def do_auto_correlation(model_name, phase, r, mode='smu-post-recon-std'):
sim_name = '{}_{:02}-{}'.format(sim_name_prefix, cosmology, phase)
filedir = os.path.join(save_dir, sim_name, 'z{}-r{}'.format(redshift, r))
if 'smu' in mode:
DDnpy = np.load(os.path.join(filedir,
'{}-auto-paircount-DD-{}.npy'
.format(model_name, mode)))
DD, _ = rebin_smu_counts(DDnpy, 'DD')
np.savetxt(os.path.join(filedir, '{}-auto-paircount-DD-{}-rebinned.txt'
.format(model_name, mode)),
DD, fmt=txtfmt)
# # create r vector from weighted average of DD pair counts
# savg_vec = s_bins_centre
# savg_vec = np.sum(savg * DD, axis=1) / np.sum(DD, axis=1)
DR_ar, _, RR_ar = analytic_random(1, 1, 1, 1, s_bins, mu_bins, L**3)
assert DD.shape == DR_ar.shape == RR_ar.shape
np.savetxt(os.path.join(filedir,
'{}-auto-paircount-DR-{}-ar.txt'
.format(model_name, mode)),
DR_ar, fmt=txtfmt)
np.savetxt(os.path.join(filedir,
'{}-auto-paircount-RR-{}-ar.txt'
.format(model_name, mode)),
RR_ar, fmt=txtfmt)
xi_s_mu = ls_estimator(DD, DR_ar, DR_ar, RR_ar, RR_ar)
xi_0 = tpcf_multipole(xi_s_mu, mu_bins, order=0)
xi_2 = tpcf_multipole(xi_s_mu, mu_bins, order=2)
xi_0_txt = np.vstack([s_bins_centre, xi_0]).T
xi_2_txt = np.vstack([s_bins_centre, xi_2]).T
for output, tag in zip([xi_s_mu, xi_0_txt, xi_2_txt],
['xi', 'xi_0', 'xi_2']):
np.savetxt(os.path.join(filedir, '{}-auto-{}-{}-ar.txt'
.format(model_name, tag, mode)),
output, fmt=txtfmt)
def multipoles(self, s: np.array, mu: np.array):
if self.list_analytical_moments:
self.s_mu = real2redshift.simps_integrate(
s, mu, self.sim_measurement_best_fit.tpcf.mean,
self.jointpdf_los)
else:
self.s_mu = real2redshift.simps_integrate(
s, mu, self.sim_measurement.tpcf.mean, self.jointpdf_los)
monopole = tpcf_multipole(self.s_mu, mu, order=0)
quadrupole = tpcf_multipole(self.s_mu, mu, order=2)
hexadecapole = tpcf_multipole(self.s_mu, mu, order=4)
#self.wedges = tpcf_wedges(self.s_mu, mu)
return monopole, quadrupole, hexadecapole
def compute_xi2(x,
y,
z,
L,
s_min,
s_max,
n_sbins,
fn_save,
nmubins=15,
nthreads=1):
print("Computing xi_2")
# Set up bins (log)
sbins = np.logspace(np.log10(smin), np.log10(smax),
nsbins + 1) # note the + 1 to nbins
s_avg = 10**(0.5 * (np.log10(sbins)[1:] + np.log10(sbins)[:-1]))
# Use halotools to compute the quadrupole, as in this example:
# https://halotools.readthedocs.io/en/latest/api/halotools.mock_observables.tpcf_multipole.html
sample = np.vstack((x, y, z)).T
mu_bins = np.linspace(0, 1, nmubins)
xi_s_mu = s_mu_tpcf(sample, sbins, mu_bins, period=L)
xi_2 = tpcf_multipole(xi_s_mu, mu_bins, order=1) # Order 1 is quadrupole
print("Saving")
os.makedirs(os.path.dirname(savename), exist_ok=True)
results = np.array([s_avg, xi_2])
np.savetxt(savename, results.T, delimiter=',', fmt=['%f', '%e'])
def multipoles(mu, s_mu):
'''
Computes monopole, quadrupole and hexadecapole of the redshift space correlation function
Args:
s : array of s distances in Mpc/h
mu : array of mu angular bins (between 0 and 1)
Returns:
monopole: monopole evaluated at the given s bins
quadrupole: quadrupole evaluated at the given s bins
hexadecapole: hexadecapole evaluated at the given s bins
'''
monopole = tpcf_multipole(s_mu, mu, order=0)
quadrupole = tpcf_multipole(s_mu, mu, order=2)
hexadecapole = tpcf_multipole(s_mu, mu, order=4)
return monopole, quadrupole, hexadecapole
def xi_rsd(x, y, z, L, smin, smax, nsbins, savename, nthreads=1, order=1):
print("Computing xi_2")
#LOG
sbins = np.logspace(np.log10(smin), np.log10(smax),
nsbins + 1) # note the + 1 to nbins
s_avg = 10**(0.5 * (np.log10(sbins)[1:] + np.log10(sbins)[:-1]))
#LINEAR
#sbins = np.linspace(smin, smax, sbins + 1) # note the + 1 to nbins
#s_avg = 0.5*(sbins[1:] + sbins[:-1])
sample = np.vstack((x, y, z)).T
nmubins = 15
mu_bins = np.linspace(0, 1, nmubins)
xi_s_mu = s_mu_tpcf(sample, sbins, mu_bins, period=L)
xi_2 = tpcf_multipole(xi_s_mu, mu_bins, order=order)
print("Saving")
os.makedirs(os.path.dirname(savename), exist_ok=True)
print(xi_2)
results = np.array([s_avg, xi_2])
np.savetxt(savename, results.T, delimiter=',', fmt=['%f', '%e'])
import numpy as np
from halotools.mock_observables import tpcf, s_mu_tpcf, tpcf_multipole
import matplotlib.pyplot as plt
h = 0.6726
b = 2.23
pos = np.fromfile('sample_input_gal_mx3_float32_0-1100_mpc.dat',
dtype=np.float32).reshape(-1, 4)[:, 1:4]*h
s_bins, mu_bins = np.arange(5, 155, 5), np.arange(0, 1.05, 0.05)
r = (s_bins[:-1] + s_bins[1:])/2
xi = tpcf(pos, s_bins, period=1100)
xi_s_mu = s_mu_tpcf(pos, s_bins, mu_bins, period=1100)
xi_0 = tpcf_multipole(xi_s_mu, mu_bins, order=0)
xi_2 = tpcf_multipole(xi_s_mu, mu_bins, order=2)
fig, ax = plt.subplots()
ax.plot(r, xi*np.square(r), 'o:', label='xi')
ax.plot(r, xi_0*np.square(r), '+:', label='xi_0')
ax.plot(r, xi_2*np.square(r), 'x-.', label='xi_2')
fig.legend()
fig.savefig('correlation.pdf')
dd_all = np.zeros((len(s_bins) - 1) * (len(mu_bins) - 1))
for xyz in ['xyz', 'yzx', 'zxy']:
pos = return_xyz_formatted_array(
x=mock[xyz[0]], y=mock[xyz[1]], z=mock[xyz[2]],
velocity=mock['v'+xyz[2]], velocity_distortion_dimension='z',
period=boxsize, redshift=redshift, cosmology=cosmology)[select]
pos = pos.astype(float)
dd_all += DDsmu(1, n_threads, s_bins, 1, len(mu_bins) - 1, pos[:, 0],
pos[:, 1], pos[:, 2], periodic=True, boxsize=boxsize)[
'npairs'] / 3.0
xi = xi_from_dd(dd_all, len(pos), boxsize, s_bins, mu_bins)
n_jk = 10
for order in [0, 2, 4]:
table['xi{}'.format(order)] = tpcf_multipole(xi, mu_bins, order=order)
table['xi{}_jk'.format(order)] = np.zeros((len(table), n_jk**3))
for i_x, i_y, i_z in tqdm.tqdm(itertools.product(
range(n_jk), range(n_jk), range(n_jk)), total=n_jk**3):
select = ~((pos[:, 0] < boxsize / n_jk * i_x) |
(pos[:, 0] >= boxsize / n_jk * (i_x + 1)) |
(pos[:, 1] < boxsize / n_jk * i_y) |
(pos[:, 1] >= boxsize / n_jk * (i_y + 1)) |
(pos[:, 2] < boxsize / n_jk * i_z) |
(pos[:, 2] >= boxsize / n_jk * (i_z + 1)))
dd_auto = DDsmu(1, 4, s_bins, 1, len(mu_bins) - 1, pos[:, 0][select],
pos[:, 1][select], pos[:, 2][select], periodic=True,
boxsize=boxsize)['npairs']
dd_cross = DDsmu(0, 4, s_bins, 1, len(mu_bins) - 1,
pos[:, 0][~select], pos[:, 1][~select],
def do_subcross_correlation(model, n_sub=3): # n defines number of subvolums
'''
cross-correlation between 1/n_sub^3 of a box to the whole box
n_sub^3 * 16 results are used for emperically estimating covariance matrix
'''
# setting halocat properties to be compatibble with halotools
sim_name = model.mock.header['SimName']
Lbox = model.mock.Lbox
redshift = model.mock.redshift
model_name = model.model_name
gt = model.mock.galaxy_table
ND1 = len(gt)
s_bins = np.arange(0, 150 + step_s_bins, step_s_bins)
s_bins_centre = (s_bins[:-1] + s_bins[1:]) / 2
mu_bins = np.arange(0, 1 + step_mu_bins, step_mu_bins)
filedir = os.path.join(save_dir, sim_name,
'z{}-r{}'.format(redshift, model.r))
for i, j, k in itertools.product(range(n_sub), repeat=3):
linind = i * n_sub**2 + j * n_sub + k # linearised index
# read in pair counts file which has fine bins
D1D2 = np.load(
os.path.join(
filedir,
'{}-cross_{}-paircount-D1D2.npy'.format(model_name, linind)))
# print('Re-binning {} of {} cross-correlation into ({}, {})...'
# .format(linind+1, n_sub**3, s_bins.size-1, mu_bins.size-1))
# set up bins using specifications, re-bin the counts
npairs_D1D2 = rebin(D1D2)
# save re-binned pair ounts
np.savetxt(os.path.join(
filedir, '{}-cross_{}-paircount-D1D2-rebinned.txt'.format(
model_name, linind)),
npairs_D1D2,
fmt=txtfmt)
# read R1D2 counts and re-bin
if use_analytic_randoms:
npairs_R1D2 = np.loadtxt(
os.path.join(
filedir, '{}-cross_{}-paircount-R1D2.txt'.format(
model_name, linind)))
if not use_analytic_randoms or debug_mode:
R1D2 = np.load(
os.path.join(
filedir, '{}-cross_{}-paircount-R1D2.npy'.format(
model_name, linind)))
npairs_R1D2 = rebin(R1D2)
# save re-binned pair ounts
np.savetxt(os.path.join(
filedir, '{}-cross_{}-paircount-R1D2-rebinned.txt'.format(
model_name, linind)),
npairs_R1D2,
fmt=txtfmt)
# calculate cross-correlation from counts using dp estimator
nD1 = ND1 / Lbox.prod()
nR1 = nD1
xi_s_mu = dp_estimator(nD1, nR1, npairs_D1D2, npairs_R1D2)
# print('Calculating cross-correlation for subvolume {} of {}...'
# .format(linind+1, np.power(n_sub, 3)))
xi_0 = tpcf_multipole(xi_s_mu, mu_bins, order=0)
xi_2 = tpcf_multipole(xi_s_mu, mu_bins, order=2)
xi_0_txt = np.vstack([s_bins_centre, xi_0]).transpose()
xi_2_txt = np.vstack([s_bins_centre, xi_2]).transpose()
# save to text
np.savetxt(os.path.join(
filedir, '{}-cross_{}-xi_s_mu.txt'.format(model_name, linind)),
xi_s_mu,
fmt=txtfmt)
np.savetxt(os.path.join(
filedir, '{}-cross_{}-xi_0.txt'.format(model_name, linind)),
xi_0_txt,
fmt=txtfmt)
np.savetxt(os.path.join(
filedir, '{}-cross_{}-xi_2.txt'.format(model_name, linind)),
xi_2_txt,
fmt=txtfmt)
def do_auto_correlation(model):
'''
read in counts, and generate xi_s_mu using bins specified
using the PH (natural) estimator for periodic sim boxes instead of LS
'''
# setting halocat properties to be compatibble with halotools
sim_name = model.mock.header['SimName']
redshift = model.mock.redshift
model_name = model.model_name
s_bins = np.arange(0, 150 + step_s_bins, step_s_bins)
s_bins_centre = (s_bins[:-1] + s_bins[1:]) / 2
mu_bins = np.arange(0, 1 + step_mu_bins, step_mu_bins)
filedir = os.path.join(save_dir, sim_name,
'z{}-r{}'.format(redshift, model.r))
# read in pair counts file which has fine bins
filepath1 = os.path.join(filedir,
'{}-auto-paircount-DD.npy'.format(model_name))
DD = np.load(filepath1)
ND = len(model.mock.galaxy_table)
NR = ND
# re-count pairs in new bins, re-bin the counts
# print('Re-binning auto DD counts into ({}, {})...'
# .format(s_bins.size-1, mu_bins.size-1))
npairs_DD = rebin(DD)
# save re-binned pair ounts
np.savetxt(os.path.join(
filedir, '{}-auto-paircount-DD-rebinned.txt'.format(model_name)),
npairs_DD,
fmt=txtfmt)
if use_analytic_randoms:
filepath2 = os.path.join(filedir,
'{}-auto-paircount-RR.txt'.format(model_name))
npairs_RR = np.loadtxt(filepath2)
if not use_analytic_randoms or debug_mode:
# rebin RR.npy counts
RR = np.load(
os.path.join(filedir,
'{}-auto-paircount-RR.npy'.format(model_name)))
npairs_RR = rebin(RR)
# save re-binned pair ounts
np.savetxt(os.path.join(
filedir, '{}-auto-paircount-RR-rebinned.txt'.format(model_name)),
npairs_RR,
fmt=txtfmt)
xi_s_mu = ph_estimator(ND, NR, npairs_DD, npairs_RR)
# print('Calculating first two orders of auto-correlation multipoles...')
xi_0 = tpcf_multipole(xi_s_mu, mu_bins, order=0)
xi_2 = tpcf_multipole(xi_s_mu, mu_bins, order=2)
xi_0_txt = np.vstack([s_bins_centre, xi_0]).transpose()
xi_2_txt = np.vstack([s_bins_centre, xi_2]).transpose()
# save to text
# print('Saving auto-correlation texts to: {}'.format(filedir))
np.savetxt(os.path.join(filedir, '{}-auto-xi_s_mu.txt'.format(model_name)),
xi_s_mu,
fmt=txtfmt)
np.savetxt(os.path.join(filedir, '{}-auto-xi_0.txt'.format(model_name)),
xi_0_txt,
fmt=txtfmt)
np.savetxt(os.path.join(filedir, '{}-auto-xi_2.txt'.format(model_name)),
xi_2_txt,
fmt=txtfmt)
return xi_s_mu, xi_0_txt, xi_2_txt
def save_tpcfs(r,
s,
mu,
pos,
vel,
los_direction,
cosmology,
boxsize,
saveto,
n_wedges=3):
print('Computing real space correlation function...')
tpcf_real = tpcf_tools.compute_real_tpcf(r, pos, vel, boxsize)
print('Done!')
print('Computing redshift space correlation function...')
tpcf_s_mu = tpcf_tools.compute_tpcf_s_mu(s, mu, pos, vel, los_direction,
cosmology, boxsize)
print('Done!')
print('Computing multipoles...')
monopole = tpcf_multipole(tpcf_s_mu, mu, order=0)
quadrupole = tpcf_multipole(tpcf_s_mu, mu, order=2)
hexadecapole = tpcf_multipole(tpcf_s_mu, mu, order=4)
print('Done!')
# wedges for mu
n_mu_bins_per_wedge = 50
mu_wedges = np.concatenate([
np.linspace(i * (1. / n_wedges),
(i + 1) * 1. / n_wedges - 0.001, n_mu_bins_per_wedge)
for i in range(n_wedges)
], )
mu_wedges[-1] = 1.
print('Computing wedges...')
tpcf_s_mu_wedges = tpcf_tools.compute_tpcf_s_mu(s, mu_wedges, pos, vel,
los_direction, cosmology,
boxsize)
wedges = tpcf_tools.tpcf_wedges(tpcf_s_mu_wedges,
mu_wedges,
n_wedges=n_wedges)
print('Done!')
tpcf_dict = {
'real': {
'tpcf': tpcf_real,
'r': r,
},
'redsfhit': {
's': s,
'mu': mu,
'tpcf_s_mu': tpcf_s_mu,
'monopole': monopole,
'quadrupole': quadrupole,
'hexadecapole': hexadecapole,
'wedges': wedges
}
}
with open(saveto + '.pickle', 'wb') as fp:
pickle.dump(tpcf_dict, fp, protocol=pickle.HIGHEST_PROTOCOL)
def do_subcross_correlation(linind, phase, r, model_name,
mode='smu-post-recon-std',
use_shifted_randoms=True):
sim_name = '{}_{:02}-{}'.format(sim_name_prefix, cosmology, phase)
filedir = os.path.join(save_dir, sim_name, 'z{}-r{}'.format(redshift, r))
print('r = {}, x-correlation subvolume {}...'.format(r, linind))
DDnpy = np.load(os.path.join(filedir, '{}-cross_{}-paircount-DD-{}.npy'
.format(model_name, linind, mode)))
DD, _ = rebin_smu_counts(DDnpy, 'DD') # re-bin and re-weight
np.savetxt(os.path.join(filedir,
'{}-cross_{}-paircount-DD-{}-rebinned.txt'
.format(model_name, linind, mode)),
DD, fmt=txtfmt)
if use_shifted_randoms:
DRnpy = np.load(os.path.join(filedir,
'{}-cross_{}-paircount-DR-{}-sr.npy'
.format(model_name, linind, mode)))
RDnpy = np.load(os.path.join(filedir,
'{}-cross_{}-paircount-RD-{}-sr.npy'
.format(model_name, linind, mode)))
DR, _ = rebin_smu_counts(DRnpy, 'DR')
RD, _ = rebin_smu_counts(RDnpy, 'RD')
for txt, tag in zip([DR, RD], ['DR', 'RD']):
np.savetxt(os.path.join(
filedir, '{}-cross_{}-paircount-{}-{}-sr_rebinned.txt'
.format(model_name, linind, tag, mode)),
txt, fmt=txtfmt)
RR_list = []
for n in range(random_multiplier):
RRnpy = np.load(os.path.join(
filedir, '{}-cross_{}_{}-paircount-RR-{}-sr.npy'
.format(model_name, linind, n, mode)))
RR, _ = rebin_smu_counts(RRnpy, 'RR')
RR_list.append(RR)
RR = np.mean(RR_list, axis=0) # shifted, could be co-adding zeros
np.savetxt(os.path.join(
filedir, '{}-cross_{}-paircount-RR-{}-sr_rebinned.txt'
.format(model_name, linind, mode)),
RR, fmt=txtfmt)
# use analytic RR as denominator in LS estimator
_, _, RR_ar = analytic_random(1, 1, 1, 1, s_bins, mu_bins, L**3)
np.savetxt(os.path.join(
filedir,
'{}-cross_{}-paircount-RR-{}-ar.txt'
.format(model_name, linind, mode)),
RR_ar, fmt=txtfmt)
assert DD.shape == DR.shape == RD.shape == RR.shape == RR_ar.shape
xi_s_mu = ls_estimator(DD, DR, RD, RR, RR_ar)
xi_0 = tpcf_multipole(xi_s_mu, mu_bins, order=0)
xi_2 = tpcf_multipole(xi_s_mu, mu_bins, order=2)
xi_0_txt = np.vstack([s_bins_centre, xi_0]).T
xi_2_txt = np.vstack([s_bins_centre, xi_2]).T
for output, tag in zip([xi_s_mu, xi_0_txt, xi_2_txt],
['xi', 'xi_0', 'xi_2']):
np.savetxt(os.path.join(
filedir, '{}-cross_{}-{}-{}-sr.txt'
.format(model_name, linind, tag, mode)),
output, fmt=txtfmt)
elif 'post' not in mode: # pre-recon covariance, use analytic randoms
DR, RD, RR = analytic_random(1, 1, 1, 1, s_bins, mu_bins, L**3)
for output, tag in zip([DR, RD, RR], ['DR', 'RD', 'RR']):
np.savetxt(os.path.join(
filedir, '{}-cross_{}-paircount-{}-{}-ar.txt'
.format(model_name, linind, tag, mode)),
output, fmt=txtfmt)
# calculate cross-correlation from counts using ls estimator
xi_s_mu = ls_estimator(DD, DR, RD, RR, RR)
xi_0 = tpcf_multipole(xi_s_mu, mu_bins, order=0)
xi_2 = tpcf_multipole(xi_s_mu, mu_bins, order=2)
xi_0_txt = np.vstack([s_bins_centre, xi_0]).T
xi_2_txt = np.vstack([s_bins_centre, xi_2]).T
for output, tag in zip([xi_s_mu, xi_0_txt, xi_2_txt],
['xi', 'xi_0', 'xi_2']):
np.savetxt(os.path.join(
filedir, '{}-cross_{}-{}-{}-ar.txt'
.format(model_name, linind, tag, mode)),
output, fmt=txtfmt)