Source code for yt.fields.xray_emission_fields

import os

import numpy as np

from yt.config import ytcfg
from yt.fields.derived_field import DerivedField
from yt.funcs import mylog, only_on_root, parse_h5_attr
from yt.units.yt_array import YTArray, YTQuantity
from yt.utilities.cosmology import Cosmology
from yt.utilities.exceptions import YTException, YTFieldNotFound
from yt.utilities.linear_interpolators import (
from yt.utilities.on_demand_imports import _h5py as h5py

data_version = {"cloudy": 2, "apec": 3}

data_url = ""

def _get_data_file(table_type, data_dir=None):
    data_file = "%s_emissivity_v%d.h5" % (table_type, data_version[table_type])
    if data_dir is None:
        supp_data_dir = ytcfg.get("yt", "supp_data_dir")
        data_dir = supp_data_dir if os.path.exists(supp_data_dir) else "."
    data_path = os.path.join(data_dir, data_file)
    if not os.path.exists(data_path):
        msg = "Failed to find emissivity data file {}! Please download from {}".format(
        raise OSError(msg)
    return data_path

[docs]class EnergyBoundsException(YTException): def __init__(self, lower, upper): self.lower = lower self.upper = upper def __str__(self): return f"Energy bounds are {self.lower:e} to {self.upper:e} keV."
[docs]class ObsoleteDataException(YTException): def __init__(self, table_type): data_file = "%s_emissivity_v%d.h5" % (table_type, data_version[table_type]) self.msg = "X-ray emissivity data is out of date.\n" self.msg += f"Download the latest data from {data_url}/{data_file}." def __str__(self): return self.msg
[docs]class XrayEmissivityIntegrator: r"""Class for making X-ray emissivity fields. Uses hdf5 data tables generated from Cloudy and AtomDB/APEC. Initialize an XrayEmissivityIntegrator object. Parameters ---------- table_type : string The type of data to use when computing the emissivity values. If "cloudy", a file called "cloudy_emissivity.h5" is used, for photoionized plasmas. If, "apec", a file called "apec_emissivity.h5" is used for collisionally ionized plasmas. These files contain emissivity tables for primordial elements and for metals at solar metallicity for the energy range 0.1 to 100 keV. redshift : float, optional The cosmological redshift of the source of the field. Default: 0.0. data_dir : string, optional The location to look for the data table in. If not supplied, the file will be looked for in the location of the YT_DEST environment variable or in the current working directory. use_metals : boolean, optional If set to True, the emissivity will include contributions from metals. Default: True """ def __init__(self, table_type, redshift=0.0, data_dir=None, use_metals=True): filename = _get_data_file(table_type, data_dir=data_dir) only_on_root(, "Loading emissivity data from %s", filename) in_file = h5py.File(filename, mode="r") if "info" in in_file.attrs: only_on_root(, parse_h5_attr(in_file, "info")) if parse_h5_attr(in_file, "version") != data_version[table_type]: raise ObsoleteDataException(table_type) else: only_on_root(, "X-ray '%s' emissivity data version: %s." % (table_type, parse_h5_attr(in_file, "version")), ) self.log_T = in_file["log_T"][:] self.emissivity_primordial = in_file["emissivity_primordial"][:] if "log_nH" in in_file: self.log_nH = in_file["log_nH"][:] if use_metals: self.emissivity_metals = in_file["emissivity_metals"][:] self.ebin = YTArray(in_file["E"], "keV") in_file.close() self.dE = np.diff(self.ebin) self.emid = 0.5 * (self.ebin[1:] + self.ebin[:-1]).to("erg") self.redshift = redshift
[docs] def get_interpolator(self, data_type, e_min, e_max, energy=True): data = getattr(self, f"emissivity_{data_type}") if not energy: data = data[..., :] / self.emid.v e_min = YTQuantity(e_min, "keV") * (1.0 + self.redshift) e_max = YTQuantity(e_max, "keV") * (1.0 + self.redshift) if (e_min - self.ebin[0]) / e_min < -1e-3 or ( e_max - self.ebin[-1] ) / e_max > 1e-3: raise EnergyBoundsException(self.ebin[0], self.ebin[-1]) e_is, e_ie = np.digitize([e_min, e_max], self.ebin) e_is = np.clip(e_is - 1, 0, self.ebin.size - 1) e_ie = np.clip(e_ie, 0, self.ebin.size - 1) my_dE = self.dE[e_is:e_ie].copy() # clip edge bins if the requested range is smaller my_dE[0] -= e_min - self.ebin[e_is] my_dE[-1] -= self.ebin[e_ie] - e_max interp_data = (data[..., e_is:e_ie] * my_dE).sum(axis=-1) if data.ndim == 2: emiss = UnilinearFieldInterpolator( np.log10(interp_data), [self.log_T[0], self.log_T[-1]], "log_T", truncate=True, ) else: emiss = BilinearFieldInterpolator( np.log10(interp_data), [self.log_nH[0], self.log_nH[-1], self.log_T[0], self.log_T[-1]], ["log_nH", "log_T"], truncate=True, ) return emiss
[docs]def add_xray_emissivity_field( ds, e_min, e_max, redshift=0.0, metallicity=("gas", "metallicity"), table_type="cloudy", data_dir=None, cosmology=None, dist=None, ftype="gas", ): r"""Create X-ray emissivity fields for a given energy range. Parameters ---------- e_min : float The minimum energy in keV for the energy band. e_min : float The maximum energy in keV for the energy band. redshift : float, optional The cosmological redshift of the source of the field. Default: 0.0. metallicity : str or tuple of str or float, optional Either the name of a metallicity field or a single floating-point number specifying a spatially constant metallicity. Must be in solar units. If set to None, no metals will be assumed. Default: ("gas", "metallicity") table_type : string, optional The type of emissivity table to be used when creating the fields. Options are "cloudy" or "apec". Default: "cloudy" data_dir : string, optional The location to look for the data table in. If not supplied, the file will be looked for in the location of the YT_DEST environment variable or in the current working directory. cosmology : :class:`~yt.utilities.cosmology.Cosmology`, optional If set and redshift > 0.0, this cosmology will be used when computing the cosmological dependence of the emission fields. If not set, yt's default LCDM cosmology will be used. dist : (value, unit) tuple or :class:`~yt.units.yt_array.YTQuantity`, optional The distance to the source, used for making intensity fields. You should only use this if your source is nearby (not cosmological). Default: None ftype : string, optional The field type to use when creating the fields, default "gas" This will create at least three fields: "xray_emissivity_{e_min}_{e_max}_keV" (erg s^-1 cm^-3) "xray_luminosity_{e_min}_{e_max}_keV" (erg s^-1) "xray_photon_emissivity_{e_min}_{e_max}_keV" (photons s^-1 cm^-3) and if a redshift or distance is specified it will create two others: "xray_intensity_{e_min}_{e_max}_keV" (erg s^-1 cm^-3 arcsec^-2) "xray_photon_intensity_{e_min}_{e_max}_keV" (photons s^-1 cm^-3 arcsec^-2) These latter two are really only useful when making projections. Examples -------- >>> import yt >>> ds = yt.load("sloshing_nomag2_hdf5_plt_cnt_0100") >>> yt.add_xray_emissivity_field(ds, 0.5, 2) >>> p = yt.ProjectionPlot( ... ds, "x", ("gas", "xray_emissivity_0.5_2_keV"), table_type="apec" ... ) >>> """ if not isinstance(metallicity, float) and metallicity is not None: try: metallicity = ds._get_field_info(*metallicity) except YTFieldNotFound as e: raise RuntimeError( f"Your dataset does not have a {metallicity} field! " + "Perhaps you should specify a constant metallicity instead?" ) from e if table_type == "cloudy": # Cloudy wants to scale by nH**2 other_n = "H_nuclei_density" else: # APEC wants to scale by nH*ne other_n = "El_number_density" def _norm_field(field, data): return data[ftype, "H_nuclei_density"] * data[ftype, other_n] ds.add_field( (ftype, "norm_field"), _norm_field, units="cm**-6", sampling_type="local" ) my_si = XrayEmissivityIntegrator(table_type, data_dir=data_dir, redshift=redshift) em_0 = my_si.get_interpolator("primordial", e_min, e_max) emp_0 = my_si.get_interpolator("primordial", e_min, e_max, energy=False) if metallicity is not None: em_Z = my_si.get_interpolator("metals", e_min, e_max) emp_Z = my_si.get_interpolator("metals", e_min, e_max, energy=False) def _emissivity_field(field, data): with np.errstate(all="ignore"): dd = { "log_nH": np.log10(data[ftype, "H_nuclei_density"]), "log_T": np.log10(data[ftype, "temperature"]), } my_emissivity = np.power(10, em_0(dd)) if metallicity is not None: if isinstance(metallicity, DerivedField): my_Z = data[].to("Zsun") else: my_Z = metallicity my_emissivity += my_Z * np.power(10, em_Z(dd)) my_emissivity[np.isnan(my_emissivity)] = 0 return data[ftype, "norm_field"] * YTArray(my_emissivity, "erg*cm**3/s") emiss_name = (ftype, f"xray_emissivity_{e_min}_{e_max}_keV") ds.add_field( emiss_name, function=_emissivity_field, display_name=fr"\epsilon_{{X}} ({e_min}-{e_max} keV)", sampling_type="local", units="erg/cm**3/s", ) def _luminosity_field(field, data): return data[emiss_name] * data[ftype, "mass"] / data[ftype, "density"] lum_name = (ftype, f"xray_luminosity_{e_min}_{e_max}_keV") ds.add_field( lum_name, function=_luminosity_field, display_name=fr"\rm{{L}}_{{X}} ({e_min}-{e_max} keV)", sampling_type="local", units="erg/s", ) def _photon_emissivity_field(field, data): dd = { "log_nH": np.log10(data[ftype, "H_nuclei_density"]), "log_T": np.log10(data[ftype, "temperature"]), } my_emissivity = np.power(10, emp_0(dd)) if metallicity is not None: if isinstance(metallicity, DerivedField): my_Z = data[].to("Zsun") else: my_Z = metallicity my_emissivity += my_Z * np.power(10, emp_Z(dd)) return data[ftype, "norm_field"] * YTArray(my_emissivity, "photons*cm**3/s") phot_name = (ftype, f"xray_photon_emissivity_{e_min}_{e_max}_keV") ds.add_field( phot_name, function=_photon_emissivity_field, display_name=fr"\epsilon_{{X}} ({e_min}-{e_max} keV)", sampling_type="local", units="photons/cm**3/s", ) fields = [emiss_name, lum_name, phot_name] if redshift > 0.0 or dist is not None: if dist is None: if cosmology is None: if hasattr(ds, "cosmology"): cosmology = ds.cosmology else: cosmology = Cosmology() D_L = cosmology.luminosity_distance(0.0, redshift) angular_scale = 1.0 / cosmology.angular_scale(0.0, redshift) dist_fac = ds.quan( 1.0 / (4.0 * np.pi * D_L * D_L * angular_scale * angular_scale).v, "rad**-2", ) else: redshift = 0.0 # Only for local sources! try: # normal behaviour, if dist is a YTQuantity dist = ds.quan(dist.value, dist.units) except AttributeError as e: try: dist = ds.quan(*dist) except (RuntimeError, TypeError): raise TypeError( "dist should be a YTQuantity or a (value, unit) tuple!" ) from e angular_scale = dist / ds.quan(1.0, "radian") dist_fac = ds.quan( 1.0 / (4.0 * np.pi * dist * dist * angular_scale * angular_scale).v, "rad**-2", ) ei_name = (ftype, f"xray_intensity_{e_min}_{e_max}_keV") def _intensity_field(field, data): I = dist_fac * data[emiss_name] return I.in_units("erg/cm**3/s/arcsec**2") ds.add_field( ei_name, function=_intensity_field, display_name=fr"I_{{X}} ({e_min}-{e_max} keV)", sampling_type="local", units="erg/cm**3/s/arcsec**2", ) i_name = (ftype, f"xray_photon_intensity_{e_min}_{e_max}_keV") def _photon_intensity_field(field, data): I = (1.0 + redshift) * dist_fac * data[phot_name] return I.in_units("photons/cm**3/s/arcsec**2") ds.add_field( i_name, function=_photon_intensity_field, display_name=fr"I_{{X}} ({e_min}-{e_max} keV)", sampling_type="local", units="photons/cm**3/s/arcsec**2", ) fields += [ei_name, i_name] for field in fields:"Adding ('%s','%s') field.", field[0], field[1]) return fields