density_redshifts = c2t.get_dens_redshifts(density_dir, z_low, z_high, bracket=True)
xfrac_redshifts = c2t.get_xfrac_redshifts(xfrac_dir, z_low, z_high, bracket=True)
#List all the data files
dens_files = [density_dir + '%.3fn_all.dat' % z for z in density_redshifts]
vel_files = [velocity_dir + '%.3fv_all.dat' % z for z in density_redshifts]
xfrac_files = [xfrac_dir + 'xfrac3d_%.3f.bin' % z for z in xfrac_redshifts]
#Make the ionization fraction lightcone
xfrac_lightcone, z = c2t.make_lightcone(xfrac_files, z_low, z_high)
#Make the density lightcone
dens_lightcone, z = c2t.make_lightcone(dens_files, z_low, z_high)
#Combine ionization fraction and density to make a dT lightcone
dT_lightcone = c2t.calc_dt_lightcone(xfrac_lightcone, dens_lightcone, \
lowest_z=z.min())
#Make a velocity lightcone
vel_lightcone, z = c2t.make_velocity_lightcone(vel_files, dens_files, \
z_low, z_high)
#Apply redshift space distortions. This is done in the same way as for
#coeval data volumes. Just be sure to set periodic to False and
#to specify the the velocity_axis argument (see the documentation
#of get_distorted_dt for more information)
rsd_dT = c2t.get_distorted_dt(dT_lightcone, vel_lightcone, z, \
num_particles=30, los_axis=2, velocity_axis=0, \
periodic=False)
#Save the results
c2t.save_cbin(output_dir + 'lightcone_rsd.cbin', rsd_dT)
import numpy as np
import c2raytools as c2t
import argparse
import sys
import os
import glob
def parse_options():
parser = argparse.ArgumentParser(prog='make_dt_lightcone', formatter_class=argparse.ArgumentDefaultsHelpFormatter)
parser.add_argument('--xfrac', '-x', type=str, default = None, help='The lightcone file containing the ionized fractions.')
parser.add_argument('--density', '-d', type=str, default = None, help='The lightcone file containing the density.')
parser.add_argument('--output', '-o', type=str, help='The name of the output file.',\
default='dt_lightcone.cbin')
parser.add_argument('--min_z', type=float, default = None, help='The lowest_redshift.')
parser.add_argument('--boxsize', '-b', type=float, default=425, help='The side of the box in Mpc/h.')
args = parser.parse_args()
return args
if __name__ == '__main__':
if len(sys.argv) <= 1:
print 'No arguments given. Use -h to print help.'
sys.exit(2)
args = parse_options()
c2t.set_verbose(True)
c2t.set_sim_constants(args.boxsize)
xfrac, xfile_type = c2t.get_data_and_type(args.xfrac, cbin_bits = 32, cbin_order = 'c')
density, dfile_type = c2t.get_data_and_type(args.density, cbin_bits = 32, cbin_order = 'c')
dt_lightcone = c2t.calc_dt_lightcone(xfrac, density, args.min_z)
c2t.save_cbin(args.output, dt_lightcone)
#First we need lists of all the available ionization fraction and density files.
#Here, we use python's built-in glob command, which makes a list of all such files:
xfrac_files = glob.glob(xfrac_dir + '/xfrac3d_*.bin')
density_files = glob.glob(density_dir + '/*n_all.dat')
#Make the ionization fraction lightcone
xfrac_lightcone, z = c2t.make_lightcone(xfrac_files, z_low = 7.059, z_high = 7.3)
#Make the density lightcone
density_lightcone, z = c2t.make_lightcone(density_files, z_low = 7.059, z_high = 7.3)
#The dT lightcone is made by combining density and ionization fraction.
#If you already have a bunch of dT files, you can make a lightcone directly
#using the make_lightcone method
dt_lightcone = c2t.calc_dt_lightcone(xfrac_lightcone, density_lightcone, lowest_z = z.min())
print dt_lightcone.shape
#Calculate the mean dT along the line-of-sight of the lightcone
dT_mean = c2t.apply_func_along_los(dt_lightcone, func=np.mean, los_axis=2)
#Plot the dT volume
pl.subplot(121)
pl.imshow(dt_lightcone[0,:,:], extent=[z.min(),z.max(), 0, c2t.conv.LB], aspect='auto')
pl.colorbar()
pl.xlabel('$z$')
pl.ylabel('Mpc')
pl.subplot(122)
pl.plot(z, dT_mean)
pl.xlabel('Redshift')
pl.ylabel('Mean brightness temperature')
