cov = cov[-emu.n_bins:, :][:, -emu.n_bins:]
#em_params.update( cosmo_param_dict)
fixed_params.update(em_params)
#fixed_params.update(cosmo_param_dict)
em_params = cosmo_param_dict
param_names = [k for k in em_params.iterkeys() if k not in fixed_params]
nwalkers = 500
nsteps = 20000
nburn = 0
savedir = '/scratch/users/swmclau2/PearceMCMC/'
#chain_fname = path.join(savedir, '%d_walkers_%d_steps_chain_cosmo_zheng_xi_lowmsat.npy'%(nwalkers, nsteps ))
chain_fname = path.join(
savedir, '%d_walkers_%d_steps_xigg_r%d_%d_rmin_emu2_jk.npy' %
(nwalkers, nsteps, boxno, realization))
with open(chain_fname, 'w') as f:
f.write('#' + '\t'.join(param_names) + '\n')
print 'starting mcmc'
np.random.seed(0)
for pos in run_mcmc_iterator([emu], param_names, [y], [cov], rpoints, fixed_params = fixed_params,nwalkers = nwalkers,\
nsteps = nsteps, nburn = nburn):#, ncores = 1):#, resume_from_previous = chain_fname):
with open(chain_fname, 'a') as f:
np.savetxt(f, pos)
savedir = '/home/swmclau2/scratch/PearceMCMC/'
chain_fname = path.join(
savedir,
'%d_walkers_%d_steps_chain_shuffle_sham_no_ab_sh.npy' % (nwalkers, nsteps))
with open(chain_fname, 'w') as f:
f.write('#' + '\t'.join(param_names) + '\n')
for pos in run_mcmc_iterator(emu,
cat,
param_names,
y,
cov,
rpoints,
obs_nd,
obs_nd_err,
'calc_analytic_nd',
fixed_params=fixed_params,
nwalkers=nwalkers,
nsteps=nsteps,
nburn=nburn): #,\
#resume_from_previous = path.join(savedir, '%d_walkers_%d_steps_chain_shuffled_sham_no_ab.npy'%(nwalkers, nsteps))):
with open(chain_fname, 'a') as f:
np.savetxt(f, pos)
#np.savetxt(path.join(savedir, '%d_walkers_%d_steps_chain_shuffled_sham_3.npy'%(nwalkers, nsteps)), chain)
#np.savetxt(path.join(savedir, '%d_walkers_%d_steps_truth_ld_errors_2.npy'%(nwalkers, nsteps)),\
# np.array([em_params[p] for p in param_names]))
#np.savetxt(path.join(savedir, '%d_walkers_%d_steps_fixed_old_errors_2.npy'%(nwalkers, nsteps)),\
print cat.calc_number_density(em_params)
print cat.calc_analytic_nd(em_params)
from sys import exit
exit(0)
nwalkers = 200
nsteps = 5000
nburn = 0
savedir = '/home/swmclau2/scratch/PearceMCMC/'
chain_fname = path.join(
savedir,
'%d_walkers_%d_steps_chain_vpeak_sham_no_ab_2.npy' % (nwalkers, nsteps))
with open(chain_fname, 'w') as f:
f.write('#' + '\t'.join(param_names) + '\n')
for pos in run_mcmc_iterator(emu, cat, param_names, y, cov, rpoints,obs_nd, obs_nd_err,'calc_analytic_nd', fixed_params = fixed_params,nwalkers = nwalkers, nsteps = nsteps, nburn = nburn,\
resume_from_previous = path.join(savedir, '%d_walkers_%d_steps_chain_vpeak_sham_no_ab.npy'%(nwalkers, nsteps))):
with open(chain_fname, 'a') as f:
np.savetxt(f, pos)
#np.savetxt(path.join(savedir, '%d_walkers_%d_steps_chain_shuffled_sham_3.npy'%(nwalkers, nsteps)), chain)
#np.savetxt(path.join(savedir, '%d_walkers_%d_steps_truth_ld_errors_2.npy'%(nwalkers, nsteps)),\
# np.array([em_params[p] for p in param_names]))
#np.savetxt(path.join(savedir, '%d_walkers_%d_steps_fixed_old_errors_2.npy'%(nwalkers, nsteps)),\
# np.array([fixed_params[p] for p in param_names if p in fixed_params]))