def LoadPlotfile(filenames):
nwalkers_0 = -1
ndim_0 = -1
iters = -1
iter = -1
for filename in filenames:
pf = pymc.UqPlotfile()
pf.Read(filename)
nwalkers = pf.NWALKERS()
ndim = pf.NDIM()
if nwalkers_0 < 0:
nwalkers_0 = nwalkers
else:
if nwalkers != nwalkers_0:
print 'Plotfiles incompatible'
if ndim_0 < 0:
ndim_0 = ndim
else:
if ndim != ndim_0:
print 'Plotfiles incompatible'
iter1 = pf.ITER()
if iter < 0:
iter = iter1
else:
if iter1 != iter + iters:
print 'plotfiles out of sequence'
iters1 = pf.NITERS()
if iters < 0:
iters = iters1
else:
iters += iters1
ret = np.zeros((nwalkers, iters, ndim))
for filename in filenames:
print('Loading plotfile: ' + filename)
pf = pymc.UqPlotfile()
pf.Read(filename)
iters1 = pf.NITERS()
iter1 = pf.ITER()
p0 = pf.LoadEnsemble(iter1, iters1)
for walker in range(0, nwalkers):
for it in range(0, iters1):
for dim in range(0, ndim):
index = walker + nwalkers * it + nwalkers * iters1 * dim
ret[walker, iter1 + it - iter, dim] = p0[index]
return ret, nwalkers, ndim, iters, iter
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 LoadPlotfile(driver,filename):
if rank == 0:
print('Loading plotfile: '+filename)
pf = pymc.UqPlotfile()
pf.Read_serial(filename)
if rank == 0:
print('Done Loading plotfile: '+filename)
t_nwalkers = pf.NWALKERS()
t_ndim = pf.NDIM()
t_iters = 1
rstate = cPickle.loads(pf.RSTATE())
iter = pf.ITER() + pf.NITERS() - 1
p0 = pf.LoadEnsemble(iter, t_iters)
ret = []
for walker in range(0, t_nwalkers):
ret.append(np.zeros(t_ndim))
for dim in range(0, t_ndim):
ret[walker][dim] = p0[walker + t_nwalkers*dim]
return ret, iter, rstate
def WritePlotfile(x, np, filename):
nSteps = len(x) / np
if nSteps == 0:
print 'Not enough data for even one sample'
exit()
if np * nSteps != len(x):
print 'len(x) not an integer mult of np'
exit()
nwalkers = 1
rstateString = ''
step = 0
pf = pymc.UqPlotfile(x, np, nwalkers, step, nSteps, rstateString)
print 'writing ', filename, nSteps
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 LoadPlotfile(filename):
if rank == 0:
print('Loading plotfile: ' + filename)
pf = pymc.UqPlotfile()
pf.Read(filename)
nwalkers = pf.NWALKERS()
ndim = pf.NDIM()
iters = pf.NITERS()
iter = pf.ITER()
p0 = pf.LoadEnsemble(iter, iters)
ret = []
for walker in range(0, nwalkers):
for it in range(0, iters):
ret.append(np.zeros(ndim))
for dim in range(0, ndim):
index = walker + nwalkers * it + nwalkers * iters * dim
ret[-1][dim] = p0[index]
return ret
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)
def LoadPlotfile(filename, iters_in = -1):
if rank == 0:
print('Loading plotfile: '+filename)
pf = pymc.UqPlotfile()
pf.Read(filename)
t_nwalkers = pf.NWALKERS()
t_ndim = pf.NDIM()
t_iters = pf.NITERS()
if iters_in > 0:
t_iters = iters_in
rstate = 0
try:
rstate = cPickle.loads(pf.RSTATE())
except EOFError:
pass
except:
raise
iter = pf.ITER() + pf.NITERS() - t_iters
p0 = pf.LoadEnsemble(iter,t_iters)
ret = np.zeros(t_nwalkers*t_iters*t_ndim).reshape(t_nwalkers,t_iters,t_ndim)
for walker in range(0,t_nwalkers):
for it in range(0,t_iters):
for dim in range(0,t_ndim):
index = walker + t_nwalkers*it + t_nwalkers*t_iters*dim
ret[walker,it,dim] = p0[index]
if rank == 0:
print('Finished loading plotfile: '+filename)
return ret, iter, rstate
def LoadPlotfile(filenames):
nwalkers_0 = -1
ndim_0 = -1
iters = -1
iter = -1
for filename in filenames:
pf = pymc.UqPlotfile()
pf.Read(filename)
nwalkers = pf.NWALKERS()
ndim = pf.NDIM()
if nwalkers_0 < 0:
nwalkers_0 = nwalkers
else:
if nwalkers != nwalkers_0:
print 'Plotfiles incompatible'
if ndim_0 < 0:
ndim_0 = ndim
else:
if ndim != ndim_0:
print 'Plotfiles incompatible'
iter1 = pf.ITER()
if iter < 0:
iter = iter1
else:
if iter1 != iter + iters:
print 'plotfiles out of sequence'
iters1 = pf.NITERS()
if iters < 0:
iters = iters1
else:
iters += iters1
ret = np.zeros((nwalkers, iters, ndim))
iterFirst = iter
itersPrev = 0
print 'iterFirst:', iterFirst
print 'nwalkers', nwalkers
print 'iters', iters
print 'ndim', ndim
for filename in filenames:
print('Loading plotfile: ' + filename)
pf = pymc.UqPlotfile()
pf.Read(filename)
iter1 = pf.ITER()
iters1 = pf.NITERS()
p0 = pf.LoadEnsemble(iter1, iters1)
for walker in range(0, nwalkers):
for it in range(0, iters1):
for dim in range(0, ndim):
#index = walker + nwalkers*(it-iter1) + nwalkers*iters1*dim
index = walker + nwalkers * it + nwalkers * iters1 * dim
if ((it == 0 and walker == 0 and dim == 0)
or (it == iters1 - 1 and walker == nwalkers - 1
and dim == ndim - 1)):
print 'record, index', index, 'len(p0)', len(p0)
print ' ret w,i,d:', walker, iter1 + it + itersPrev, dim
ret[walker, iter1 + it + itersPrev, dim] = p0[index]
#itersPrev = iters1 # uncomment if we are combining a bunch of pltfiles starting from 0, rather than a sequence
return ret, nwalkers, ndim, iters, iter