help="file to read the zfactors")
parser.add_argument("-m", "--masses", type=float, nargs="+", required=True,
help="list of masses for each level")
parser.add_argument("-v", "--verbose", action="store_true",
help="increase output verbosity")
args = parser.parse_args()
if args.verbose:
logging.basicConfig(format='%(levelname)s: %(message)s', level=logging.DEBUG)
logging.debug("Verbose debuging mode activated")
else:
logging.basicConfig(format='%(levelname)s: %(message)s', level=logging.INFO)
N = len(args.masses)
raw_Zs = zfactor.read_coeffs_file(args.overlapsfile)
assert len(raw_Zs)==N*N, "Length missmatch in levels and coeffs"
print raw_Zs
Zs = np.matrix(raw_Zs.identities.values.reshape((N, N))).T
print Zs
print "blah"
for i in range(N):
for j in range(N):
print "Correlator_{}{}".format(i,j)
amps = [Zs[i,level]*Zs[j,level] for level in range(N)]
print "newaps", amps
cor = fakecor.make_fake_cor(args.configs, args.times, amps, args.masses)
cor.writefullfile(args.output_stub+"{}_{}".format(i,j), comp=True)
logging.info("done")
def sh_optimized_zfacts():
shops = readops(args.single_hadron_ops)
mhops = readops(args.full_hadron_ops)
rotco = overlaps(read_coeffs_file(args.rotation_coeffs))
fullz = overlaps(read_file(args.full_zfactors))
indicies = [mhops.index(o)+1 for o in shops]
OptZ = {}
# Main calculation below
# TODO this should be done as matrix multiplication, would be WAY faster but this works.
for m in range(1,rotco.levels+1):
value = np.array([np.abs(np.array(np.matrix( np.conj(rotco.get_level(m))) * np.matrix([fullz.get_entry(i,l) for i in indicies]).T))**2 for l in range(1,fullz.levels+1)]).flatten()
if np.all(value==0):
break
OptZ[m] = value
with open(args.ordering) as orderfile:
ordering = [int(i.strip()) for i in orderfile.readlines()]
N = len(OptZ.keys())
if args.number:
N = min(N,args.number)
if args.columns:
Ncols = args.columns
else:
Ncols = ncols(N)
rows = int(math.ceil(float(N)/Ncols))
if not args.seperate:
fig, ax = plt.subplots(ncols=Ncols, nrows=rows)
with open(args.SHordering) as SHorderfile:
SHordering = [int(i.strip()) for i in SHorderfile.readlines()]
for index, m in enumerate(SHordering):
if index >= N:
break
i = (index)/Ncols
j = (index) % Ncols
if args.seperate:
fig, axe = plt.subplots(1)
else:
if N <= Ncols:
axe=ax[j]
else:
axe=ax[i][j]
reordered = [OptZ[m+1][reorderedlevel] for reorderedlevel in ordering]
axe.bar(range(len(reordered)), reordered, 1.0, color="b")
# axe.set_title("SH-opt level{}".format(index))
axe.set_ylim((0,max(reordered)))
axe.set_ylabel("$|Z|^2$", fontweight='bold', fontsize=30)
axe.set_xlabel("Level", fontweight='bold', fontsize=30)
axe.tick_params(axis='both', which='major', labelsize=20)
plt.tight_layout()
if args.seperate:
outfilename = args.output_stub+"_{}.eps".format(index)
logging.info("Saving plot to {}".format(outfilename))
plt.savefig(outfilename)
plt.clf()
if args.seperate:
return
if args.output_stub:
logging.info("Saving unreordered shopt_zfactors to {}".format(args.output_stub+".nonreordered.out"))
with open(args.output_stub+".out", 'w') as outfile:
for level,d in OptZ.iteritems():
outfile.write("{}, {}\n".format(level, ", ".join(map(str,d))))
logging.info("Saving shcandidates to {}".format(args.output_stub+".singleresonances"))
with open(args.output_stub+".singleresonances", 'w') as resfile:
for level,d in OptZ.iteritems():
fixd = np.nan_to_num(d)
if max(fixd) > 0:
resfile.write("{}, {}\n".format(level, np.argmax(fixd)))
plt.rcParams.update({'font.size': 10})
fig.set_size_inches(18.5,8.5)
plt.tight_layout()
if args.eps:
logging.info("Saving plot to {}".format(args.output_stub+".eps"))
plt.savefig(args.output_stub+".eps")
else:
logging.info("Saving plot to {}".format(args.output_stub+".png"))
plt.savefig(args.output_stub+".png",dpi=100)
else:
plt.tight_layout()
plt.show()
def alt_zfactor(corwild, zrotfile, rotfile, ops, t0, outputstub,
maxlevels=None, normalize=False, reconstruct_stub=None, inputemass=None):
# zrots = read_zrots(zrotfile)
fit_values = read_level_fits(zrotfile)
N = len(fit_values)
N = len(ops)
levels_to_make = range(min(N, maxlevels, len(fit_values)))
raw_v = zfactor.read_coeffs_file(rotfile)
v = np.matrix(raw_v.identities.values.reshape((N, N))).T
roterror = np.matrix(raw_v.error.values.reshape((N, N))).T
cormat, errmat = build_cor_mat_error(corwild, ops, t0)
Zs = {}
err = {}
ABS = np.abs
def nothing(a):
return a
if args.complex:
ABS = nothing
for level in levels_to_make:
zr = fit_values.amp[level]
#err[level] = zrots.error[level]*np.ones(N)
for op in range(N):
v_n = (v[:, level])
ev_n = np.ravel(roterror[:, level])
Zs[level] = [ABS((cormat[j]*(v_n)).flat[0])*np.sqrt(zr) for j in range(len(ops))]
err[level] = [ABS((cormat[j]*(v_n)).flat[0])*np.sqrt(fit_values.amp_error[level]) +
ABS((errmat[j]*(v_n)).flat[0])*np.sqrt(zr)
for j in range(len(ops))]
#err[level] = np.sqrt(fit_values.amp_error[level])*ABS(v_n)+np.sqrt(zr)*ABS(ev_n)
# normalized_Zs = zfactor.normalize_Zs(Zs, normalize)
A = np.array(Zs.values())
if normalize:
maximums = np.array([max(np.abs(A[:, i])) for i in range(len(Zs[0]))])
normalized_Zs = {k: np.abs(values)/maximums for k, values in Zs.iteritems()}
normalized_err = {k: np.abs(values)/maximums for k, values in err.iteritems()}
else:
normalized_Zs = Zs
normalized_err = err
# print err
# print normalized_err
if(outputstub):
logging.info("Writing alt_zfactors to {}".format(outputstub+".out"))
with open(outputstub+".out", 'w') as outfile:
outfile.write("# normalized Zfactors\n")
for level in levels_to_make:
for j in range(N):
if args.complex:
outfile.write("{:d}{:03d} ({},{}) ({},{})\n".format(j+1, level+1,
np.real(normalized_Zs[level][j]), np.imag(normalized_Zs[level][j]),
np.real(normalized_err[level][j]), np.imag(normalized_err[level][j])))
else:
outfile.write("{:d}{:03d} {} {}\n".format(j+1, level+1,
normalized_Zs[level][j], normalized_err[level][j]))
if(reconstruct_stub):
reconstructed_correaltors(Zs, err, fit_values, ops, reconstruct_stub)