres')
plt.show()
#Read priors
prior = params.priors[meson]
#Read trange
trange = params.trange['mres']
#Fit
#args = ((g, trange, T, mres_dat, prior, draws) for g in range(len(draws)))
#pool = multi.Pool()
#p = pool.map_async(mres_fit, args)
# sort by bootstrap number
#output = np.sort(np.array(p.get()), axis=0)
result = []
for g in range(len(draws)):
mres_dat_bs = mres_dat[draws[g]]
mres_dat_bs = c51.make_gvars(mres_dat_bs)
#Randomize priors
bsp = c51.dict_of_tuple_to_gvar(
prior
) #{'mres': gv.gvar(prior[0]+prior[1]*np.random.randn(), prior[1])}
#Fit
fitfcn = c51.fit_function(T)
fit = c51.fitscript_v2(trange,
T,
mres_dat_bs,
bsp,
fitfcn.mres_fitfcn,
result_flag='off')
result.append([g, fit])
output = np.sort(np.array(result), axis=0)
return output
def decay_bs(params, meson, draws):
print 'decay ', meson
ens = params.ens
ml = params.ml
ms = params.ms
loc = params.data_loc
# read data
decay_dat = c51.fold(c51.open_data(loc['file_loc'], loc['spec_'+meson]))
decay_ss = np.squeeze(decay_dat[:,:,0,:])
decay_ps = np.squeeze(decay_dat[:,:,1,:])
T = 2*len(decay_ss[0])
if params.plot_data_flag == 'on':
# unfolded correlator data
c51.scatter_plot(np.arange(len(decay_ss[0])), c51.make_gvars(decay_ss), meson+' ss folded')
c51.scatter_plot(np.arange(len(decay_ps[0])), c51.make_gvars(decay_ps), meson+' ps folded')
# effective mass
eff = c51.effective_plots(T)
meff_ss = eff.effective_mass(c51.make_gvars(decay_ss), 1, 'cosh')
meff_ps = eff.effective_mass(c51.make_gvars(decay_ps), 1, 'cosh')
xlim = [3, len(meff_ss)-2]
ylim = c51.find_yrange(meff_ss, xlim[0], xlim[1])
c51.scatter_plot(np.arange(len(meff_ss)), meff_ss, meson+' ss effective mass', xlim = xlim, ylim = ylim)
ylim = c51.find_yrange(meff_ps, xlim[0], xlim[1])
c51.scatter_plot(np.arange(len(meff_ps)), meff_ps, meson+' ps effective mass', xlim = xlim, ylim = ylim)
# scaled correlator
E0 = params.priors[meson]['E0'][0]
scaled_ss = eff.scaled_correlator(c51.make_gvars(decay_ss), E0, phase=1.0)
scaled_ps = eff.scaled_correlator(c51.make_gvars(decay_ps), E0, phase=1.0)
ylim = c51.find_yrange(scaled_ss, xlim[0], xlim[1])
c51.scatter_plot(np.arange(len(scaled_ss)), scaled_ss, meson+' ss scaled correlator (take sqrt to get Z0_s)', xlim = xlim, ylim = ylim)
ylim = c51.find_yrange(scaled_ps, xlim[0], xlim[1])
c51.scatter_plot(np.arange(len(scaled_ps)), scaled_ps, meson+' ps scaled correlator (divide by Z0_s to get Z0_p)', xlim = xlim, ylim = ylim)
plt.show()
# concatenate data
decay_ss_ps = np.concatenate((decay_ss, decay_ps), axis=1)
# priors
priors = params.priors[meson]
# read trange
trange = params.trange['twopt']
#Fit
#args = ((g, trange, T, decay_ss_ps, priors, draws) for g in range(len(draws)))
#pool = multi.Pool()
#p = pool.map_async(decay_fit, args)
## sort via bootstrap number
#output = np.sort(np.array(p.get()), axis=0)
result = []
for g in range(len(draws)):
# resample decay data
decay_bs = decay_ss_ps[draws[g]]
decay_bs = c51.make_gvars(decay_bs)
# priors
bsp = c51.dict_of_tuple_to_gvar(priors)
#Fit
fitfcn = c51.fit_function(T, nstates=2)
fit = c51.fitscript_v2(trange, T, decay_bs, bsp, fitfcn.twopt_fitfcn_ss_ps, result_flag='off')
fit = [g, fit]
result.append(fit)
output = np.sort(np.array(result), axis=0)
return output
def read_data(params):
# read data
twopt_dat = c51.fold(c51.open_data(params.data_loc['file_loc'], params.data_loc['phiqq_'+params.hadron]))
T = 2*len(twopt_dat[0])
if params.plot_data_flag == 'on':
# unfolded correlator data
c51.scatter_plot(np.arange(len(twopt_dat[0])), c51.make_gvars(twopt_dat), params.hadron+' folded')
# effective mass
eff = c51.effective_plots(T)
meff = eff.effective_mass(c51.make_gvars(twopt_dat), 1, 'cosh')
xlim = [2, len(meff)]
ylim = c51.find_yrange(meff, xlim[0], xlim[1])
ylim = [0.0, 0.7]
c51.scatter_plot(np.arange(len(meff)), meff, params.hadron+' effective mass', xlim = xlim, ylim = ylim)
# scaled correlator
E0 = params.priors[params.hadron]['E0'][0]
scaled = eff.scaled_correlator(c51.make_gvars(twopt_dat), E0, phase=1.0)
c51.scatter_plot(np.arange(len(scaled)), scaled, params.hadron+' scaled correlator (A0 = Z0_s*Z0_p)')
return twopt_dat, T
def decay_axial(pr, meson, draws):
if meson == 'pion':
shortname = 'll'
elif meson == 'kaon':
shortname = 'ls'
# read data
twopt_dat = c51.open_data(pr.data_loc['file_loc'], pr.data_loc['spec_'+meson])
twopt_ss = np.squeeze(twopt_dat[:,:,0,:])
twopt_ps = np.squeeze(twopt_dat[:,:,1,:])
axial_dat = np.squeeze(c51.open_data(pr.data_loc['file_loc'], pr.data_loc['axial_'+shortname]))
T = len(twopt_ss[0])
if pr.plot_data_flag == 'on':
# unfolded correlator data
c51.scatter_plot(np.arange(len(twopt_ss[0])), c51.make_gvars(twopt_ss), 'two point no fold')
c51.scatter_plot(np.arange(len(axial_dat[0])), c51.make_gvars(axial_dat), 'axial_'+shortname+' no fold')
# fold data
axial_dat = c51.fold(axial_dat, phase=-1.0)
twopt_ss = c51.fold(twopt_ss, phase=1.0)
twopt_ps = c51.fold(twopt_ps, phase=1.0)
if pr.plot_data_flag == 'on':
# folded correlator data
c51.scatter_plot(np.arange(len(twopt_ss[0])), c51.make_gvars(twopt_ss), 'two point folded')
c51.scatter_plot(np.arange(len(axial_dat[0])), c51.make_gvars(axial_dat), 'axial_'+shortname+' folded')
# effective mass
eff = c51.effective_plots(T)
meff = eff.effective_mass(c51.make_gvars(twopt_ss), 1, 'cosh')
meff_axial = eff.effective_mass(c51.make_gvars(axial_dat)[1:], 1, 'cosh')
xlim = [3, len(meff)]
ylim = c51.find_yrange(meff, xlim[0], xlim[1])
c51.scatter_plot(np.arange(len(meff)), meff, 'two pt effective mass', xlim = xlim, ylim = ylim)
ylim = c51.find_yrange(meff, xlim[0], xlim[1])
c51.scatter_plot(np.arange(len(meff_axial))+1, meff_axial, 'axial_'+shortname+' effective mass', xlim = xlim, ylim = ylim)
# scaled correlator
E0 = pr.priors[meson]['E0'][0]
scaled = eff.scaled_correlator(c51.make_gvars(twopt_ss), E0, phase=1.0)
scaled_axial = eff.scaled_correlator(c51.make_gvars(axial_dat)[1:], E0, phase=-1.0)
c51.scatter_plot(np.arange(len(scaled)), scaled, 'two pt scaled correlator (take sqrt to get Z0)')
c51.scatter_plot(np.arange(len(scaled_axial))+1, scaled_axial, 'axial_'+shortname+' scaled correlator (divide by Z0 to get F0)')
# concatenate
decay_axial_ss = np.concatenate((axial_dat, twopt_ss), axis=1)
# read priors
priors = pr.priors[meson]
# read trange
trange = pr.trange['decay_axial']
# fit
args = ((g, trange, T, decay_axial_ss, priors, draws) for g in range(len(draws)))
pool = multi.Pool()
p = pool.map_async(decay_axial_fit, args)
# sort via bootstrap number
output = np.sort(np.array(p.get()), axis=0)
return output
def fittwo_pt(params, twopt_dat, T):
# make data
twopt_gv = c51.make_gvars(twopt_dat)
# priors
priors = params.priors[params.hadron]
priors_gv = c51.dict_of_tuple_to_gvar(priors)
# read trange
trange = params.trange['twopt']
# fit
fitfcn = c51.fit_function(T, nstates=1)
fit = c51.fitscript_v2(trange, T, twopt_gv, priors_gv, fitfcn.twopt_fitfcn_phiqq, params.print_fit_flag)
return np.array([[0, fit]])
def decay_fit(args):
g, trange, T, decay_ss_sp_dat, priors, draws = args
# resample decay data
decay_bs = decay_ss_sp_dat[draws[g]]
decay_bs = c51.make_gvars(decay_bs)
# priors
bsp = c51.dict_of_tuple_to_gvar(priors)
#Fit
fitfcn = c51.fit_function(T, nstates=2)
fit = c51.fitscript_v2(trange, T, decay_bs, bsp, fitfcn.twopt_fitfcn_ss_ps, result_flag='off')
fit = [g, fit]
return fit
def decay_axial_fit(args):
g, trange, T, decay_axial_ss, priors, draws = args
# resample
decay_axial_ss = c51.make_gvars(decay_axial_ss[draws[g]])
# make priors
bsp = c51.dict_of_tuple_to_gvar(priors)
# fit
fitfcn = c51.fit_function(T, nstates=2)
fit = c51.fitscript_v2(trange, T, decay_axial_ss, bsp, fitfcn.axial_twoptss_fitfcn, result_flag='off')
# record nbs
fit = [g, fit]
return fit
def fit_proton(pr, p_avg, T):
# priors
priors = c51.dict_of_tuple_to_gvar(pr.priors['proton'])
# trange
trange = pr.trange['proton']
# make data
p_data = np.concatenate((p_avg[:,:,0,0], p_avg[:,:,3,0]), axis=1)
p_data = c51.make_gvars(p_data)
# fit
fitfcn = c51.fit_function(T, nstates=6)
fit = c51.fitscript_v2(trange, T, p_data, priors, fitfcn.twopt_fitfcn_ss_ps, pr.print_fit_flag)
return np.array([[0, fit]])
def read_data(filename, dpath_pion, dpath_kaon, plot='off'):
pion = c51.open_data(filename, dpath_pion)
kaon = c51.open_data(filename, dpath_kaon)
#Fold meson data
pion = c51.fold(pion)
kaon = c51.fold(kaon)
pion_ss = c51.make_gvars(pion[:, :, 0, 0])
pion_ps = c51.make_gvars(pion[:, :, 1, 0])
kaon_ss = c51.make_gvars(kaon[:, :, 0, 0])
kaon_ps = c51.make_gvars(kaon[:, :, 1, 0])
if plot == 'on':
dat = pion_ps
E0 = 0.237
meff = c51.effective_mass(dat, 1, 'cosh')
x = np.arange(len(meff))
xlim = [4, 15]
ylim = c51.find_yrange(meff, xlim[0], xlim[1])
c51.scatter_plot(x, meff, 'meff', xlim=xlim, ylim=ylim)
scaled2pt = c51.scaled_correlator(dat, E0)
ylim = c51.find_yrange(scaled2pt, xlim[0], xlim[1])
c51.scatter_plot(x, scaled2pt, 'scaled 2pt', xlim=xlim, ylim=ylim)
ylim = c51.find_yrange(dat, xlim[0], xlim[1])
c51.scatter_plot(x, dat, 'data', xlim=xlim, ylim=ylim)
else:
pass
pion_ss_ps = np.concatenate((pion[:, :, 0, 0], pion[:, :, 1, 0]), axis=1)
kaon_ss_ps = np.concatenate((kaon[:, :, 0, 0], kaon[:, :, 1, 0]), axis=1)
pion_ss_ps_gv = c51.make_gvars(pion_ss_ps)
kaon_ss_ps_gv = c51.make_gvars(kaon_ss_ps)
return pion_ss_ps_gv, kaon_ss_ps_gv
def read_data(filename, dpath_pion, dpath_kaon, plot='off'):
pion = c51.open_data(filename, dpath_pion)
kaon = c51.open_data(filename, dpath_kaon)
#Fold meson data
pion = c51.fold(pion)
kaon = c51.fold(kaon)
pion_ss = c51.make_gvars(pion[:,:,0,0])
pion_ps = c51.make_gvars(pion[:,:,1,0])
kaon_ss = c51.make_gvars(kaon[:,:,0,0])
kaon_ps = c51.make_gvars(kaon[:,:,1,0])
if plot=='on':
dat = pion_ps
E0 = 0.237
meff = c51.effective_mass(dat,1,'cosh')
x = np.arange(len(meff))
xlim = [4,15]
ylim = c51.find_yrange(meff, xlim[0], xlim[1])
c51.scatter_plot(x, meff, 'meff', xlim = xlim, ylim = ylim)
scaled2pt = c51.scaled_correlator(dat, E0)
ylim = c51.find_yrange(scaled2pt, xlim[0], xlim[1])
c51.scatter_plot(x, scaled2pt, 'scaled 2pt', xlim=xlim, ylim=ylim)
ylim = c51.find_yrange(dat, xlim[0], xlim[1])
c51.scatter_plot(x, dat, 'data', xlim=xlim, ylim=ylim)
else: pass
pion_ss_ps = np.concatenate((pion[:,:,0,0],pion[:,:,1,0]), axis=1)
kaon_ss_ps = np.concatenate((kaon[:,:,0,0],kaon[:,:,1,0]), axis=1)
pion_ss_ps_gv = c51.make_gvars(pion_ss_ps)
kaon_ss_ps_gv = c51.make_gvars(kaon_ss_ps)
return pion_ss_ps_gv, kaon_ss_ps_gv
def mres_fit(args):
g, trange, T, mres_dat, prior, draws = args
print g
#Resample mres data
mres_dat_bs = mres_dat[draws[g]]
mres_dat_bs = c51.make_gvars(mres_dat_bs)
print 'bs'
#Randomize priors
bsp = c51.dict_of_tuple_to_gvar(prior) #{'mres': gv.gvar(prior[0]+prior[1]*np.random.randn(), prior[1])}
#Fit
fitfcn = c51.fit_function(T)
fit = c51.fitscript_v2(trange, T, mres_dat_bs, bsp, fitfcn.mres_fitfcn, result_flag='off')
result = [g, fit]
return result
def mres_bs(params, meson, draws):
print 'mres', meson
ens = params.ens
ml = params.ml
ms = params.ms
loc = params.data_loc
#Read data
mp = c51.open_data(loc['file_loc'], loc['mres_'+meson+'_mp'])
pp = c51.open_data(loc['file_loc'], loc['mres_'+meson+'_pp'])
T = len(pp[0])
mres_dat = mp/pp
# plot mres
if params.plot_data_flag == 'on':
c51.scatter_plot(np.arange(len(mres_dat[0])), c51.make_gvars(mres_dat), meson+' mres')
plt.show()
#Read priors
prior = params.priors[meson]
#Read trange
trange = params.trange['mres']
#Fit
#args = ((g, trange, T, mres_dat, prior, draws) for g in range(len(draws)))
#pool = multi.Pool()
#p = pool.map_async(mres_fit, args)
# sort by bootstrap number
#output = np.sort(np.array(p.get()), axis=0)
result = []
for g in range(len(draws)):
mres_dat_bs = mres_dat[draws[g]]
mres_dat_bs = c51.make_gvars(mres_dat_bs)
#Randomize priors
bsp = c51.dict_of_tuple_to_gvar(prior) #{'mres': gv.gvar(prior[0]+prior[1]*np.random.randn(), prior[1])}
#Fit
fitfcn = c51.fit_function(T)
fit = c51.fitscript_v2(trange, T, mres_dat_bs, bsp, fitfcn.mres_fitfcn, result_flag='off')
result.append([g, fit])
output = np.sort(np.array(result), axis=0)
return output
def decay_axial_fit(args):
g, trange, T, decay_axial_ss, priors, draws = args
# resample
decay_axial_ss = c51.make_gvars(decay_axial_ss[draws[g]])
# make priors
bsp = c51.dict_of_tuple_to_gvar(priors)
# fit
fitfcn = c51.fit_function(T, nstates=2)
fit = c51.fitscript_v2(trange,
T,
decay_axial_ss,
bsp,
fitfcn.axial_twoptss_fitfcn,
result_flag='off')
# record nbs
fit = [g, fit]
return fit
def decay_fit(args):
g, trange, T, decay_ss_sp_dat, priors, draws = args
# resample decay data
decay_bs = decay_ss_sp_dat[draws[g]]
decay_bs = c51.make_gvars(decay_bs)
# priors
bsp = c51.dict_of_tuple_to_gvar(priors)
#Fit
fitfcn = c51.fit_function(T, nstates=2)
fit = c51.fitscript_v2(trange,
T,
decay_bs,
bsp,
fitfcn.twopt_fitfcn_ss_ps,
result_flag='off')
fit = [g, fit]
return fit
def mres_fit(args):
g, trange, T, mres_dat, prior, draws = args
print g
#Resample mres data
mres_dat_bs = mres_dat[draws[g]]
mres_dat_bs = c51.make_gvars(mres_dat_bs)
print 'bs'
#Randomize priors
bsp = c51.dict_of_tuple_to_gvar(
prior
) #{'mres': gv.gvar(prior[0]+prior[1]*np.random.randn(), prior[1])}
#Fit
fitfcn = c51.fit_function(T)
fit = c51.fitscript_v2(trange,
T,
mres_dat_bs,
bsp,
fitfcn.mres_fitfcn,
result_flag='off')
result = [g, fit]
return result
def mres_bs(params, meson, draws):
#Read data
mp = c51.open_data(params.data_loc['file_loc'], params.data_loc['mres_'+meson+'_mp'])
pp = c51.open_data(params.data_loc['file_loc'], params.data_loc['mres_'+meson+'_pp'])
T = len(pp)
mres_dat = mp/pp
# plot mres
if params.plot_data_flag == 'on':
c51.scatter_plot(np.arange(len(mres_dat[0])), c51.make_gvars(mres_dat), meson+' folded mres')
#Read priors
prior = params.priors[meson]
#Read trange
print params.priors
trange = params.trange['mres']
print trange
#Fit
args = ((g, trange, T, mres_dat, prior, draws) for g in range(len(draws)))
pool = multi.Pool()
p = pool.map_async(mres_fit, args)
# sort by bootstrap number
output = np.sort(np.array(p.get()), axis=0)
return output
def read_proton(pr):
# read data
p_up = c51.open_data(pr.data_loc['file_loc'], pr.data_loc['proton_spin_up'])
p_dn = c51.open_data(pr.data_loc['file_loc'], pr.data_loc['proton_spin_dn'])
pnp_up = c51.open_data(pr.data_loc['file_loc'], pr.data_loc['proton_np_spin_up'])
pnp_dn = c51.open_data(pr.data_loc['file_loc'], pr.data_loc['proton_np_spin_dn'])
p_savg = c51.ispin_avg(p_up, p_dn)
pnp_savg = c51.ispin_avg(pnp_up, pnp_dn)
p_avg = c51.parity_avg(p_savg, pnp_savg, phase=-1.0)
T = len(p_avg[0])
p_avg = p_avg[:, :T/2] # keep only first half of data ('folded' length)
if pr.plot_data_flag == 'on':
# folded correlator data
p_ss = p_avg[:,:,0,0]
p_ps = p_avg[:,:,3,0]
c51.scatter_plot(np.arange(len(p_ss[0])), c51.make_gvars(p_ss), 'proton ss folded')
c51.scatter_plot(np.arange(len(p_ps[0])), c51.make_gvars(p_ps), 'proton ps folded')
# effective mass
eff = c51.effective_plots(T)
meff_ss = eff.effective_mass(c51.make_gvars(p_ss)[1:], 1, 'cosh')
meff_ps = eff.effective_mass(c51.make_gvars(p_ps)[1:], 1, 'cosh')
xlim = [1, len(meff_ss)] #*2/5]
#ylim = [0.7, 1.1]
ylim = [0.3, 0.9]
#ylim = c51.find_yrange(meff_ss, xlim[0], xlim[1])
c51.scatter_plot(np.arange(len(meff_ss))+1, meff_ss, 'proton ss effective mass', xlim = xlim, ylim = ylim)
#ylim = c51.find_yrange(meff_ps, xlim[0], xlim[1])
c51.scatter_plot(np.arange(len(meff_ps))+1, meff_ps, 'proton ps effective mass', xlim = xlim, ylim = ylim)
# scaled correlator
E0 = pr.priors['proton']['E0'][0]
scaled_ss = eff.scaled_correlator(c51.make_gvars(p_ss), E0, phase=1.0)
scaled_ps = eff.scaled_correlator(c51.make_gvars(p_ps), E0, phase=1.0)
ylim = c51.find_yrange(scaled_ss, xlim[0], xlim[1]/2)
c51.scatter_plot(np.arange(len(scaled_ss)), scaled_ss, 'proton ss scaled correlator (take sqrt to get Z0_s)', xlim = xlim, ylim = ylim)
ylim = c51.find_yrange(scaled_ps, xlim[0], xlim[1]/2)
c51.scatter_plot(np.arange(len(scaled_ps)), scaled_ps, 'proton ps scaled correlator (divide by Z0_s to get Z0_p)', xlim = xlim, ylim = ylim)
plt.show()
return p_avg, T
def read_proton(pr):
# read data
p_up = c51.open_data(pr.data_loc['file_loc'], pr.data_loc['proton_spin_up'])
p_dn = c51.open_data(pr.data_loc['file_loc'], pr.data_loc['proton_spin_dn'])
pnp_up = c51.open_data(pr.data_loc['file_loc'], pr.data_loc['proton_np_spin_up'])
pnp_dn = c51.open_data(pr.data_loc['file_loc'], pr.data_loc['proton_np_spin_dn'])
p_savg = c51.ispin_avg(p_up, p_dn)
pnp_savg = c51.ispin_avg(pnp_up, pnp_dn)
p_avg = c51.parity_avg(p_savg, pnp_savg, phase=-1.0)
T = len(p_avg[0])
p_avg = p_avg[:, :T/2] # keep only first half of data ('folded' length)
if pr.plot_data_flag == 'on':
# folded correlator data
p_ss = p_avg[:,:,0,0]
p_ps = p_avg[:,:,3,0]
c51.scatter_plot(np.arange(len(p_ss[0])), c51.make_gvars(p_ss), 'proton ss folded')
c51.scatter_plot(np.arange(len(p_ps[0])), c51.make_gvars(p_ps), 'proton ps folded')
# effective mass
eff = c51.effective_plots(T)
meff_ss = eff.effective_mass(c51.make_gvars(p_ss)[1:], 1, 'cosh')
meff_ps = eff.effective_mass(c51.make_gvars(p_ps)[1:], 1, 'cosh')
xlim = [1, len(meff_ss)] #*2/5]
ylim = [0.6, 1.2]
#ylim = c51.find_yrange(meff_ss, xlim[0], xlim[1])
c51.scatter_plot(np.arange(len(meff_ss))+1, meff_ss, 'proton ss effective mass', xlim = xlim, ylim = ylim)
#ylim = c51.find_yrange(meff_ps, xlim[0], xlim[1])
c51.scatter_plot(np.arange(len(meff_ps))+1, meff_ps, 'proton ps effective mass', xlim = xlim, ylim = ylim)
# scaled correlator
E0 = pr.priors['proton']['E0'][0]
scaled_ss = eff.scaled_correlator(c51.make_gvars(p_ss), E0, phase=1.0)
scaled_ps = eff.scaled_correlator(c51.make_gvars(p_ps), E0, phase=1.0)
ylim = c51.find_yrange(scaled_ss, xlim[0], xlim[1])
c51.scatter_plot(np.arange(len(scaled_ss)), scaled_ss, 'proton ss scaled correlator (take sqrt to get Z0_s)', xlim = xlim, ylim = ylim)
ylim = c51.find_yrange(scaled_ps, xlim[0], xlim[1])
c51.scatter_plot(np.arange(len(scaled_ps)), scaled_ps, 'proton ps scaled correlator (divide by Z0_s to get Z0_p)', xlim = xlim, ylim = ylim)
return p_avg, T
import h5py as h5
import numpy as np
import c51lib as c51
import matplotlib.pyplot as plt
#Read meson data
filename = 'l2464f211b600m0102m0509m635a_avg.h5'
datapath = 'l2464f211b600m0102m0509m635/wf1p0_m51p2_l58_a51p5_smrw5p0_n75/spectrum/ml0p0126_ms0p0693/pion/corr'
data_ss = c51.read_data(filename, datapath, 0, 0)
data_ps = c51.read_data(filename, datapath, 1, 0)
data = np.concatenate((data_ss, data_ps), axis=1)
data = c51.make_gvars(data)
#data = data_ps
#Plot effective mass
T = len(data) * 0.5
meff = c51.effective_mass(data, 1)
x = np.arange(len(meff))
ylim = c51.find_yrange(meff, 1, 10)
#ylim = [0.47, 0.57]
xr = [1, 15]
c51.scatter_plot(x, meff, 'effective mass', xlim=[xr[0], xr[1]], ylim=ylim)
#ylim = c51.find_yrange(meff, 65, 79)
c51.scatter_plot(x,
meff,
'effective mass ps',
xlim=[T + xr[0], T + xr[1]],
ylim=ylim)
#Fit
def decay_axial(pr, meson, draws):
if meson == 'pion':
shortname = 'll'
elif meson == 'kaon':
shortname = 'ls'
# read data
twopt_dat = c51.open_data(pr.data_loc['file_loc'],
pr.data_loc['spec_' + meson])
twopt_ss = np.squeeze(twopt_dat[:, :, 0, :])
twopt_ps = np.squeeze(twopt_dat[:, :, 1, :])
axial_dat = np.squeeze(
c51.open_data(pr.data_loc['file_loc'],
pr.data_loc['axial_' + shortname]))
T = len(twopt_ss[0])
if pr.plot_data_flag == 'on':
# unfolded correlator data
c51.scatter_plot(np.arange(len(twopt_ss[0])), c51.make_gvars(twopt_ss),
'two point no fold')
c51.scatter_plot(np.arange(len(axial_dat[0])),
c51.make_gvars(axial_dat),
'axial_' + shortname + ' no fold')
# fold data
axial_dat = c51.fold(axial_dat, phase=-1.0)
twopt_ss = c51.fold(twopt_ss, phase=1.0)
twopt_ps = c51.fold(twopt_ps, phase=1.0)
if pr.plot_data_flag == 'on':
# folded correlator data
c51.scatter_plot(np.arange(len(twopt_ss[0])), c51.make_gvars(twopt_ss),
'two point folded')
c51.scatter_plot(np.arange(len(axial_dat[0])),
c51.make_gvars(axial_dat),
'axial_' + shortname + ' folded')
# effective mass
eff = c51.effective_plots(T)
meff = eff.effective_mass(c51.make_gvars(twopt_ss), 1, 'cosh')
meff_axial = eff.effective_mass(
c51.make_gvars(axial_dat)[1:], 1, 'cosh')
xlim = [3, len(meff)]
ylim = c51.find_yrange(meff, xlim[0], xlim[1])
c51.scatter_plot(np.arange(len(meff)),
meff,
'two pt effective mass',
xlim=xlim,
ylim=ylim)
ylim = c51.find_yrange(meff, xlim[0], xlim[1])
c51.scatter_plot(np.arange(len(meff_axial)) + 1,
meff_axial,
'axial_' + shortname + ' effective mass',
xlim=xlim,
ylim=ylim)
# scaled correlator
E0 = pr.priors[meson]['E0'][0]
scaled = eff.scaled_correlator(c51.make_gvars(twopt_ss), E0, phase=1.0)
scaled_axial = eff.scaled_correlator(c51.make_gvars(axial_dat)[1:],
E0,
phase=-1.0)
c51.scatter_plot(np.arange(len(scaled)), scaled,
'two pt scaled correlator (take sqrt to get Z0)')
c51.scatter_plot(
np.arange(len(scaled_axial)) + 1, scaled_axial, 'axial_' +
shortname + ' scaled correlator (divide by Z0 to get F0)')
# concatenate
decay_axial_ss = np.concatenate((axial_dat, twopt_ss), axis=1)
# read priors
priors = pr.priors[meson]
# read trange
trange = pr.trange['decay_axial']
# fit
args = ((g, trange, T, decay_axial_ss, priors, draws)
for g in range(len(draws)))
pool = multi.Pool()
p = pool.map_async(decay_axial_fit, args)
# sort via bootstrap number
output = np.sort(np.array(p.get()), axis=0)
return output
def read_baryon(pr):
# read data
baryon = pr.baryon2pt
if baryon in ['proton', 'sigma', 'xi', 'lambda']:
corr_up = c51.open_data(pr.data_loc['file_loc'],
pr.data_loc[baryon + '_spin_up'])
corr_dn = c51.open_data(pr.data_loc['file_loc'],
pr.data_loc[baryon + '_spin_dn'])
corrnp_up = c51.open_data(pr.data_loc['file_loc'],
pr.data_loc[baryon + '_np_spin_up'])
corrnp_dn = c51.open_data(pr.data_loc['file_loc'],
pr.data_loc[baryon + '_np_spin_dn'])
# spin avg
corr = 0.5 * (corr_up + corr_dn)
corrnp = 0.5 * (corrnp_up + corrnp_dn)
elif baryon in ['delta', 'sigma_st', 'xi_st', 'omega']:
corr_upup = c51.open_data(pr.data_loc['file_loc'],
pr.data_loc[baryon + '_spin_upup'])
corr_up = c51.open_data(pr.data_loc['file_loc'],
pr.data_loc[baryon + '_spin_up'])
corr_dn = c51.open_data(pr.data_loc['file_loc'],
pr.data_loc[baryon + '_spin_dn'])
corr_dndn = c51.open_data(pr.data_loc['file_loc'],
pr.data_loc[baryon + '_spin_dndn'])
corrnp_upup = c51.open_data(pr.data_loc['file_loc'],
pr.data_loc[baryon + '_np_spin_upup'])
corrnp_up = c51.open_data(pr.data_loc['file_loc'],
pr.data_loc[baryon + '_np_spin_up'])
corrnp_dn = c51.open_data(pr.data_loc['file_loc'],
pr.data_loc[baryon + '_np_spin_dn'])
corrnp_dndn = c51.open_data(pr.data_loc['file_loc'],
pr.data_loc[baryon + '_np_spin_dndn'])
# spin avg
corr = 0.25 * (corr_upup + corr_up + corr_dn + corr_dndn)
corrnp = 0.25 * (corrnp_upup + corrnp_up + corrnp_dn + corrnp_dndn)
# parity avg
corr_avg = c51.parity_avg(corr, corrnp, phase=-1.0)
T = len(corr_avg[0])
corr_avg = corr_avg[:, :T /
2] # keep only first half of data ('folded' length)
if pr.plot_data_flag == 'on':
for src in range(len(corr_avg[0, 0, 0])):
for snk in range(len(corr_avg[0, 0])):
# folded correlator data
corr_i = corr_avg[:, :, snk, src]
#c51.scatter_plot(np.arange(len(corr_i[0])), c51.make_gvars(corr_i), '%s snk_%s src_%s folded' %(baryon,str(snk),str(src)))
# effective mass
eff = c51.effective_plots(T)
meff = eff.effective_mass(
c51.make_gvars(corr_i)[1:], 1, 'cosh')
xlim = [1, len(meff)]
ylim = c51.find_yrange(meff, xlim[0], xlim[1] * 2 / 5)
c51.scatter_plot(np.arange(len(meff)) + 1,
meff,
'%s snk_%s src_%s effective mass' %
(baryon, str(snk), str(src)),
xlim=xlim,
ylim=ylim)
# scaled correlator
E0 = pr.priors[baryon]['E0'][0]
scaled = eff.scaled_correlator(c51.make_gvars(corr_i),
E0,
phase=1.0)
ylim = c51.find_yrange(scaled, xlim[0], xlim[1] * 2 / 5)
c51.scatter_plot(
np.arange(len(scaled)),
scaled,
'%s snk_%s src_%s scaled correlator (take sqrt to get Z0_s)'
% (baryon, str(snk), str(src)),
xlim=xlim,
ylim=ylim)
plt.show()
return corr_avg, T
data_dn = c51.read_data(filename, datapath, 3, 0)
data_neg = c51.ispin_avg(data_up, data_dn)
#Parity average
data_ps = c51.parity_avg(data_pos, data_neg, -1)
##READ SPIN AND PARITY AVG'D DATA
#filename = 'l2464f211b600m0102m0509m635_tune_avg.h5'
#datapath = 'prot_w6p1_n94'
#datapath = 'prot_w5p6_n94'
filename = 'l2464f211b600m0102m0509m635a_avg.h5'
datapath = 'l2464f211b600m0102m0509m635/wf1p0_m51p2_l58_a51p5_smrw5p0_n75/spectrum/ml0p0126_ms0p0693/pion/corr'
data_ss = c51.read_data(filename, datapath, 0, 0)
data_ps = c51.read_data(filename, datapath, 3, 0)
data = np.concatenate((data_ss, data_ps), axis=1)
data = c51.make_gvars(data)
#data = data_ps
#Plot effective mass
T = len(data)*0.5
meff = c51.effective_mass(data, 1)
x = np.arange(len(meff))
ylim = c51.find_yrange(meff, 1, 10)
#ylim = [0.47, 0.57]
xr = [1,15]
c51.scatter_plot(x, meff, 'effective mass', xlim=[xr[0],xr[1]], ylim=ylim)
#ylim = c51.find_yrange(meff, 65, 79)
c51.scatter_plot(x, meff, 'effective mass ps', xlim=[T+xr[0],T+xr[1]], ylim=ylim)
#Fit
inputs = c51.read_yaml('temp.yml')
def decay_bs(params, meson, draws):
print 'decay ', meson
ens = params.ens
ml = params.ml
ms = params.ms
loc = params.data_loc
# read data
decay_dat = c51.fold(c51.open_data(loc['file_loc'], loc['spec_' + meson]))
decay_ss = np.squeeze(decay_dat[:, :, 0, :])
decay_ps = np.squeeze(decay_dat[:, :, 1, :])
T = 2 * len(decay_ss[0])
if params.plot_data_flag == 'on':
# unfolded correlator data
c51.scatter_plot(np.arange(len(decay_ss[0])), c51.make_gvars(decay_ss),
meson + ' ss folded')
c51.scatter_plot(np.arange(len(decay_ps[0])), c51.make_gvars(decay_ps),
meson + ' ps folded')
# effective mass
eff = c51.effective_plots(T)
meff_ss = eff.effective_mass(c51.make_gvars(decay_ss), 1, 'cosh')
meff_ps = eff.effective_mass(c51.make_gvars(decay_ps), 1, 'cosh')
xlim = [3, len(meff_ss) - 2]
ylim = c51.find_yrange(meff_ss, xlim[0], xlim[1])
c51.scatter_plot(np.arange(len(meff_ss)),
meff_ss,
meson + ' ss effective mass',
xlim=xlim,
ylim=ylim)
ylim = c51.find_yrange(meff_ps, xlim[0], xlim[1])
c51.scatter_plot(np.arange(len(meff_ps)),
meff_ps,
meson + ' ps effective mass',
xlim=xlim,
ylim=ylim)
# scaled correlator
E0 = params.priors[meson]['E0'][0]
scaled_ss = eff.scaled_correlator(c51.make_gvars(decay_ss),
E0,
phase=1.0)
scaled_ps = eff.scaled_correlator(c51.make_gvars(decay_ps),
E0,
phase=1.0)
ylim = c51.find_yrange(scaled_ss, xlim[0], xlim[1])
c51.scatter_plot(np.arange(len(scaled_ss)),
scaled_ss,
meson +
' ss scaled correlator (take sqrt to get Z0_s)',
xlim=xlim,
ylim=ylim)
ylim = c51.find_yrange(scaled_ps, xlim[0], xlim[1])
c51.scatter_plot(np.arange(len(scaled_ps)),
scaled_ps,
meson +
' ps scaled correlator (divide by Z0_s to get Z0_p)',
xlim=xlim,
ylim=ylim)
plt.show()
# concatenate data
decay_ss_ps = np.concatenate((decay_ss, decay_ps), axis=1)
# priors
priors = params.priors[meson]
# read trange
trange = params.trange['twopt']
#Fit
#args = ((g, trange, T, decay_ss_ps, priors, draws) for g in range(len(draws)))
#pool = multi.Pool()
#p = pool.map_async(decay_fit, args)
## sort via bootstrap number
#output = np.sort(np.array(p.get()), axis=0)
result = []
for g in range(len(draws)):
# resample decay data
decay_bs = decay_ss_ps[draws[g]]
decay_bs = c51.make_gvars(decay_bs)
# priors
bsp = c51.dict_of_tuple_to_gvar(priors)
#Fit
fitfcn = c51.fit_function(T, nstates=2)
fit = c51.fitscript_v2(trange,
T,
decay_bs,
bsp,
fitfcn.twopt_fitfcn_ss_ps,
result_flag='off')
fit = [g, fit]
result.append(fit)
output = np.sort(np.array(result), axis=0)
return output