# Licensed under a 3-clause BSD style license - see LICENSE.rst
"""Gammacat open TeV source catalog.
https://github.com/gammapy/gamma-cat
"""
import logging
import numpy as np
from astropy import units as u
from astropy.table import Table
from gammapy.estimators import FluxPoints
from gammapy.modeling.models import Model, SkyModel
from gammapy.utils.scripts import make_path
from .core import SourceCatalog, SourceCatalogObject, format_flux_points_table
__all__ = ["SourceCatalogGammaCat", "SourceCatalogObjectGammaCat"]
log = logging.getLogger(__name__)
[docs]
class SourceCatalogObjectGammaCat(SourceCatalogObject):
"""One object from the gamma-cat source catalog.
Catalog is represented by `~gammapy.catalog.SourceCatalogGammaCat`.
"""
_source_name_key = "common_name"
def __str__(self):
return self.info()
@property
def flux_points(self):
"""Flux points (`~gammapy.estimators.FluxPoints`)."""
return FluxPoints.from_table(
table=self.flux_points_table,
reference_model=self.sky_model(),
format="gadf-sed",
)
[docs]
def info(self, info="all"):
"""Information string.
Parameters
----------
info : {'all', 'basic', 'position, 'model'}
Comma separated list of options
"""
if info == "all":
info = "basic,position,model"
ss = ""
ops = info.split(",")
if "basic" in ops:
ss += self._info_basic()
if "position" in ops:
ss += self._info_position()
if "model" in ops:
ss += self._info_morph()
ss += self._info_spectral_fit()
ss += self._info_spectral_points()
return ss
def _info_basic(self):
"""Print basic info."""
d = self.data
return (
f"\n*** Basic info ***\n\n"
f"Catalog row index (zero-based): {self.row_index}\n"
f"Common name: {self.name}\n"
f"Gamma names: {d.gamma_names}\n"
f"Fermi names: {d.fermi_names}\n"
f"Other names: {d.other_names}\n"
f"Location: {d.where}\n"
f"Class: {d.classes}\n\n"
f"TeVCat ID: {d.tevcat_id}\n"
f"TeVCat 2 ID: {d.tevcat2_id}\n"
f"TeVCat name: {d.tevcat_name}\n\n"
f"TGeVCat ID: {d.tgevcat_id}\n"
f"TGeVCat name: {d.tgevcat_name}\n\n"
f"Discoverer: {d.discoverer}\n"
f"Discovery date: {d.discovery_date}\n"
f"Seen by: {d.seen_by}\n"
f"Reference: {d.reference_id}\n"
)
def _info_position(self):
"""Print position information."""
d = self.data
return (
f"\n*** Position info ***\n\n"
f"SIMBAD:\n"
f"RA: {d.ra:.3f}\n"
f"DEC: {d.dec:.3f}\n"
f"GLON: {d.glon:.3f}\n"
f"GLAT: {d.glat:.3f}\n"
f"\nMeasurement:\n"
f"RA: {d.pos_ra:.3f}\n"
f"DEC: {d.pos_dec:.3f}\n"
f"GLON: {d.pos_glon:.3f}\n"
f"GLAT: {d.pos_glat:.3f}\n"
f"Position error: {d.pos_err:.3f}\n"
)
def _info_morph(self):
"""Print morphology information."""
d = self.data
return (
f"\n*** Morphology info ***\n\n"
f"Morphology model type: {d.morph_type}\n"
f"Sigma: {d.morph_sigma:.3f}\n"
f"Sigma error: {d.morph_sigma_err:.3f}\n"
f"Sigma2: {d.morph_sigma2:.3f}\n"
f"Sigma2 error: {d.morph_sigma2_err:.3f}\n"
f"Position angle: {d.morph_pa:.3f}\n"
f"Position angle error: {d.morph_pa_err:.3f}\n"
f"Position angle frame: {d.morph_pa_frame}\n"
)
def _info_spectral_fit(self):
"""Print spectral information."""
d = self.data
ss = "\n*** Spectral info ***\n\n"
ss += f"Significance: {d.significance:.3f}\n"
ss += f"Livetime: {d.livetime:.3f}\n"
spec_type = d["spec_type"]
ss += f"\nSpectrum type: {spec_type}\n"
if spec_type == "pl":
ss += f"norm: {d.spec_pl_norm:.3} +- {d.spec_pl_norm_err:.3} (stat) +- {d.spec_pl_norm_err_sys:.3} (sys) cm-2 s-1 TeV-1\n" # noqa: E501
ss += f"index: {d.spec_pl_index:.3} +- {d.spec_pl_index_err:.3} (stat) +- {d.spec_pl_index_err_sys:.3} (sys)\n" # noqa: E501
ss += f"reference: {d.spec_pl_e_ref:.3}\n"
elif spec_type == "pl2":
ss += f"flux: {d.spec_pl2_flux.value:.3} +- {d.spec_pl2_flux_err.value:.3} (stat) +- {d.spec_pl2_flux_err_sys.value:.3} (sys) cm-2 s-1\n" # noqa: E501
ss += f"index: {d.spec_pl2_index:.3} +- {d.spec_pl2_index_err:.3} (stat) +- {d.spec_pl2_index_err_sys:.3} (sys)\n" # noqa: E501
ss += f"e_min: {d.spec_pl2_e_min:.3}\n"
ss += f"e_max: {d.spec_pl2_e_max:.3}\n"
elif spec_type == "ecpl":
ss += f"norm: {d.spec_ecpl_norm.value:.3g} +- {d.spec_ecpl_norm_err.value:.3g} (stat) +- {d.spec_ecpl_norm_err_sys.value:.03g} (sys) cm-2 s-1 TeV-1\n" # noqa: E501
ss += f"index: {d.spec_ecpl_index:.3} +- {d.spec_ecpl_index_err:.3} (stat) +- {d.spec_ecpl_index_err_sys:.3} (sys)\n" # noqa: E501
ss += f"e_cut: {d.spec_ecpl_e_cut.value:.3} +- {d.spec_ecpl_e_cut_err.value:.3} (stat) +- {d.spec_ecpl_e_cut_err_sys.value:.3} (sys) TeV\n" # noqa: E501
ss += f"reference: {d.spec_ecpl_e_ref:.3}\n"
elif spec_type == "none":
pass
else:
raise ValueError(f"Invalid spec_type: {spec_type}")
ss += f"\nEnergy range: ({d.spec_erange_min.value:.3}, {d.spec_erange_max.value:.3}) TeV\n"
ss += f"theta: {d.spec_theta:.3}\n"
ss += "\n\nDerived fluxes:\n"
ss += f"Spectral model norm (1 TeV): {d.spec_dnde_1TeV:.3} +- {d.spec_dnde_1TeV_err:.3} (stat) cm-2 s-1 TeV-1\n" # noqa: E501
ss += f"Integrated flux (>1 TeV): {d.spec_flux_1TeV.value:.3} +- {d.spec_flux_1TeV_err.value:.3} (stat) cm-2 s-1\n" # noqa: E501
ss += f"Integrated flux (>1 TeV): {d.spec_flux_1TeV_crab:.3f} +- {d.spec_flux_1TeV_crab_err:.3f} (% Crab)\n" # noqa: E501
ss += f"Integrated flux (1-10 TeV): {d.spec_eflux_1TeV_10TeV.value:.3} +- {d.spec_eflux_1TeV_10TeV_err.value:.3} (stat) erg cm-2 s-1\n" # noqa: E501
return ss
def _info_spectral_points(self):
"""Print spectral points information."""
d = self.data
ss = "\n*** Spectral points ***\n\n"
ss += f"SED reference ID: {d.sed_reference_id}\n"
ss += f"Number of spectral points: {d.sed_n_points}\n"
ss += f"Number of upper limits: {d.sed_n_ul}\n\n"
table = self.flux_points_table
if table is None:
ss += "\nNo spectral points available for this source."
else:
lines = format_flux_points_table(table).pformat(max_width=-1, max_lines=-1)
ss += "\n".join(lines)
return ss + "\n"
[docs]
def spectral_model(self):
"""Source spectral model (`~gammapy.modeling.models.SpectralModel`).
Parameter errors are statistical errors only.
"""
data = self.data
spec_type = data["spec_type"]
if spec_type == "pl":
tag = "PowerLawSpectralModel"
pars = {
"amplitude": data["spec_pl_norm"],
"index": data["spec_pl_index"],
"reference": data["spec_pl_e_ref"],
}
errs = {
"amplitude": data["spec_pl_norm_err"],
"index": data["spec_pl_index_err"],
}
elif spec_type == "pl2":
e_max = data["spec_pl2_e_max"]
DEFAULT_E_MAX = u.Quantity(1e5, "TeV")
if np.isnan(e_max.value) or e_max.value == 0:
e_max = DEFAULT_E_MAX
tag = "PowerLaw2SpectralModel"
pars = {
"amplitude": data["spec_pl2_flux"],
"index": data["spec_pl2_index"],
"emin": data["spec_pl2_e_min"],
"emax": e_max,
}
errs = {
"amplitude": data["spec_pl2_flux_err"],
"index": data["spec_pl2_index_err"],
}
elif spec_type == "ecpl":
tag = "ExpCutoffPowerLawSpectralModel"
pars = {
"amplitude": data["spec_ecpl_norm"],
"index": data["spec_ecpl_index"],
"lambda_": 1.0 / data["spec_ecpl_e_cut"],
"reference": data["spec_ecpl_e_ref"],
}
errs = {
"amplitude": data["spec_ecpl_norm_err"],
"index": data["spec_ecpl_index_err"],
"lambda_": data["spec_ecpl_e_cut_err"] / data["spec_ecpl_e_cut"] ** 2,
}
elif spec_type == "none":
return None
else:
raise ValueError(f"Invalid spec_type: {spec_type}")
model = Model.create(tag, "spectral", **pars)
for name, value in errs.items():
model.parameters[name].error = value
return model
[docs]
def spatial_model(self):
"""Source spatial model (`~gammapy.modeling.models.SpatialModel`)."""
# TODO : support array input if it should vary along the energy axis.
d = self.data
morph_type = d["morph_type"]
pars = {"lon_0": d["glon"], "lat_0": d["glat"], "frame": "galactic"}
errs = {
"lat_0": self.data["pos_err"],
"lon_0": self.data["pos_err"] / np.cos(self.data["glat"]),
}
if morph_type == "point":
tag = "PointSpatialModel"
elif morph_type == "gauss":
# TODO: add infos back once model support elongation
# pars['x_stddev'] = d['morph_sigma']
# pars['y_stddev'] = d['morph_sigma']
# if not np.isnan(d['morph_sigma2']):
# pars['y_stddev'] = d['morph_sigma2']
# if not np.isnan(d['morph_pa']):
# # TODO: handle reference frame for rotation angle
# pars['theta'] = Angle(d['morph_pa'], 'deg').rad
tag = "GaussianSpatialModel"
pars["sigma"] = d["morph_sigma"]
elif morph_type == "shell":
tag = "ShellSpatialModel"
# TODO: probably we shouldn't guess a shell width here!
pars["radius"] = 0.8 * d["morph_sigma"]
pars["width"] = 0.2 * d["morph_sigma"]
elif morph_type == "none":
return None
else:
raise ValueError(f"Invalid morph_type: {morph_type!r}")
model = Model.create(tag, "spatial", **pars)
for name, value in errs.items():
model.parameters[name].error = value
return model
[docs]
def sky_model(self):
"""Source sky model (`~gammapy.modeling.models.SkyModel`)."""
return SkyModel(
spatial_model=self.spatial_model(),
spectral_model=self.spectral_model(),
name=self.name,
)
def _add_source_meta(self, table):
"""Copy over some information to `table.meta`."""
d = self.data
m = table.meta
m["origin"] = "Data from gamma-cat"
m["source_id"] = d["source_id"]
m["common_name"] = d["common_name"]
m["reference_id"] = d["reference_id"]
@property
def flux_points_table(self):
"""Differential flux points (`~gammapy.estimators.FluxPoints`)."""
d = self.data
table = Table()
table.meta["SED_TYPE"] = "dnde"
self._add_source_meta(table)
valid = np.isfinite(d["sed_e_ref"].value)
if valid.sum() == 0:
return None
table["e_ref"] = d["sed_e_ref"]
table["e_min"] = d["sed_e_min"]
table["e_max"] = d["sed_e_max"]
table["dnde"] = d["sed_dnde"]
table["dnde_err"] = d["sed_dnde_err"]
table["dnde_errn"] = d["sed_dnde_errn"]
table["dnde_errp"] = d["sed_dnde_errp"]
table["dnde_ul"] = d["sed_dnde_ul"]
# Only keep rows that actually contain information
table = table[valid]
for colname in table.colnames:
if not np.isfinite(table[colname]).any():
table.remove_column(colname)
return table
[docs]
class SourceCatalogGammaCat(SourceCatalog):
"""Gammacat open TeV source catalog.
See: https://github.com/gammapy/gamma-cat
One source is represented by `~gammapy.catalog.SourceCatalogObjectGammaCat`.
Parameters
----------
filename : str
Path to the gamma-cat fits file.
Examples
--------
Load the catalog data:
>>> import matplotlib.pyplot as plt
>>> import astropy.units as u
>>> from gammapy.catalog import SourceCatalogGammaCat
>>> cat = SourceCatalogGammaCat()
Access a source by name:
>>> source = cat['Vela Junior']
Access source spectral data and plot it:
>>> ax = plt.subplot()
>>> energy_range = [1, 10] * u.TeV
>>> source.spectral_model().plot(energy_range, ax=ax) # doctest: +SKIP
>>> source.spectral_model().plot_error(energy_range, ax=ax) # doctest: +SKIP
>>> source.flux_points.plot(ax=ax) # doctest: +SKIP
"""
tag = "gamma-cat"
description = "An open catalog of gamma-ray sources"
source_object_class = SourceCatalogObjectGammaCat
[docs]
def __init__(self, filename="$GAMMAPY_DATA/catalogs/gammacat/gammacat.fits.gz"):
filename = make_path(filename)
table = Table.read(filename, hdu=1)
source_name_key = "common_name"
source_name_alias = ("other_names", "gamma_names")
super().__init__(
table=table,
source_name_key=source_name_key,
source_name_alias=source_name_alias,
)
