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]))