def WritePlotfile(samples, ndim, outFilePrefix, nwalkers, step, nSteps,
nDigits, rstate):
if nDigits > 0:
fmt = "%0" + str(nDigits) + "d"
lastStep = step + nSteps - 1
filename = outFilePrefix + '_' + (fmt % step) + '_' + (fmt % lastStep)
else:
filename = outFilePrefix
if rank == 0:
print('Writing plotfile: ' + filename)
C_array_size = nSteps * ndim * nwalkers
x_for_c = pymc.DoubleVec(C_array_size)
for walker in range(0, nwalkers):
for it in range(0, nSteps):
for dim in range(0, ndim):
index = walker + nwalkers * it + nwalkers * nSteps * dim
x_for_c[index] = samples[dim, step + it]
if rstate == None:
rstateString = ''
else:
rstateString = cPickle.dumps(rstate)
pf = pymc.UqPlotfile(x_for_c, ndim, nwalkers, step, nSteps,
rstateString)
pf.Write(filename)
def WritePlotfile(driver, outFilePrefix, nwalkers, step, nSteps, nDigits,
rstate):
fmt = "%0" + str(nDigits) + "d"
lastStep = step + nSteps - 1
filename = outFilePrefix + '_' + (fmt % step) + '_' + (fmt % lastStep)
if rank == 0:
print('Writing plotfile: ' + filename)
x = driver.sampler.chain
ndim = driver.NumParams()
C_array_size = nSteps * ndim * nwalkers
x_for_c = pymc.DoubleVec(C_array_size)
for walker in range(0, nwalkers):
for it in range(0, nSteps):
for dim in range(0, ndim):
index = walker + nwalkers * it + nwalkers * nSteps * dim
x_for_c[index] = x[walker, it, dim]
if rstate == None:
rstateString = ''
else:
rstateString = cPickle.dumps(rstate)
pf = pymc.UqPlotfile(x_for_c, ndim, nwalkers, step, nSteps, rstateString)
pf.Write(filename)
def WritePlotfile(x, filename, ndim, nwalkers, step, nSteps, rstate):
print('Writing plotfile: ' + filename)
C_array_size = nSteps * ndim * nwalkers
x_for_c = pymc.DoubleVec(C_array_size)
for walker in range(0, nwalkers):
for it in range(0, nSteps):
for dim in range(0, ndim):
index = walker + nwalkers * it + nwalkers * nSteps * dim
x_for_c[index] = x[walker, it, dim]
if rstate == None:
rstateString = ''
else:
rstateString = cPickle.dumps(rstate)
pf = pymc.UqPlotfile(x_for_c, ndim, nwalkers, step, nSteps, rstateString)
pf.Write(filename)
def WritePlotfile(x, ndim, outFilePrefix, nwalkers, step, nSteps, nDigits,
rstate):
fmt = "%0" + str(nDigits) + "d"
lastStep = step + nSteps - 1
filename = outFilePrefix + '_' + (fmt % step) + '_' + (fmt % lastStep)
C_array_size = nSteps * ndim * nwalkers
x_for_c = pymc.DoubleVec(C_array_size)
for walker in range(0, nwalkers):
for it in range(0, nSteps):
for dim in range(0, ndim):
index = walker + nwalkers * it + nwalkers * nSteps * dim
x_for_c[index] = x[walker, it, dim]
if rstate is None:
rstateString = ''
else:
rstateString = cPickle.dumps(rstate)
pf = pymc.UqPlotfile(x_for_c, ndim, nwalkers, step, nSteps, rstateString)
pf.Write(filename)
nwalkers = 1
rstateString = ''
step = 0
pf = pymc.UqPlotfile(x, np, nwalkers, step, nSteps, rstateString)
print 'writing ', filename, nSteps
pf.Write(filename)
sampleFile = sys.argv[1]
f = open(sampleFile)
ll = f.readlines()
N = 0
x = []
for L in ll:
t = string.split(string.strip(L))
if N == 0:
N = len(t)
if len(t) != N:
print 'Input has a line with different number of args than in the first line'
exit()
x.append(t)
xd = pymc.DoubleVec(len(x) * N)
for i in range(len(x)):
for j in range(N):
idx = j * len(x) + i
xd[idx] = float(x[i][j])
outfile = sys.argv[2]
WritePlotfile(xd, N, outfile)