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#!/usr/bin/env python3
#
# Based on 'coolfunc_calc.sh' from 'chandra-acis-analysis/mass_profile'.
#
# Aaron LI
# Created: 2016-06-19
# Updated: 2016-07-11
#
# Change logs:
# 2016-07-11:
# * Use a default config to allow a minimal user config
# 2016-07-04:
# * Use "AstroParams"
# * Update to use 3-column temperature profile
# * Update documentation
# * Update sample configuration file
# 2016-06-27:
# * Minor style fixes
# * Change 'tprofile' to 't_profile'
#
"""
Calculate the *cooling function* profile with respect to the
given *temperature profile* and the average abundance, redshift,
and column density nH, using the XSPEC model 'wabs*apec'.
Emission measure:
EM = \int n_e n_H dV ~= (n_e^2 / ratio_eH) V [ cm^-3 ]
where 'ratio_eH' is the ratio of electron density to proton density (n_H).
APEC normalization returned by XSPEC is simply the *emission measure* of
the gas scaled by the distance:
eta = (\int n_e n_H dV) / (4 pi (D_A (1+z))^2)
The flux calculated with the XSPEC `flux` command has dimension:
Flux: [ photon s^-1 cm^-2 ] or [ erg s^-2 cm^-2 ]
If we let EM=1 and then set the APEC's normalization,
the cooling function is therefore derived by calculating the flux
using the XSPEC `flux` command, and the cooling function has
dimension of [ FLUX / EM ].
See also the documentation of `deproject_sbp.py` for more details.
"""
import argparse
import subprocess
import sys
import os
from datetime import datetime
import numpy as np
import astropy.units as au
from astropy.cosmology import FlatLambdaCDM
from configobj import ConfigObj
from astro_params import AstroParams
config_default = """
## Configuration file for `calc_coolfunc.py`
# temperature profile fitted & extrapolated by model: [r, T]
t_profile = t_profile.txt
# average abundance (unit: solar)
abundance = -1
# abundance table (default: grsa)
abund_table = grsa
# redshift of the object
redshift = -1
# H column density (unit: 10^22 cm^-2)
nh = -1
# energy range within which to calculate the cooling function (unit: keV)
energy_low = 0.7
energy_high = 7.0
# output file of the XSPEC script for cooling function calculation
xspec_script = coolfunc.xcm
# output file of the cooling function profile: [r, CF]
coolfunc = coolfunc_profile.txt
"""
def gen_xspec_script(outfile, data):
"""
Generate the XSPEC script for cooling function profile calculation.
Arguments:
* outfile: output file to save the XSPEC script
* data: dictionary used to format the template XSPEC script
"""
xspec_script = """
# Calculate the cooling function profile w.r.t the temperature profile.
#
# Generated by: %(prog_name)s
# Date: %(cur_date)s
# debug (off)
chatter 0
set xs_return_results 1
set xs_echo_script 0
# set tcl_precision 12
query yes
abund %(abund_table)s
dummyrsp 0.01 100.0 4096 linear
# use model 'wabs*apec'
model wabs*apec & %(nh)s & 1.0 & %(abundance)s & %(redshift)s & %(apec_norm)s & /*
# input and output files
set tpro_fn "%(t_profile)s"
set cf_fn "%(coolfunc)s"
if { [ file exists $cf_fn ] } {
exec rm -fv $cf_fn
}
# open files
set tpro_fd [ open $tpro_fn r ]
set cf_fd [ open $cf_fn w ]
# output file header
puts $cf_fd "# radius flux(%(energy_low)s-%(energy_high)s)"
# read data from temperature profile line by line
while { [ gets $tpro_fd line ] != -1 } {
if {[ regexp -- {^\s*#} $line ] == 1} {
# ignore comment line
continue
}
scan $line "%%f %%f %%f" radius radius_err temperature
#puts "radius: $radius, temperature: $temperature
# set temperature value
newpar 2 $temperature
flux %(energy_low)s %(energy_high)s
tclout flux 1
scan $xspec_tclout "%%f %%f %%f %%f" _ _ _ cf_data
#puts "cf_data: $cf_data"
puts $cf_fd "$radius $cf_data"
}
# close & exit
close $tpro_fd
close $cf_fd
tclexit
""" % data
open(outfile, "w").write(xspec_script)
def calc_apec_norm(z):
"""
Calculate the normalization of the APEC model.
Reference:
https://heasarc.gsfc.nasa.gov/docs/xanadu/xspec/manual/XSmodelApec.html
"""
cosmo = FlatLambdaCDM(H0=AstroParams.H0, Om0=AstroParams.OmegaM0)
D_A = cosmo.angular_diameter_distance(z).to(au.cm).value
norm = 1.0e-14 / (4*np.pi * (D_A * (1+z))**2)
return norm
def calc_coolfunc(xspec_script, verbose=True):
if verbose:
print("Invoke XSPEC to calculate cooling function profile ...")
subprocess.run(args=["xspec", "-", xspec_script],
stdout=subprocess.DEVNULL)
def main():
parser = argparse.ArgumentParser(
description="Calculate the cooling function profile " +
"w.r.t the temperature profile")
parser.add_argument("config", nargs="?", default="coolfunc.conf",
help="config for cooling function calculation " +
"(default: coolfunc.conf)")
args = parser.parse_args()
config = ConfigObj(config_default.splitlines())
config_user = ConfigObj(args.config)
config.merge(config_user)
redshift = config.as_float("redshift")
config_data = {
"prog_name": os.path.basename(sys.argv[0]),
"cur_date": datetime.now().isoformat(),
#
"t_profile": config["t_profile"],
"abundance": config.as_float("abundance"),
"abund_table": config.get("abund_table", "grsa"),
"redshift": redshift,
"nh": config.as_float("nh"),
"energy_low": float(config.get("energy_low", 0.7)),
"energy_high": float(config.get("energy_high", 0.7)),
"xspec_script": config["xspec_script"],
"coolfunc": config["coolfunc"],
"apec_norm": calc_apec_norm(z=redshift),
}
gen_xspec_script(outfile=config["xspec_script"], data=config_data)
calc_coolfunc(xspec_script=config["xspec_script"])
if __name__ == "__main__":
main()
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