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mc3d.py
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mc3d.py
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import sys
sys.path = ['/global/u2/h/husni/PZ_Project',
'/global/u2/h/husni/PZ_Project',
'',
'/global/homes/h/husni/.local/lib/python3.8/site-packages',
'/global/homes/h/husni/.local/bin',
'/opt/lsst/software/stack/stack/miniconda3-py38_4.9.2-0.4.3/Linux64/sims_almanac/master-g021b69e146+616205b9df/python',
'/opt/lsst/software/stack/stack/miniconda3-py38_4.9.2-0.4.3/Linux64/sims_downtimeModel/master-g55f72efa65+3e384ed16a/python',
'/opt/lsst/software/stack/stack/miniconda3-py38_4.9.2-0.4.3/Linux64/sims_cloudModel/master-ge3724df529+632df0f48d/python',
'/opt/lsst/software/stack/stack/miniconda3-py38_4.9.2-0.4.3/Linux64/sims_seeingModel/master-ga4bf72ea44+6e62bc95d5/python',
'/opt/lsst/software/stack/stack/miniconda3-py38_4.9.2-0.4.3/Linux64/sims_featureScheduler/master-g5f42dc1c76+c0a10aa3f3/python',
'/opt/lsst/software/stack/stack/miniconda3-py38_4.9.2-0.4.3/Linux64/sims_skybrightness_pre/2.13.0.sims-11-g9ab127b+5f00cb8bf4/python',
'/opt/lsst/software/stack/stack/miniconda3-py38_4.9.2-0.4.3/Linux64/sims_skybrightness_data/2017.05.05-2-gf1b2499/python',
'/opt/lsst/software/stack/stack/miniconda3-py38_4.9.2-0.4.3/Linux64/sims_skybrightness/2.13.0.sims-7-g57b020e+ba01f1af57/python',
'/opt/lsst/software/stack/stack/miniconda3-py38_4.9.2-0.4.3/Linux64/python_extinction/master-g3504403c44+15e725ac18/lib/python',
'/opt/lsst/software/stack/stack/miniconda3-py38_4.9.2-0.4.3/Linux64/astropy_helpers/3.0.2.lsst-1-g9c76ab2/lib/python',
'/opt/lsst/software/stack/stack/miniconda3-py38_4.9.2-0.4.3/Linux64/astropy_helpers/3.0.2.lsst-1-g9c76ab2',
'/opt/lsst/software/stack/stack/miniconda3-py38_4.9.2-0.4.3/Linux64/sncosmo/1.3.0.lsst2-5-gea39e10+3c1685c4f7/lib/python',
'/opt/lsst/software/stack/stack/miniconda3-py38_4.9.2-0.4.3/Linux64/sims_catUtils/2.13.0.sims-16-g9f88571c+4cf1f4b6fb/python',
'/opt/lsst/software/stack/stack/miniconda3-py38_4.9.2-0.4.3/Linux64/sims_survey_fields/2.13.0.sims-1-g3f5255d+616205b9df/python',
'/opt/lsst/software/stack/stack/miniconda3-py38_4.9.2-0.4.3/Linux64/scarlet_extensions/lsst-dev-g9d18589735+5de2e29f4b/lib/python',
'/opt/lsst/software/stack/stack/miniconda3-py38_4.9.2-0.4.3/Linux64/sims_coordUtils/2.13.0.sims-7-gc9b9334+d5a977bfcb/python',
'/opt/lsst/software/stack/stack/miniconda3-py38_4.9.2-0.4.3/Linux64/sims_photUtils/2.13.0.sims-5-ge14a266+aba1a31c29/python',
'/opt/lsst/software/stack/stack/miniconda3-py38_4.9.2-0.4.3/Linux64/pymssql/2.1.1-2-g168068f+ad9f4941ed/lib/python',
'/opt/lsst/software/stack/stack/miniconda3-py38_4.9.2-0.4.3/Linux64/sims_catalogs/2.13.0.sims-9-g8bb9136+47a81b2cae/python',
'/opt/lsst/software/stack/stack/miniconda3-py38_4.9.2-0.4.3/Linux64/sims_utils/2.13.0.sims-46-g370dc29+872406ca88/python',
'/opt/lsst/software/stack/stack/miniconda3-py38_4.9.2-0.4.3/Linux64/palpy/1.8.1-1-ga780397/lib/python',
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'/opt/lsst/software/stack/stack/miniconda3-py38_4.9.2-0.4.3/Linux64/meas_extensions_photometryKron/21.0.0-3-ge02ed75+2dd4ab1e4d/python',
'/opt/lsst/software/stack/stack/miniconda3-py38_4.9.2-0.4.3/Linux64/ctrl_bps/21.0.0-13-g0c9ff3e+5a28569b12/python',
'/opt/lsst/software/stack/stack/miniconda3-py38_4.9.2-0.4.3/Linux64/ctrl_mpexec/21.0.0-25-g2bc75c1+ab0f4fc97f/python',
'/opt/lsst/software/stack/stack/miniconda3-py38_4.9.2-0.4.3/Linux64/ctrl_orca/21.0.0-2-gfca2c14+fcd967797e/python',
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'/opt/lsst/software/stack/stack/miniconda3-py38_4.9.2-0.4.3/Linux64/verify/21.0.0-8-ga0979ac+3aab7553ee/python',
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'/opt/lsst/software/stack/stack/miniconda3-py38_4.9.2-0.4.3/Linux64/ip_isr/21.0.0-14-g07a2928+2dd4ab1e4d/python',
'/opt/lsst/software/stack/stack/miniconda3-py38_4.9.2-0.4.3/Linux64/meas_astrom/21.0.0-4-g591bb35+2dd4ab1e4d/python',
'/opt/lsst/software/stack/stack/miniconda3-py38_4.9.2-0.4.3/Linux64/kht/lsst-dev-g14ffe67dc2+fe93bf5141/cpp/build',
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'/opt/lsst/software/stack/stack/miniconda3-py38_4.9.2-0.4.3/Linux64/proxmin/lsst-dev-g79c0498783/lib/python',
'/opt/lsst/software/stack/stack/miniconda3-py38_4.9.2-0.4.3/Linux64/scarlet/lsst-dev-g965bb5fbbf+f31336177f/lib/python',
'/opt/lsst/software/stack/stack/miniconda3-py38_4.9.2-0.4.3/Linux64/meas_extensions_scarlet/21.0.0-12-g771b9a2+644d7c70fa/python',
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'/opt/lsst/software/stack/stack/miniconda3-py38_4.9.2-0.4.3/Linux64/shapelet/21.0.0-3-g4be5c26+2a0303cc17/python',
'/opt/lsst/software/stack/stack/miniconda3-py38_4.9.2-0.4.3/Linux64/meas_modelfit/21.0.0-2-gecfae73+c0704111f2/python',
'/opt/lsst/software/stack/stack/miniconda3-py38_4.9.2-0.4.3/Linux64/astro_metadata_translator/0.1.0-25-gffa9b84+f5e6047307/python',
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'/opt/lsst/software/stack/stack/miniconda3-py38_4.9.2-0.4.3/Linux64/obs_test/21.0.0-4-ge8a399c+7d01a1857e/python',
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'/opt/lsst/software/stack/stack/miniconda3-py38_4.9.2-0.4.3/Linux64/daf_butler/21.0.0-69-g3ff10e88+06509c8b61/python',
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'/opt/lsst/software/stack/stack/miniconda3-py38_4.9.2-0.4.3/Linux64/meas_algorithms/21.0.0-20-g8cd22d88+ae1e48c0d5/python',
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'/opt/lsst/software/stack/stack/miniconda3-py38_4.9.2-0.4.3/Linux64/log/21.0.0-3-g7d9da8d+616205b9df/python',
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'/opt/lsst/software/stack/stack/miniconda3-py38_4.9.2-0.4.3/Linux64/sconsUtils/21.0.0-7-gd4ecef8/python',
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'/opt/lsst/software/stack/stack/miniconda3-py38_4.9.2-0.4.3/Linux64/afw/21.0.0-27-g37a8c363b+1e633d4884/python',
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'/opt/lsst/software/stack/conda/miniconda3-py38_4.9.2/envs/lsst-scipipe-0.4.3/eups/python',
'/opt/mods/lib/python3.6/site-packages',
'/opt/ovis/lib/python3.6/site-packages',
'/opt/lsst/software/stack/stack/miniconda3-py38_4.9.2-0.4.3/Linux64/meas_extensions_convolved/21.0.0-2-g7713827+138fd9ef6c/python',
'/opt/lsst/software/stack/stack/miniconda3-py38_4.9.2-0.4.3/Linux64/fgcm/lsst-dev-g14fa2066fb/lib/python',
'/opt/lsst/software/stack/supreme',
'/opt/lsst/software/stack/conda/miniconda3-py38_4.9.2/envs/lsst-scipipe-0.4.3/lib/python38.zip',
'/opt/lsst/software/stack/conda/miniconda3-py38_4.9.2/envs/lsst-scipipe-0.4.3/lib/python3.8',
'/opt/lsst/software/stack/conda/miniconda3-py38_4.9.2/envs/lsst-scipipe-0.4.3/lib/python3.8/lib-dynload',
'/opt/lsst/software/stack/conda/miniconda3-py38_4.9.2/envs/lsst-scipipe-0.4.3/lib/python3.8/site-packages',
'/opt/lsst/software/stack/conda/miniconda3-py38_4.9.2/envs/lsst-scipipe-0.4.3/lib/python3.8/site-packages/IPython/extensions',
'/global/u2/h/husni/.ipython']
import numpy as np
import pandas as pd;
from collections import namedtuple
from pprint import pprint;
import sys;
from copy import deepcopy;
import pickle;
import pyccl as ccl
import emcee
from fisher import Fisher, FullPlot, marginalize, plot_contours
from multiprocessing import Pool
obj = pickle.load(open('/global/u2/h/husni/PZ_Project/debuggedFisher.p','rb'))
data = np.array(obj.ccl_cls['C_ell']).reshape(15, 15).T
def lnprob(theta):
cosmo = ccl.Cosmology(Omega_c=theta[1]-0.049,
Omega_b=0.049,
h=theta[2],
sigma8=theta[0],
n_s=0.9645,
transfer_function='eisenstein_hu')
theory = np.array(obj.makeEmceeCells(cosmo)).T;
diff = np.array(data) - np.array(theory)
return -sum(np.dot(diff[l], np.dot(obj.invcov_list[l], diff[l]))/2
for l in range(15)) + lnprior(theta)
def lnprior(theta):
X = {'sigma_8':theta[0], 'omega_m':theta[1], 'h':theta[2]}
mu = {'sigma_8':0.831, 'omega_m':0.3156, 'h':0.6727}
sigma = {'sigma_8':0.14, 'omega_m':0.2, 'h':0.063}
return sum([
np.log(1/(np.sqrt(2*np.pi)*sigma[i])) - (X[i]-mu[i])**2/(2*(sigma[i]**2)) for i in ['sigma_8', 'omega_m', 'h']
])
ndim = 3
nwalkers = 64
nsteps = 100000
fid = np.array([0.831, 0.3156, 0.6727])
p00 = fid + 0.05 * numpy.random.randn(nwalkers, ndim)
filename = "/global/u2/h/husni/PZ_Project/mc3d.h5"
backend = emcee.backends.HDFBackend(filename)
backend.reset(nwalkers, ndim)
with Pool() as pool:
sampler = emcee.EnsembleSampler(nwalkers, ndim, lnprob, pool=pool, backend=backend)
sampler.run_mcmc(p00, nsteps)