From 18c9a3c27e1e39e42b5390b42194e12d6875c282 Mon Sep 17 00:00:00 2001
From: Aaron LI <aaronly.me@outlook.com>
Date: Fri, 24 Jun 2016 14:20:37 +0800
Subject: Add calc_mass_potential.py: currently only calculate the gas mass
 profile

---
 calc_mass_potential.py | 329 +++++++++++++++++++++++++++++++++++++++++++++++++
 1 file changed, 329 insertions(+)
 create mode 100755 calc_mass_potential.py

diff --git a/calc_mass_potential.py b/calc_mass_potential.py
new file mode 100755
index 0000000..22c3ccd
--- /dev/null
+++ b/calc_mass_potential.py
@@ -0,0 +1,329 @@
+#!/usr/bin/env python3
+#
+# Weitian LI
+# Created: 2016-06-24
+# Updated: 2016-06-24
+#
+
+"""
+Calculate the (gas and gravitational) mass profile and gravitational
+potential profile from the electron number density profile.
+The temperature profile is required.
+
+References:
+[1] Ettori et al, 2013, Space Science Review, 177, 119-154
+
+
+Sample configuration file:
+------------------------------------------------------------
+## Configuration for `calc_mass_potential.py`
+## Date: 2016-06-24
+
+# redshift used for pixel to distance conversion
+redshift = <REDSHIFT>
+
+# electron density profile
+ne_profile = ne_profile.txt
+
+# cooling function profile
+cf_profile = coolfunc_profile.txt
+# unit of the CF profile radius (default: pixel)
+cf_unit = "pixel"
+
+# temperature profile
+t_profile = t_profile.txt
+# unit of the T profile radius (default: pixel)
+t_unit = "pixel"
+
+# number of data points for the output profile calculation
+num_dp = 100
+
+# output gas mass profile
+m_gas_profile = mass_gas_profile.txt
+
+------------------------------------------------------------
+"""
+
+import argparse
+
+import numpy as np
+import astropy.units as au
+import scipy.interpolate as interpolate
+import scipy.integrate as integrate
+from configobj import ConfigObj
+
+from astro_params import AstroParams, ChandraPixel
+from projection import Projection
+
+
+class DensityProfile:
+    """
+    Utilize the 3D (electron number or gas mass) density profile to
+    calculate the following quantities:
+    * 2D projected surface brightness (requires cooling function profile)
+    * gas mass profile (integrated, M_gas(<r))
+    * gravitational mass profile (M(<r); requires temperature profile)
+    * gravitational potential profile (cut at the largest available radius)
+
+    NOTE:
+    * The radii (of density profile and cooling function profile)
+      should have unit [ cm ]
+    * The density should have unit [ cm^-3 ] or [ g cm^-3 ]
+    """
+    # allowed density profile types
+    DENSITY_TYPES = ["electron", "gas"]
+    # input density data: [r, r_err, d]
+    r = None
+    r_err = None
+    d = None
+    # electron number density
+    ne = None
+    # gas mass density
+    rho_gas = None
+    # cooling function profile
+    cf_radius = None
+    cf_value = None
+    # temperature profile
+    t_radius = None
+    t_value = None
+    # interpolated profiles
+    d_interp = None
+    cf_interp = None
+    t_interp = None
+    # generated radial data points for profile calculation
+    radius = None
+    radius_err = None
+    # gas mass profile: M_gas(<r); same length as the above 'radius'
+    m_gas = None
+    # total (gravitational) mass profile: M_total(<r)
+    m_total = None
+    # potential profile (cut at the largest available radius)
+    potential = None
+
+    def __init__(self, density, density_type="electron"):
+        self.load_data(data=density, density_type=density_type)
+
+    def load_data(self, data, density_type="electron"):
+        if density_type not in self.DENSITY_TYPES:
+            raise ValueError("invalid density_types: %s" % density_type)
+        # 3-column density profile: [r, r_err, density]
+        self.r = data[:, 0].copy()
+        self.r_err = data[:, 1].copy()
+        self.d = data[:, 2].copy()
+        self.density_type = density_type
+
+    def load_cf_profile(self, data):
+        # 2-column cooling function profile: r[cm], cf[flux/EM]
+        self.cf_radius = data[:, 0].copy()
+        self.cf_value = data[:, 1].copy()
+
+    def load_t_profile(self, data):
+        # 2-column temperature profile: r[cm], T[keV]
+        self.t_radius = data[:, 0].copy()
+        self.t_value = data[:, 1].copy()
+
+    def calc_brightness(self):
+        """
+        Project the electron number density or gas mass density profile
+        to calculate the 2D surface brightness profile.
+        """
+        if self.cf_radius is None or self.cf_value is None:
+            raise ValueError("cooling function profile missing")
+        ne = self.calc_electron_density()
+        # flux per unit volume
+        flux = self.cf_interp(self.r) * ne ** 2 / AstroParams.ratio_ne_np
+        # project the 3D flux
+        projector = Projection(rout=self.r+self.r_err)
+        brightness = projector.project(flux)
+        return brightness
+
+    def calc_electron_density(self):
+        """
+        Calculate the electron number density from the gas mass density
+        if necessary.
+        """
+        if self.density_type == "electron":
+            self.ne = self.d.copy()
+        elif self.density_type == "gas":
+            self.ne = self.d / AstroParams.m_atom / AstroParams.mu_e
+        return self.ne
+
+    def calc_gas_density(self):
+        """
+        Calculate the gas mass density from the electron number density
+        if necessary.
+        """
+        if self.density_type == "electron":
+            self.rho_gas = self.d * AstroParams.mu_e * AstroParams.m_atom
+        elif self.density_type == "gas":
+            self.rho_gas = self.d.copy()
+        return self.rho_gas
+
+    def interpolate(self):
+        """
+        Interpolate the density profile, cooling function profile,
+        and temperature profile.
+
+        NOTE:
+        * Linear interpolation may be bad because the total mass calculation
+          needs to take the derivative of electron density profile and
+          temperature profile.  Therefore, smooth spline is a better choice.
+        * Allow cooling function profile and temperature profile to be
+          extrapolated by filling with the last value if necessary.
+
+        XXX:
+        * How to extrapolate the smooth spline if necessary ??
+        """
+        # density profile
+        # insert a data point at radius of zero
+        self.d_interp = interpolate.interp1d(
+            x=np.concatenate([[0.0], self.r]),
+            y=np.concatenate([[self.d[0]], self.d]),
+            kind="linear",
+            bounds_error=False, fill_value=self.d[-1],
+            assume_sorted=True)
+        if self.ne is not None:
+            self.ne_interp = interpolate.interp1d(
+                x=np.concatenate([[0.0], self.r]),
+                y=np.concatenate([[self.ne[0]], self.ne]),
+                kind="linear",
+                bounds_error=False, fill_value=self.ne[-1],
+                assume_sorted=True)
+        if self.rho_gas is not None:
+            self.rho_gas_interp = interpolate.interp1d(
+                x=np.concatenate([[0.0], self.r]),
+                y=np.concatenate([[self.rho_gas[0]], self.rho_gas]),
+                kind="linear",
+                bounds_error=False, fill_value=self.rho_gas[-1],
+                assume_sorted=True)
+        # cooling function profile
+        self.cf_interp = interpolate.interp1d(
+            x=self.cf_radius, y=self.cf_value, kind="linear",
+            bounds_error=False, fill_value=self.cf_value[-1],
+            assume_sorted=True)
+        # temperature profile
+        self.t_interp = interpolate.interp1d(
+            x=self.t_radius, y=self.t_value, kind="linear",
+            bounds_error=False, fill_value=self.t_value[-1],
+            assume_sorted=True)
+
+    def gen_radius(self, num=100):
+        """
+        Generate radial points for following mass and potential calculation.
+
+        The generated radial points are logarithmic-evenly distributed.
+        """
+        rout = self.r + self.r_err
+        rout_new = np.logspace(np.log10(rout[0]), np.log10(rout[-1]),
+                               num=num, base=10.0)
+        rin_new = np.concatenate([[0.0], rout_new[:-1]])
+        self.radius = (rout_new + rin_new) / 2.0
+        self.radius_err = (rout_new - rin_new) / 2.0
+
+    def calc_mass_gas(self, verbose=False):
+        """
+        Calculate the gas mass profile, i.e., the mass of the gas within
+        each radius.
+
+        Reference: ref.[1], eq.(9)
+        """
+        def _f_rho_gas(r):
+            return self.rho_gas_interp(r) * 4*np.pi * r**2
+        #
+        m_gas = np.zeros(self.radius.shape)
+        if verbose:
+            print("Calculating the gas mass profile (#%d) ... " % len(m_gas))
+        for i, r in enumerate(self.radius):
+            if verbose and (i+1) % 10 == 0:
+                print("%d..." % (i+1), end="", flush=True)
+            # integrated gas mass [ g ]
+            m_gas[i] = integrate.quad(_f_rho_gas, a=0.0, b=r,
+                                      epsabs=1.0e5, epsrel=1.e-2)[0]
+        if verbose:
+            print("DONE!", flush=True)
+        self.m_gas = m_gas
+        return m_gas
+
+    def calc_mass_total(self, verbose=True):
+        """
+        Calculate the total mass (i.e., gravitational mass) profile,
+        under the assumption of hydrostatic equilibrium (HE).
+
+        References: ref.[1], eq.(5,6,7)
+        """
+        if self.cf_radius is None or self.cf_value is None:
+            raise ValueError("cooling function profile required")
+        if self.t_radius is None or self.t_value is None:
+            raise ValueError("temperature profile required")
+        #
+        m_total = np.zeros(self.radius.shape)
+        if verbose:
+            print("Calculating the total mass profile (#%d) ... " %
+                  len(m_total))
+            # TODO:
+        self.m_total = m_total
+        return m_total
+
+    def save(self, profile, outfile):
+        if profile == "mass_gas":
+            data = np.column_stack([self.radius,
+                                    self.radius_err,
+                                    self.m_gas])
+            header = "radius[cm]  radius_err[cm]  mass_gas(<r)[g]"
+        else:
+            raise ValueError("unknown profile name: %s" % profile)
+        np.savetxt(outfile, data, header=header)
+
+
+def main():
+    parser = argparse.ArgumentParser(
+            description="Calculate the mass and potential profiles")
+    parser.add_argument("config", nargs="?", default="mass_potential.conf",
+                        help="config for mass and potential profiles " +
+                             "calculation (default: mass_potential.conf)")
+    args = parser.parse_args()
+
+    config = ConfigObj(args.config)
+
+    redshift = config.as_float("redshift")
+    pixel = ChandraPixel(z=redshift)
+
+    ne_profile = np.loadtxt(config["ne_profile"])
+
+    cf_profile = np.loadtxt(config["cf_profile"])
+    cf_unit = "pixel"
+    try:
+        cf_unit = config["cf_unit"]
+    except KeyError:
+        pass
+    if cf_unit == "pixel":
+        conv_factor = pixel.get_length().to(au.cm).value
+    else:
+        conv_factor = au.Unit(cf_unit).to(au.cm)
+    cf_profile[:, 0] *= conv_factor
+
+    t_profile = np.loadtxt(config["t_profile"])
+    t_unit = "pixel"
+    try:
+        t_unit = config["t_unit"]
+    except KeyError:
+        pass
+    if t_unit == "pixel":
+        conv_factor = pixel.get_length().to(au.cm).value
+    else:
+        conv_factor = au.Unit(t_unit).to(au.cm)
+    t_profile[:, 0] *= conv_factor
+
+    density_profile = DensityProfile(density=ne_profile,
+                                     density_type="electron")
+    density_profile.load_cf_profile(cf_profile)
+    density_profile.load_t_profile(t_profile)
+    density_profile.calc_gas_density()
+    density_profile.interpolate()
+    density_profile.gen_radius(num=config.as_int("num_dp"))
+    density_profile.calc_mass_gas(verbose=True)
+    density_profile.save(profile="mass_gas", outfile=config["m_gas_profile"])
+
+
+if __name__ == "__main__":
+    main()
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