path: root/fg21sim/extragalactic/clusters/main.py

# Copyright (c) 2017-2019 Weitian LI <wt@liwt.net>
# MIT License

"""
Simulate the diffuse radio emissions from galaxy clusters.

NOTE
----
Only implement the *giant radio halos* generated by the merger-induced
turbulence accelerations.  Other types of diffuse radio emissions are not
considered yet, e.g., mini-halos, radio relics.

NOTE
----
Only support to simulate in sky patches, not full-sky mode.
"""

import os
import logging
from collections import OrderedDict

import numpy as np

from . import helper
from .psformalism import PSFormalism
from .formation import ClusterFormation
from .halo import RadioHaloAM
from .emission import HaloEmission
from ...sky import get_sky
from ...share import CONFIGS, COSMO
from ...utils.io import dataframe_to_csv, pickle_dump, pickle_load
from ...utils.ds import dictlist_to_dataframe
from ...utils.convert import JyPerPix_to_K
from ...utils.units import UnitConversions as AUC


logger = logging.getLogger(__name__)


class GalaxyClusters:
    """
    Simulate the diffuse radio emissions from the galaxy clusters.

    Attributes
    ----------
    configs : `~ConfigManager`
        A `ConfigManager` instance containing default and user configurations.
        For more details, see the example configuration specifications.
    halo_configs : dict
        A dictionary containing the configurations for halo simulation.
    sky : `~SkyBase`
        The sky instance to deal with the simulation sky as well as the
        output map.
    """
    compID = "extragalactic/clusters"
    name = "galaxy clusters (halos)"

    def __init__(self, configs=CONFIGS):
        self._set_configs(configs)
        self.sky = get_sky(configs)
        self.sky.add_header("CompID", self.compID, "Emission component ID")
        self.sky.add_header("CompName", self.name, "Emission component")
        self.sky.add_header("BUNIT", "K", "[Kelvin] Data unit")
        self.sky.creator = __name__

    def _set_configs(self, configs):
        """
        Load the configs and set the corresponding class attributes.
        """
        sec = self.compID
        self.configs = configs
        self.catalog_outfile = configs.get_path(sec+"/catalog_outfile")
        self.dump_catalog_data = configs.getn(sec+"/dump_catalog_data")
        self.use_dump_catalog_data = configs.getn(
            sec+"/use_dump_catalog_data")
        self.halos_catalog_outfile = configs.get_path(
            sec+"/halos_catalog_outfile")
        self.dump_halos_data = configs.getn(sec+"/dump_halos_data")
        self.use_dump_halos_data = configs.getn(
            sec+"/use_dump_halos_data")
        self.felong_min = configs.getn(sec+"/felong_min")
        self.halo_dropout = configs.getn(sec+"/halo_dropout")
        self.prefix = configs.getn(sec+"/prefix")
        self.output_dir = configs.get_path(sec+"/output_dir")
        self.merger_mass_min = configs.getn(sec+"/merger_mass_min")
        self.time_traceback = configs.getn(sec+"/time_traceback")
        self.kT_out = configs.getn(sec+"/kT_out")
        self.make_maps = configs.getn(sec+"/make_maps")

        self.frequencies = configs.frequencies
        self.filename_pattern = configs.getn("output/filename_pattern")
        self.clobber = configs.getn("output/clobber")

        sec = "extragalactic/halos"
        self.eta_b = configs.getn(sec+"/x_cr")
        self.genuine_emfacc_th = configs.getn(sec+"/genuine_emfacc_th")
        self.genuine_index_th = configs.getn(sec+"/genuine_index_th")

        if self.use_dump_halos_data and (not self.use_dump_catalog_data):
            self.use_dump_catalog_data = True
            logger.warning("Forced to use existing cluster catalog, "
                           "due to 'use_dump_halos_data=True'")

        logger.info("Loaded and set up configurations")

    def _simulate_catalog(self):
        """
        Simulate the (z, mass) catalog of the cluster distribution
        according to the Press-Schechter formalism.

        Catalog Items
        -------------
        z : redshifts
        mass_dm : [Msun] dark matter halo mass
        mass : [Msun] cluster total mass

        Attributes
        ----------
        catalog : list[dict]
        comments : list[str]
        """
        logger.info("Simulating the clusters (z, mass) catalog ...")
        psform = PSFormalism(configs=self.configs)
        psform.calc_dndlnm()
        psform.write()
        counts = psform.calc_cluster_counts(coverage=self.sky.area)
        z, mass, self.comments = psform.sample_z_m(counts)
        fdm = 1 - COSMO.baryon_fraction
        self.catalog = [OrderedDict([("z", z_),
                                     ("mass_dm", m_),
                                     ("mass", m_ / fdm)])
                        for z_, m_ in zip(z, mass)]
        self.comments += [
            "",
            "z - redshift",
            "mass_dm - [Msun] dark matter halo mass",
            "mass - [Msun] cluster total mass",
        ]
        logger.info("Simulated a catalog of %d clusters" % counts)

    def _process_catalog(self):
        """
        Do some basic processes to the catalog:

        * Calculate the cosmic age at cluster's redshift
        * Generate random positions within the sky for each cluster;
        * Generate random elongated fraction;
        * Generate random rotation angle.

        Catalog Items
        -------------
        age : [Gyr] cosmic age at cluster's redshift, ~ cluster age
        lon : [deg] longitudes
        lat : [deg] latitudes
        felong : elongated fraction, defined as the ratio of
                 elliptical semi-major axis to semi-minor axis
        rotation : [deg] rotation angle; uniformly distributed within
                   [0, 360.0)

        NOTE
        ----
        felong (elongated fraction) ::
            Adopt a definition (felong = b/a) similar to the Hubble
            classification for the elliptical galaxies.  Considering that
            radio halos are generally regular, ``felong`` is thus restricted
            within [0.6, 1.0], and sampled from a cut and absolute normal
            distribution centered at 1.0 with sigma ~0.4/3 (<= 3σ).
        """
        logger.info("Preliminary processes to the catalog ...")
        num = len(self.catalog)
        lon, lat = self.sky.random_points(n=num)
        sigma = (1.0 - self.felong_min) / 3.0
        felong = 1.0 - np.abs(np.random.normal(scale=sigma, size=num))
        felong[felong < self.felong_min] = self.felong_min
        rotation = np.random.uniform(low=0.0, high=360.0, size=num)

        for i, cdict in enumerate(self.catalog):
            cdict.update([
                ("age", COSMO.age(cdict["z"])),
                ("lon", lon[i]),
                ("lat", lat[i]),
                ("felong", felong[i]),
                ("rotation", rotation[i]),
            ])

        self.comments += [
            "age - [Gyr] cosmic age at z; ~ cluster age",
            "lon, lat - [deg] longitudes and latitudes",
            "felong - elongated fraction (= b/a)",
            "rotation - [deg] ellipse rotation angle",
        ]
        logger.info("Added catalog items: age, lon, lat, felong, rotation.")

    def _calc_cluster_info(self):
        """
        Calculate some basic information for each cluster.

        Catalog Items
        -------------
        DA : [Mpc] angular diameter distance
        Rvir : [kpc] virial radius
        Rvir_angular : [arcsec] angular virial radius
        kT : [keV] ICM mean temperature
        B : [uG] magnetic field
        """
        logger.info("Calculating basic information for each cluster ...")
        for cdict in self.catalog:
            z, mass = cdict["z"], cdict["mass"]
            Rvir = helper.radius_cluster(mass, z)  # [kpc]
            DA = COSMO.DA(z)  # [Mpc]
            theta = Rvir / (DA*1e3) * AUC.rad2arcsec  # [arcsec]
            kT = helper.kT_cluster(mass, z, kT_out=self.kT_out)  # [keV]
            B = helper.magnetic_field(mass, z, eta_b=self.eta_b,
                                      kT_out=self.kT_out)  # [uG]
            cdict.update([
                ("DA", DA),  # [Mpc]
                ("Rvir", Rvir),  # [kpc]
                ("Rvir_angular", theta),  # [arcsec]
                ("kT", kT),  # [keV]
                ("B", B),  # [uG]
            ])

        self.comments += [
            "DA - [Mpc] angular diameter distance",
            "Rvir - [kpc] virial radius",
            "Rvir_angular - [arcsec] angular virial radius",
            "kT - [keV] ICM mean temperature",
            "B - [uG] magnetic field",
        ]

    def _simulate_mergers(self):
        """
        Simulate the formation history of each cluster to build their
        merger histories.

        Catalog Items
        -------------
        merger_num : number of merger events within the traced period
        merger_mass1, merger_mass2 :
            [Msun] masses of the main and sub clusters of each merger.
        merger_z, merger_t : redshifts and cosmic times [Gyr]
            of each merger event, in backward time ordering.
        """
        logger.info("Simulating merger histories for each cluster ...")
        num = len(self.catalog)
        num_hasmerger = 0
        fdm = 1 - COSMO.baryon_fraction
        for i, cdict in enumerate(self.catalog):
            ii = i + 1
            if ii % 100 == 0:
                logger.info("[%d/%d] %.1f%% ..." % (ii, num, 100*ii/num))
            z0, M0 = cdict["z"], cdict["mass"]
            zmax = COSMO.redshift(COSMO.age(z0) - self.time_traceback)
            clform = ClusterFormation(M0=M0*fdm, z0=z0, zmax=zmax,
                                      merger_mass_min=self.merger_mass_min)
            clform.simulate_mtree(main_only=True)
            mergers = clform.mergers()
            if mergers:
                num_hasmerger += 1
                cdict.update([
                    ("merger_num",   len(mergers)),
                    ("merger_mass1", [ev["M_main"]/fdm for ev in mergers]),
                    ("merger_mass2", [ev["M_sub"]/fdm for ev in mergers]),
                    ("merger_z",     [ev["z"] for ev in mergers]),
                    ("merger_t",     [ev["age"] for ev in mergers]),
                ])
            else:
                cdict.update([
                    ("merger_num",   0),
                    ("merger_mass1", []),
                    ("merger_mass2", []),
                    ("merger_z",     []),
                    ("merger_t",     []),
                ])

        self.comments += [
            "merger_num - number of merger events",
            "merger_mass1 - [Msun] main cluster mass of each merger",
            "merger_mass2 - [Msun] sub cluster mass of each merger",
            "merger_z - redshift of each merger",
            "merger_t - [Gyr] cosmic time at each merger",
        ]
        logger.info("%d (%.1f%%) clusters experienced recent mergers." %
                    (num_hasmerger, 100*num_hasmerger/num))

    def _simulate_halo1(self, clinfo):
        """
        Calculate the radio halo information for the given cluster.

        Parameters
        ----------
        clinfo : dict
            The cluster information from ``self._simulate_mergers()``.

        Returns
        -------
        haloinfo : dict
            The calculated radio halo information.
        """
        merger_num = clinfo["merger_num"]
        M_obs, z_obs = clinfo["mass"], clinfo["z"]
        M1 = clinfo["merger_mass1"][merger_num-1]
        z1 = clinfo["merger_z"][merger_num-1]
        logger.debug("M(%.2e)@z(%.3f) -> M(%.2e)@z(%.3f) with %d merger(s)" %
                     (M1, z1, M_obs, z_obs, merger_num))
        halo = RadioHaloAM(M_obs=M_obs, z_obs=z_obs,
                           M_main=clinfo["merger_mass1"],
                           M_sub=clinfo["merger_mass2"],
                           z_merger=clinfo["merger_z"],
                           merger_num=merger_num,
                           configs=self.configs)
        spectrum = halo.calc_electron_spectrum()
        spectrum_fiducial = halo.calc_electron_spectrum(fiducial=True)
        theta = halo.radius / (clinfo["DA"]*1e3) * AUC.rad2arcsec  # [arcsec]

        haloinfo = OrderedDict(
            **clinfo,
            Rhalo=halo.radius,  # [kpc]
            Rhalo_angular=theta,  # [arcsec]
            spectrum=spectrum,  # [cm^-3]
            spectrum_fiducial=spectrum_fiducial,  # [cm^-3]
            gamma=halo.gamma,  # Lorentz factors
            Ke=halo.injection_rate,  # [cm^-3 Gyr^-1]
        )
        return haloinfo

    def _simulate_halos(self):
        """
        Calculate the radio halo information for each cluster that has mergers.

        Attributes
        ----------
        halos : list[dict]
            Simulated data for each cluster with mergers.
        """
        idx_hasmerger = [idx for idx, cdict in enumerate(self.catalog)
                         if cdict["merger_num"] > 0]
        num = len(idx_hasmerger)
        logger.info("Simulating halos for %d clusters with mergers ..." % num)

        self.halos = []
        for i, idx in enumerate(idx_hasmerger):
            ii = i + 1
            if ii % 50 == 0:
                logger.info("[%d/%d] %.1f%% ..." % (ii, num, 100*ii/num))
            haloinfo = self._simulate_halo1(self.catalog[idx])
            self.halos.append(haloinfo)

        logger.info("Simulated radio halos.")

    def _calc_halos_emission(self):
        """
        Calculate radio emissions at needed frequencies.
        """
        logger.info("Calculating the emission of radio halos ...")
        num = len(self.halos)
        for i, hdict in enumerate(self.halos):
            ii = i + 1
            if ii % 100 == 0:
                logger.info("[%d/%d] %.1f%% ..." % (ii, num, 100*ii/num))

            haloem = HaloEmission(gamma=hdict["gamma"], n_e=hdict["spectrum"],
                                  B=hdict["B"], radius=hdict["Rhalo"],
                                  redshift=hdict["z"])
            freq = self.frequencies
            em = haloem.calc_emissivity(freq)
            power = haloem.calc_power(freq, emissivity=em)
            flux = haloem.calc_flux(freq)
            Tb_mean = haloem.calc_brightness_mean(
                    freq, flux=flux, pixelsize=self.sky.pixelsize)

            freq2 = freq - freq*0.1
            em2 = haloem.calc_emissivity(freq2)
            index = -(np.log(em2)-np.log(em)) / (np.log(freq2)-np.log(freq))

            haloem.n_e = hdict["spectrum_fiducial"]
            em_fiducial = haloem.calc_emissivity(freq)
            em_facc = em / em_fiducial

            hdict.update([
                ("frequency", freq),  # [MHz]
                ("spec_index", index),
                ("emissivity", em),  # [erg/s/cm^3/Hz]
                ("emissivity_facc", em_facc),
                ("power", power),  # [W/Hz]
                ("flux", flux),  # [Jy]
                ("Tb_mean", Tb_mean),  # [K]
            ])

        logger.info("Calculated halo emissions.")

    def _identify_halos(self):
        """
        Determine the formation/genuineness of each radio halo.

        A halo is genuine if both its emissivity acceleration factor >=
        genuine_emfacc_th and its spectral index <= genuine_index_th
        at any frequency.
        """
        logger.info("Identify the genuineness of radio halos ...")
        emfacc_th = self.genuine_emfacc_th
        index_th = self.genuine_index_th
        n = 0
        for hdict in self.halos:
            emfacc = hdict["emissivity_facc"]
            index = hdict["spec_index"]
            genuine = np.any((emfacc >= emfacc_th) & (index <= index_th))
            hdict["genuine"] = genuine
            n += genuine

        logger.info("Identified %d (%.1f%%) genuine halos." %
                    (n, n*100/len(self.halos)))

    def _dropout_halos(self):
        """
        Considering that the (very) massive galaxy clusters are very rare,
        while the simulation sky area is rather small, therefore, once a
        very massive cluster appears, its associated radio halo is also
        very bright and (almost) dominate other intermediate/faint halos,
        causing the simulation results unstable and have large variation.

        If ``halo_dropout`` is given, then select the specified number of
        most luminous radio halos from the catalog, and mark them with
        a property ``drop=True``, which will then be excluded from the
        following halo drawing step, in order to obtain more stable
        simulation results.

        NOTE
        ----
        If the halo data is reloaded from a previously dumped catalog,
        the original dropout markers is just ignored.
        """
        if self.halo_dropout <= 0:
            logger.info("No need to drop out halos.")
            return

        power = np.array([hdict["power"][0] for hdict in self.halos])
        argsort = power.argsort()[::-1]  # max -> min
        idx_drop = argsort[:self.halo_dropout]
        for idx in idx_drop:
            self.halos[idx]["drop"] = True
        logger.info("Marked %d most powerful halos for dropping" %
                    self.halo_dropout)

    def _draw_halos(self):
        """
        Draw the template images for each halo, and cache them for
        simulating the superimposed halos at requested frequencies.

        NOTE
        ----
        The drawn template images are append to the dictionaries of
        the corresponding halo within the ``self.halos``.
        The templates are normalized to have *mean* value of 1.
        """
        idx_kept = [idx for idx, hdict in enumerate(self.halos)
                    if hdict["genuine"] and not hdict.get("drop", False)]
        num = len(idx_kept)
        logger.info("Draw template images for %d halos ..." % num)
        for i, idx in enumerate(idx_kept):
            hdict = self.halos[idx]
            ii = i + 1
            if ii % 100 == 0:
                logger.info("[%d/%d] %.1f%% ..." % (ii, num, 100*ii/num))
            theta_e = hdict["Rhalo_angular"] / self.sky.pixelsize
            template = helper.draw_halo(radius=theta_e,
                                        felong=hdict["felong"],
                                        rotation=hdict["rotation"])
            hdict["template"] = template
        logger.info("Drew halo template images.")

    def _save_catalog_data(self, outfile=None, dump=None, clobber=None):
        """
        Save the simulated cluster catalog (``self.catalog``) by converting
        it into a Pandas DataFrame and writing into a CSV file.

        If ``dump=True``, then the raw data (``self.catalog``) is dumped
        into a Python pickle file, making it easier to be loaded back
        for reuse.
        """
        if outfile is None:
            outfile = self.catalog_outfile
        if dump is None:
            dump = self.dump_catalog_data
        if clobber is None:
            clobber = self.clobber

        if self.use_dump_catalog_data and os.path.exists(outfile):
            os.rename(outfile, outfile+".old")

        logger.info("Converting cluster catalog into a Pandas DataFrame ...")

        # Pad the merger events to be same length
        nmax = max([cdict["merger_num"] for cdict in self.catalog])
        for cdict in self.catalog:
            n = len(cdict["merger_z"])
            if n == nmax:
                continue
            npad = nmax - n
            cdict.update([
                ("merger_mass1", cdict["merger_mass1"] + [None]*npad),
                ("merger_mass2", cdict["merger_mass2"] + [None]*npad),
                ("merger_z",     cdict["merger_z"] + [None]*npad),
                ("merger_t",     cdict["merger_t"] + [None]*npad),
            ])

        keys = list(self.catalog[0].keys())
        catalog_df = dictlist_to_dataframe(self.catalog, keys=keys)
        dataframe_to_csv(catalog_df, outfile=outfile,
                         comment=self.comments, clobber=clobber)
        logger.info("Saved cluster catalog to CSV file: %s" % outfile)

        if dump:
            outfile = os.path.splitext(outfile)[0] + ".pkl"
            if self.use_dump_catalog_data and os.path.exists(outfile):
                os.rename(outfile, outfile+".old")
            pickle_dump([self.catalog, self.comments],
                        outfile=outfile, clobber=clobber)
            logger.info("Dumped catalog raw data to file: %s" % outfile)

    def _save_halos_data(self, outfile=None, dump=None, clobber=None):
        """
        Save the simulated halo data (``self.halos``) by converting it
        into a Pandas DataFrame and writing into a CSV file.  Note that
        excessive properties (e.g., ``gamma``, ``spectrum``) are excluded
        to keep the CSV file reasonable.

        If ``dump=True``, then the raw data (``self.halos``) is dumped
        into a Python pickle file, making it possible to be loaded back
        to quickly calculate the emissions at additional frequencies.
        """
        if outfile is None:
            outfile = self.halos_catalog_outfile
        if dump is None:
            dump = self.dump_halos_data
        if clobber is None:
            clobber = self.clobber

        if self.use_dump_halos_data and os.path.exists(outfile):
            os.rename(outfile, outfile+".old")

        logger.info("Converting halos data into a Pandas DataFrame ...")
        keys_ignored = ["gamma", "spectrum", "spectrum_fiducial", "template"]
        keys = [k for k in self.halos[0].keys() if k not in keys_ignored]
        halos_df = dictlist_to_dataframe(self.halos, keys=keys)
        dataframe_to_csv(halos_df, outfile, clobber=clobber)
        logger.info("Saved halos data to CSV file: %s" % outfile)

        if dump:
            outfile = os.path.splitext(outfile)[0] + ".pkl"
            if self.use_dump_halos_data and os.path.exists(outfile):
                os.rename(outfile, outfile+".old")
            pickle_dump(self.halos, outfile=outfile, clobber=clobber)
            logger.info("Dumped halos raw data to file: %s" % outfile)

    def _outfilepath(self, frequency, **kwargs):
        """
        Generate the path/filename to the output file for writing
        the simulate sky images.

        Parameters
        ----------
        frequency : float
            The frequency of the output sky image.
            Unit: [MHz]

        Returns
        -------
        filepath : str
            The generated filepath for the output sky file.
        """
        filename = self.filename_pattern.format(
            prefix=self.prefix, frequency=frequency, **kwargs)
        filepath = os.path.join(self.output_dir, filename)
        return filepath

    def preprocess(self):
        """
        Perform the preparation procedures for the later simulations.

        Attributes
        ----------
        _preprocessed : bool
            This attribute presents and is ``True`` after the preparation
            procedures have been done.
        """
        if hasattr(self, "_preprocessed") and self._preprocessed:
            return

        logger.info("{name}: preprocessing ...".format(name=self.name))
        if self.use_dump_catalog_data:
            infile = os.path.splitext(self.catalog_outfile)[0] + ".pkl"
            logger.info("Use existing cluster catalog: %s" % infile)
            self.catalog, self.comments = pickle_load(infile)
            logger.info("Loaded cluster catalog of %d clusters" %
                        len(self.catalog))
        else:
            self._simulate_catalog()
            self._process_catalog()
            self._calc_cluster_info()
            self._simulate_mergers()

        if self.use_dump_halos_data:
            infile = os.path.splitext(self.halos_catalog_outfile)[0] + ".pkl"
            logger.info("Use existing halos data: %s" % infile)
            self.halos = pickle_load(infile)
            logger.info("Loaded data of %d halos" % len(self.halos))
            for hdict in self.halos:
                hdict["drop"] = False
            logger.info("Reset dropout status")
        else:
            self._simulate_halos()

        self._calc_halos_emission()
        self._identify_halos()
        self._dropout_halos()
        self._draw_halos()

        self._preprocessed = True

    def simulate_frequency(self, freqidx):
        """
        Simulate the superimposed radio halos image at frequency (by
        frequency index) based on the above simulated halo templates.

        Parameters
        ----------
        freqidx : int
            The index of the frequency in the ``self.frequencies`` where
            to simulate the radio halos image.

        Returns
        -------
        sky : `~SkyBase`
            The simulated sky image of radio halos as a new sky instance.
        """
        freq = self.frequencies[freqidx]
        sky = self.sky.copy()
        sky.frequency = freq
        JyPP2K = JyPerPix_to_K(freq, sky.pixelsize)

        logger.info("Simulating radio halo map at %.2f [MHz] ..." % freq)
        for hdict in self.halos:
            if "template" not in hdict:
                continue
            template = hdict["template"]  # normalized to mean of 1
            Npix = template.size
            flux = hdict["flux"][freqidx]  # [Jy]
            Tmean = (flux/Npix) * JyPP2K  # [K]
            Timg = Tmean * template  # [K]
            center = (hdict["lon"], hdict["lat"])
            sky.add(Timg, center=center)

        logger.info("Done simulate map at %.2f [MHz]." % freq)
        return sky

    def simulate(self):
        """
        Simulate the sky images of radio halos at each frequency.

        Returns
        -------
        skyfiles : list[str]
            List of the filepath to the written sky files
        """
        logger.info("Simulating {name} ...".format(name=self.name))
        skyfiles = []
        if self.make_maps:
            for idx, freq in enumerate(self.frequencies):
                sky = self.simulate_frequency(freqidx=idx)
                outfile = self._outfilepath(frequency=freq)
                sky.write(outfile)
                skyfiles.append(outfile)
        else:
            logger.warning("Map generation disabled!")

        logger.info("Done simulate {name}!".format(name=self.name))
        return skyfiles

    def postprocess(self):
        """
        Do some necessary post-simulation operations.
        """
        logger.info("{name}: postprocessing ...".format(name=self.name))
        logger.info("Save the cluster catalog ...")
        self._save_catalog_data()
        logger.info("Saving the simulated halos catalog and raw data ...")
        self._save_halos_data()