# Licensed under a 3-clause BSD style license - see LICENSE.rst
"""Spectral models for Gammapy."""
import operator
import numpy as np
from scipy.optimize import brentq
import astropy.units as u
from astropy.table import Table
from ..utils.energy import EnergyBounds
from ..utils.scripts import make_path
from ..utils.fitting import Parameter, Parameters, Model
from ..utils.interpolation import ScaledRegularGridInterpolator
from .utils import integrate_spectrum
__all__ = [
"SpectralModel",
"ConstantModel",
"CompoundSpectralModel",
"PowerLaw",
"PowerLaw2",
"ExponentialCutoffPowerLaw",
"ExponentialCutoffPowerLaw3FGL",
"PLSuperExpCutoff3FGL",
"LogParabola",
"TableModel",
"AbsorbedSpectralModel",
"Absorption",
"NaimaModel",
]
[docs]class SpectralModel(Model):
"""Spectral model base class.
Derived classes should store their parameters as
`~gammapy.utils.modeling.Parameters`
See for example return pardict of
`~gammapy.spectrum.models.PowerLaw`.
"""
[docs] def __call__(self, energy):
"""Call evaluate method of derived classes"""
kwargs = dict()
for par in self.parameters.parameters:
quantity = par.quantity
if quantity.unit.physical_type == "energy":
quantity = quantity.to(energy.unit)
kwargs[par.name] = quantity
return self.evaluate(energy, **kwargs)
def __mul__(self, model):
if not isinstance(model, SpectralModel):
model = ConstantModel(const=model)
return CompoundSpectralModel(self, model, operator.mul)
def __rmul__(self, model):
# This is needed to support e.g. 5 * model
return self.__mul__(model)
def __add__(self, model):
if not isinstance(model, SpectralModel):
model = ConstantModel(const=model)
return CompoundSpectralModel(self, model, operator.add)
def __radd__(self, model):
return self.__add__(model)
def __sub__(self, model):
if not isinstance(model, SpectralModel):
model = ConstantModel(const=model)
return CompoundSpectralModel(self, model, operator.sub)
def __rsub__(self, model):
return self.__sub__(model)
def __truediv__(self, model):
if not isinstance(model, SpectralModel):
model = ConstantModel(const=model)
return CompoundSpectralModel(self, model, operator.truediv)
def __rtruediv__(self, model):
return self.__div__(model)
def _parse_uarray(self, uarray):
from uncertainties import unumpy
values = unumpy.nominal_values(uarray)
errors = unumpy.std_devs(uarray)
return values, errors
def _convert_energy(self, energy):
if "reference" in self.parameters.names:
return energy.to(self.parameters["reference"].unit)
elif "emin" in self.parameters.names:
return energy.to(self.parameters["emin"].unit)
else:
return energy
[docs] def evaluate_error(self, energy):
"""Evaluate spectral model with error propagation.
Parameters
----------
energy : `~astropy.units.Quantity`
Energy at which to evaluate
Returns
-------
flux, flux_error : tuple of `~astropy.units.Quantity`
Tuple of flux and flux error.
"""
energy = self._convert_energy(energy)
unit = self(energy).unit
upars = self.parameters._ufloats
uarray = self.evaluate(energy.value, **upars)
return self._parse_uarray(uarray) * unit
[docs] def integral(self, emin, emax, **kwargs):
r"""Integrate spectral model numerically.
.. math::
F(E_{min}, E_{max}) = \int_{E_{min}}^{E_{max}} \phi(E) dE
If array input for ``emin`` and ``emax`` is given you have to set
``intervals=True`` if you want the integral in each energy bin.
Parameters
----------
emin, emax : `~astropy.units.Quantity`
Lower and upper bound of integration range.
**kwargs : dict
Keyword arguments passed to :func:`~gammapy.spectrum.integrate_spectrum`
"""
return integrate_spectrum(self, emin, emax, **kwargs)
[docs] def integral_error(self, emin, emax, **kwargs):
"""Integrate spectral model numerically with error propagation.
Parameters
----------
emin, emax : `~astropy.units.Quantity`
Lower adn upper bound of integration range.
**kwargs : dict
Keyword arguments passed to func:`~gammapy.spectrum.integrate_spectrum`
Returns
-------
integral, integral_error : tuple of `~astropy.units.Quantity`
Tuple of integral flux and integral flux error.
"""
emin = self._convert_energy(emin)
emax = self._convert_energy(emax)
unit = self.integral(emin, emax, **kwargs).unit
upars = self.parameters._ufloats
def f(x):
return self.evaluate(x, **upars)
uarray = integrate_spectrum(f, emin.value, emax.value, **kwargs)
return self._parse_uarray(uarray) * unit
[docs] def energy_flux(self, emin, emax, **kwargs):
r"""Compute energy flux in given energy range.
.. math::
G(E_{min}, E_{max}) = \int_{E_{min}}^{E_{max}} E \phi(E) dE
Parameters
----------
emin, emax : `~astropy.units.Quantity`
Lower and upper bound of integration range.
**kwargs : dict
Keyword arguments passed to func:`~gammapy.spectrum.integrate_spectrum`
"""
def f(x):
return x * self(x)
return integrate_spectrum(f, emin, emax, **kwargs)
[docs] def energy_flux_error(self, emin, emax, **kwargs):
r"""Compute energy flux in given energy range with error propagation.
.. math::
G(E_{min}, E_{max}) = \int_{E_{min}}^{E_{max}} E \phi(E) dE
Parameters
----------
emin, emax : `~astropy.units.Quantity`
Lower bound of integration range.
**kwargs : dict
Keyword arguments passed to :func:`~gammapy.spectrum.integrate_spectrum`
Returns
-------
energy_flux, energy_flux_error : tuple of `~astropy.units.Quantity`
Tuple of energy flux and energy flux error.
"""
emin = self._convert_energy(emin)
emax = self._convert_energy(emax)
unit = self.energy_flux(emin, emax, **kwargs).unit
upars = self.parameters._ufloats
def f(x):
return x * self.evaluate(x, **upars)
uarray = integrate_spectrum(f, emin.value, emax.value, **kwargs)
return self._parse_uarray(uarray) * unit
[docs] def to_dict(self):
"""Convert to dict."""
retval = self.parameters.to_dict()
retval["name"] = self.__class__.__name__
return retval
[docs] @classmethod
def from_dict(cls, val):
"""Create from dict."""
val_copy = val.copy()
classname = val_copy.pop("name")
parameters = Parameters.from_dict(val_copy)
model = globals()[classname]()
model.parameters = parameters
model.parameters.covariance = parameters.covariance
return model
[docs] def plot(
self,
energy_range,
ax=None,
energy_unit="TeV",
flux_unit="cm-2 s-1 TeV-1",
energy_power=0,
n_points=100,
**kwargs
):
"""Plot spectral model curve.
kwargs are forwarded to `matplotlib.pyplot.plot`
By default a log-log scaling of the axes is used, if you want to change
the y axis scaling to linear you can use::
from gammapy.spectrum.models import ExponentialCutoffPowerLaw
from astropy import units as u
pwl = ExponentialCutoffPowerLaw()
ax = pwl.plot(energy_range=(0.1, 100) * u.TeV)
ax.set_yscale('linear')
Parameters
----------
ax : `~matplotlib.axes.Axes`, optional
Axis
energy_range : `~astropy.units.Quantity`
Plot range
energy_unit : str, `~astropy.units.Unit`, optional
Unit of the energy axis
flux_unit : str, `~astropy.units.Unit`, optional
Unit of the flux axis
energy_power : int, optional
Power of energy to multiply flux axis with
n_points : int, optional
Number of evaluation nodes
Returns
-------
ax : `~matplotlib.axes.Axes`, optional
Axis
"""
import matplotlib.pyplot as plt
ax = plt.gca() if ax is None else ax
emin, emax = energy_range
energy = EnergyBounds.equal_log_spacing(emin, emax, n_points, energy_unit)
# evaluate model
flux = self(energy).to(flux_unit)
y = self._plot_scale_flux(energy, flux, energy_power)
ax.plot(energy.value, y.value, **kwargs)
self._plot_format_ax(ax, energy, y, energy_power)
return ax
[docs] def plot_error(
self,
energy_range,
ax=None,
energy_unit="TeV",
flux_unit="cm-2 s-1 TeV-1",
energy_power=0,
n_points=100,
**kwargs
):
"""Plot spectral model error band.
.. note::
This method calls ``ax.set_yscale("log", nonposy='clip')`` and
``ax.set_xscale("log", nonposx='clip')`` to create a log-log representation.
The additional argument ``nonposx='clip'`` avoids artefacts in the plot,
when the error band extends to negative values (see also
https://github.com/matplotlib/matplotlib/issues/8623).
When you call ``plt.loglog()`` or ``plt.semilogy()`` explicitely in your
plotting code and the error band extends to negative values, it is not
shown correctly. To circumvent this issue also use
``plt.loglog(nonposx='clip', nonposy='clip')``
or ``plt.semilogy(nonposy='clip')``.
Parameters
----------
ax : `~matplotlib.axes.Axes`, optional
Axis
energy_range : `~astropy.units.Quantity`
Plot range
energy_unit : str, `~astropy.units.Unit`, optional
Unit of the energy axis
flux_unit : str, `~astropy.units.Unit`, optional
Unit of the flux axis
energy_power : int, optional
Power of energy to multiply flux axis with
n_points : int, optional
Number of evaluation nodes
**kwargs : dict
Keyword arguments forwarded to `matplotlib.pyplot.fill_between`
Returns
-------
ax : `~matplotlib.axes.Axes`, optional
Axis
"""
import matplotlib.pyplot as plt
ax = plt.gca() if ax is None else ax
kwargs.setdefault("facecolor", "black")
kwargs.setdefault("alpha", 0.2)
kwargs.setdefault("linewidth", 0)
emin, emax = energy_range
energy = EnergyBounds.equal_log_spacing(emin, emax, n_points, energy_unit)
flux, flux_err = self.evaluate_error(energy).to(flux_unit)
y_lo = self._plot_scale_flux(energy, flux - flux_err, energy_power)
y_hi = self._plot_scale_flux(energy, flux + flux_err, energy_power)
where = (energy >= energy_range[0]) & (energy <= energy_range[1])
ax.fill_between(energy.value, y_lo.value, y_hi.value, where=where, **kwargs)
self._plot_format_ax(ax, energy, y_lo, energy_power)
return ax
@staticmethod
def _plot_format_ax(ax, energy, y, energy_power):
ax.set_xlabel("Energy [{}]".format(energy.unit))
if energy_power > 0:
ax.set_ylabel("E{} * Flux [{}]".format(energy_power, y.unit))
else:
ax.set_ylabel("Flux [{}]".format(y.unit))
ax.set_xscale("log", nonposx="clip")
ax.set_yscale("log", nonposy="clip")
@staticmethod
def _plot_scale_flux(energy, flux, energy_power):
try:
eunit = [_ for _ in flux.unit.bases if _.physical_type == "energy"][0]
except IndexError:
eunit = energy.unit
y = flux * np.power(energy, energy_power)
return y.to(flux.unit * eunit ** energy_power)
[docs] def spectral_index(self, energy, epsilon=1e-5):
"""Compute spectral index at given energy.
Parameters
----------
energy : `~astropy.units.Quantity`
Energy at which to estimate the index
epsilon : float
Fractional energy increment to use for determining the spectral index.
Returns
-------
index : float
Estimated spectral index.
"""
f1 = self(energy)
f2 = self(energy * (1 + epsilon))
return np.log(f1 / f2) / np.log(1 + epsilon)
[docs] def inverse(self, value, emin=0.1 * u.TeV, emax=100 * u.TeV):
"""Return energy for a given function value of the spectral model.
Calls the `scipy.optimize.brentq` numerical root finding method.
Parameters
----------
value : `~astropy.units.Quantity`
Function value of the spectral model.
emin : `~astropy.units.Quantity`
Lower bracket value in case solution is not unique.
emax : `~astropy.units.Quantity`
Upper bracket value in case solution is not unique.
Returns
-------
energy : `~astropy.units.Quantity`
Energies at which the model has the given ``value``.
"""
eunit = "TeV"
energies = []
for val in np.atleast_1d(value):
def f(x):
# scale by 1e12 to achieve better precision
energy = u.Quantity(x, eunit, copy=False)
y = self(energy).to_value(value.unit)
return 1e12 * (y - val.value)
energy = brentq(f, emin.to_value(eunit), emax.to_value(eunit))
energies.append(energy)
return u.Quantity(energies, eunit, copy=False)
[docs]class ConstantModel(SpectralModel):
r"""Constant model
.. math:: \phi(E) = k
Parameters
----------
const : `~astropy.units.Quantity`
:math:`k`
"""
__slots__ = ["const"]
def __init__(self, const):
self.const = Parameter("const", const)
super().__init__([self.const])
[docs] @staticmethod
def evaluate(energy, const):
"""Evaluate the model (static function)."""
return np.ones(np.atleast_1d(energy).shape) * const
[docs]class CompoundSpectralModel(SpectralModel):
"""Represents the algebraic combination of two
`~gammapy.spectrum.models.SpectralModel`
"""
def __init__(self, model1, model2, operator):
self.model1 = model1
self.model2 = model2
self.operator = operator
parameters = (
self.model1.parameters.parameters + self.model2.parameters.parameters
)
super().__init__(parameters)
# TODO: Think about how to deal with covariance matrix
def __str__(self):
ss = self.__class__.__name__
ss += "\n Component 1 : {}".format(self.model1)
ss += "\n Component 2 : {}".format(self.model2)
ss += "\n Operator : {}".format(self.operator)
return ss
[docs] def __call__(self, energy):
val1 = self.model1(energy)
val2 = self.model2(energy)
return self.operator(val1, val2)
[docs] def to_dict(self):
retval = dict()
retval["model1"] = self.model1.to_dict()
retval["model2"] = self.model2.to_dict()
retval["operator"] = self.operator
[docs]class PowerLaw(SpectralModel):
r"""Spectral power-law model.
.. math::
\phi(E) = \phi_0 \cdot \left( \frac{E}{E_0} \right)^{-\Gamma}
Parameters
----------
index : `~astropy.units.Quantity`
:math:`\Gamma`
amplitude : `~astropy.units.Quantity`
:math:`\phi_0`
reference : `~astropy.units.Quantity`
:math:`E_0`
Examples
--------
This is how to plot the default `PowerLaw` model::
from astropy import units as u
from gammapy.spectrum.models import PowerLaw
pwl = PowerLaw()
pwl.plot(energy_range=[0.1, 100] * u.TeV)
plt.show()
"""
__slots__ = ["index", "amplitude", "reference"]
def __init__(self, index=2.0, amplitude="1e-12 cm-2 s-1 TeV-1", reference="1 TeV"):
self.index = Parameter("index", index)
self.amplitude = Parameter("amplitude", amplitude)
self.reference = Parameter("reference", reference, frozen=True)
super().__init__([self.index, self.amplitude, self.reference])
[docs] @staticmethod
def evaluate(energy, index, amplitude, reference):
"""Evaluate the model (static function)."""
return amplitude * np.power((energy / reference), -index)
[docs] def integral(self, emin, emax, **kwargs):
r"""Integrate power law analytically.
.. math::
F(E_{min}, E_{max}) = \int_{E_{min}}^{E_{max}}\phi(E)dE = \left.
\phi_0 \frac{E_0}{-\Gamma + 1} \left( \frac{E}{E_0} \right)^{-\Gamma + 1}
\right \vert _{E_{min}}^{E_{max}}
Parameters
----------
emin, emax : `~astropy.units.Quantity`
Lower and upper bound of integration range
"""
# kwargs are passed to this function but not used
# this is to get a consistent API with SpectralModel.integral()
pars = self.parameters
if np.isclose(pars["index"].value, 1):
e_unit = emin.unit
prefactor = pars["amplitude"].quantity * pars["reference"].quantity.to(
e_unit
)
upper = np.log(emax.to_value(e_unit))
lower = np.log(emin.to_value(e_unit))
else:
val = -1 * pars["index"].value + 1
prefactor = pars["amplitude"].quantity * pars["reference"].quantity / val
upper = np.power((emax / pars["reference"].quantity), val)
lower = np.power((emin / pars["reference"].quantity), val)
return prefactor * (upper - lower)
[docs] def integral_error(self, emin, emax, **kwargs):
r"""Integrate power law analytically with error propagation.
Parameters
----------
emin, emax : `~astropy.units.Quantity`
Lower and upper bound of integration range.
Returns
-------
integral, integral_error : tuple of `~astropy.units.Quantity`
Tuple of integral flux and integral flux error.
"""
# kwargs are passed to this function but not used
# this is to get a consistent API with SpectralModel.integral()
emin = self._convert_energy(emin)
emax = self._convert_energy(emax)
unit = self.integral(emin, emax, **kwargs).unit
upars = self.parameters._ufloats
if np.isclose(upars["index"].nominal_value, 1):
prefactor = upars["amplitude"] * upars["reference"]
upper = np.log(emax.value)
lower = np.log(emin.value)
else:
val = -1 * upars["index"] + 1
prefactor = upars["amplitude"] * upars["reference"] / val
upper = np.power((emax.value / upars["reference"]), val)
lower = np.power((emin.value / upars["reference"]), val)
uarray = prefactor * (upper - lower)
return self._parse_uarray(uarray) * unit
[docs] def energy_flux(self, emin, emax):
r"""Compute energy flux in given energy range analytically.
.. math::
G(E_{min}, E_{max}) = \int_{E_{min}}^{E_{max}}E \phi(E)dE = \left.
\phi_0 \frac{E_0^2}{-\Gamma + 2} \left( \frac{E}{E_0} \right)^{-\Gamma + 2}
\right \vert _{E_{min}}^{E_{max}}
Parameters
----------
emin, emax : `~astropy.units.Quantity`
Lower and upper bound of integration range.
"""
pars = self.parameters
val = -1 * pars["index"].value + 2
if np.isclose(val, 0):
# see https://www.wolframalpha.com/input/?i=a+*+x+*+(x%2Fb)+%5E+(-2)
# for reference
temp = pars["amplitude"].quantity * pars["reference"].quantity ** 2
return temp * np.log(emax / emin)
else:
prefactor = (
pars["amplitude"].quantity * pars["reference"].quantity ** 2 / val
)
upper = (emax / pars["reference"].quantity) ** val
lower = (emin / pars["reference"].quantity) ** val
return prefactor * (upper - lower)
[docs] def energy_flux_error(self, emin, emax, **kwargs):
r"""Compute energy flux in given energy range analytically with error propagation.
Parameters
----------
emin, emax : `~astropy.units.Quantity`
Lower and upper bound of integration range.
Returns
-------
energy_flux, energy_flux_error : tuple of `~astropy.units.Quantity`
Tuple of energy flux and energy flux error.
"""
emin = self._convert_energy(emin)
emax = self._convert_energy(emax)
unit = self.energy_flux(emin, emax, **kwargs).unit
upars = self.parameters._ufloats
val = -1 * upars["index"] + 2
if np.isclose(val.nominal_value, 0):
# see https://www.wolframalpha.com/input/?i=a+*+x+*+(x%2Fb)+%5E+(-2)
# for reference
temp = upars["amplitude"] * upars["reference"] ** 2
uarray = temp * np.log(emax.value / emin.value)
else:
prefactor = upars["amplitude"] * upars["reference"] ** 2 / val
upper = (emax.value / upars["reference"]) ** val
lower = (emin.value / upars["reference"]) ** val
uarray = prefactor * (upper - lower)
return self._parse_uarray(uarray) * unit
[docs] def inverse(self, value):
"""Return energy for a given function value of the spectral model.
Parameters
----------
value : `~astropy.units.Quantity`
Function value of the spectral model.
"""
p = self.parameters
base = value / p["amplitude"].quantity
return p["reference"].quantity * np.power(base, -1.0 / p["index"].value)
[docs]class PowerLaw2(SpectralModel):
r"""Spectral power-law model with integral as amplitude parameter.
See also: https://fermi.gsfc.nasa.gov/ssc/data/analysis/scitools/source_models.html
.. math::
\phi(E) = F_0 \cdot \frac{\Gamma + 1}{E_{0, max}^{-\Gamma + 1}
- E_{0, min}^{-\Gamma + 1}} \cdot E^{-\Gamma}
Parameters
----------
index : `~astropy.units.Quantity`
Spectral index :math:`\Gamma`
amplitude : `~astropy.units.Quantity`
Integral flux :math:`F_0`.
emin : `~astropy.units.Quantity`
Lower energy limit :math:`E_{0, min}`.
emax : `~astropy.units.Quantity`
Upper energy limit :math:`E_{0, max}`.
Examples
--------
This is how to plot the default `PowerLaw2` model::
from astropy import units as u
from gammapy.spectrum.models import PowerLaw2
pwl2 = PowerLaw2()
pwl2.plot(energy_range=[0.1, 100] * u.TeV)
plt.show()
"""
__slots__ = ["index", "amplitude", "emin", "emax"]
def __init__(
self, amplitude="1e-12 cm-2 s-1", index=2, emin="0.1 TeV", emax="100 TeV"
):
self.amplitude = Parameter("amplitude", amplitude)
self.index = Parameter("index", index)
self.emin = Parameter("emin", emin, frozen=True)
self.emax = Parameter("emax", emax, frozen=True)
super().__init__([self.index, self.amplitude, self.emin, self.emax])
[docs] @staticmethod
def evaluate(energy, amplitude, index, emin, emax):
"""Evaluate the model (static function)."""
top = -index + 1
# to get the energies dimensionless we use a modified formula
bottom = emax - emin * (emin / emax) ** (-index)
return amplitude * (top / bottom) * np.power(energy / emax, -index)
[docs] def integral(self, emin, emax, **kwargs):
r"""Integrate power law analytically.
.. math::
F(E_{min}, E_{max}) = F_0 \cdot \frac{E_{max}^{\Gamma + 1} \
- E_{min}^{\Gamma + 1}}{E_{0, max}^{\Gamma + 1} \
- E_{0, min}^{\Gamma + 1}}
Parameters
----------
emin, emax : `~astropy.units.Quantity`
Lower and upper bound of integration range.
"""
pars = self.parameters
temp1 = np.power(emax, -pars["index"].value + 1)
temp2 = np.power(emin, -pars["index"].value + 1)
top = temp1 - temp2
temp1 = np.power(pars["emax"].quantity, -pars["index"].value + 1)
temp2 = np.power(pars["emin"].quantity, -pars["index"].value + 1)
bottom = temp1 - temp2
return pars["amplitude"].quantity * top / bottom
[docs] def integral_error(self, emin, emax, **kwargs):
r"""Integrate power law analytically with error propagation.
Parameters
----------
emin, emax : `~astropy.units.Quantity`
Lower and upper bound of integration range.
Returns
-------
integral, integral_error : tuple of `~astropy.units.Quantity`
Tuple of integral flux and integral flux error.
"""
emin = self._convert_energy(emin)
emax = self._convert_energy(emax)
unit = self.integral(emin, emax, **kwargs).unit
upars = self.parameters._ufloats
temp1 = np.power(emax.value, -upars["index"] + 1)
temp2 = np.power(emin.value, -upars["index"] + 1)
top = temp1 - temp2
temp1 = np.power(upars["emax"], -upars["index"] + 1)
temp2 = np.power(upars["emin"], -upars["index"] + 1)
bottom = temp1 - temp2
uarray = upars["amplitude"] * top / bottom
return self._parse_uarray(uarray) * unit
[docs] def inverse(self, value):
"""Return energy for a given function value of the spectral model.
Parameters
----------
value : `~astropy.units.Quantity`
Function value of the spectral model.
"""
p = self.parameters
amplitude, index, emin, emax = (
p["amplitude"].quantity,
p["index"].value,
p["emin"].quantity,
p["emax"].quantity,
)
# to get the energies dimensionless we use a modified formula
top = -index + 1
bottom = emax - emin * (emin / emax) ** (-index)
term = (bottom / top) * (value / amplitude)
return np.power(term.to_value(""), -1.0 / index) * emax
[docs]class ExponentialCutoffPowerLaw(SpectralModel):
r"""Spectral exponential cutoff power-law model.
.. math::
\phi(E) = \phi_0 \cdot \left(\frac{E}{E_0}\right)^{-\Gamma} \exp(-\lambda E)
Parameters
----------
index : `~astropy.units.Quantity`
:math:`\Gamma`
amplitude : `~astropy.units.Quantity`
:math:`\phi_0`
reference : `~astropy.units.Quantity`
:math:`E_0`
lambda_ : `~astropy.units.Quantity`
:math:`\lambda`
Examples
--------
This is how to plot the default `ExponentialCutoffPowerLaw` model::
from astropy import units as u
from gammapy.spectrum.models import ExponentialCutoffPowerLaw
ecpl = ExponentialCutoffPowerLaw()
ecpl.plot(energy_range=[0.1, 100] * u.TeV)
plt.show()
"""
__slots__ = ["index", "amplitude", "reference", "lambda_"]
def __init__(
self,
index=1.5,
amplitude="1e-12 cm-2 s-1 TeV-1",
reference="1 TeV",
lambda_="0.1 TeV-1",
):
self.index = Parameter("index", index)
self.amplitude = Parameter("amplitude", amplitude)
self.reference = Parameter("reference", reference, frozen=True)
self.lambda_ = Parameter("lambda_", lambda_)
super().__init__([self.index, self.amplitude, self.reference, self.lambda_])
[docs] @staticmethod
def evaluate(energy, index, amplitude, reference, lambda_):
"""Evaluate the model (static function)."""
pwl = amplitude * (energy / reference) ** (-index)
try:
cutoff = np.exp(-energy * lambda_)
except AttributeError:
from uncertainties.unumpy import exp
cutoff = exp(-energy * lambda_)
return pwl * cutoff
@property
def e_peak(self):
r"""Spectral energy distribution peak energy (`~astropy.utils.Quantity`).
This is the peak in E^2 x dN/dE and is given by:
.. math::
E_{Peak} = (2 - \Gamma) / \lambda
"""
p = self.parameters
reference = p["reference"].quantity
index = p["index"].quantity
lambda_ = p["lambda_"].quantity
if index >= 2:
return np.nan * reference.unit
else:
return (2 - index) / lambda_
[docs]class ExponentialCutoffPowerLaw3FGL(SpectralModel):
r"""Spectral exponential cutoff power-law model used for 3FGL.
Note that the parametrization is different from `ExponentialCutoffPowerLaw`:
.. math::
\phi(E) = \phi_0 \cdot \left(\frac{E}{E_0}\right)^{-\Gamma}
\exp \left( \frac{E_0 - E}{E_{C}} \right)
Parameters
----------
index : `~astropy.units.Quantity`
:math:`\Gamma`
amplitude : `~astropy.units.Quantity`
:math:`\phi_0`
reference : `~astropy.units.Quantity`
:math:`E_0`
ecut : `~astropy.units.Quantity`
:math:`E_{C}`
Examples
--------
This is how to plot the default `ExponentialCutoffPowerLaw3FGL` model::
from astropy import units as u
from gammapy.spectrum.models import ExponentialCutoffPowerLaw3FGL
ecpl_3fgl = ExponentialCutoffPowerLaw3FGL()
ecpl_3fgl.plot(energy_range=[0.1, 100] * u.TeV)
plt.show()
"""
__slots__ = ["index", "amplitude", "reference", "ecut"]
def __init__(
self,
index=1.5,
amplitude="1e-12 cm-2 s-1 TeV-1",
reference="1 TeV",
ecut="10 TeV",
):
self.index = Parameter("index", index)
self.amplitude = Parameter("amplitude", amplitude)
self.reference = Parameter("reference", reference, frozen=True)
self.ecut = Parameter("ecut", ecut)
super().__init__([self.index, self.amplitude, self.reference, self.ecut])
[docs] @staticmethod
def evaluate(energy, index, amplitude, reference, ecut):
"""Evaluate the model (static function)."""
pwl = amplitude * (energy / reference) ** (-index)
try:
cutoff = np.exp((reference - energy) / ecut)
except AttributeError:
from uncertainties.unumpy import exp
cutoff = exp((reference - energy) / ecut)
return pwl * cutoff
[docs]class PLSuperExpCutoff3FGL(SpectralModel):
r"""Spectral super exponential cutoff power-law model used for 3FGL.
.. math::
\phi(E) = \phi_0 \cdot \left(\frac{E}{E_0}\right)^{-\Gamma_1}
\exp \left( \left(\frac{E_0}{E_{C}} \right)^{\Gamma_2} -
\left(\frac{E}{E_{C}} \right)^{\Gamma_2}
\right)
Parameters
----------
index_1 : `~astropy.units.Quantity`
:math:`\Gamma_1`
index_2 : `~astropy.units.Quantity`
:math:`\Gamma_2`
amplitude : `~astropy.units.Quantity`
:math:`\phi_0`
reference : `~astropy.units.Quantity`
:math:`E_0`
ecut : `~astropy.units.Quantity`
:math:`E_{C}`
Examples
--------
This is how to plot the default `PLSuperExpCutoff3FGL` model::
from astropy import units as u
from gammapy.spectrum.models import PLSuperExpCutoff3FGL
secpl_3fgl = PLSuperExpCutoff3FGL()
secpl_3fgl.plot(energy_range=[0.1, 100] * u.TeV)
plt.show()
"""
__slots__ = ["index_1", "index_2", "amplitude", "reference", "ecut"]
def __init__(
self,
index_1=1.5,
index_2=2,
amplitude="1e-12 cm-2 s-1 TeV-1",
reference="1 TeV",
ecut="10 TeV",
):
self.index_1 = Parameter("index_1", index_1)
self.index_2 = Parameter("index_2", index_2)
self.amplitude = Parameter("amplitude", amplitude)
self.reference = Parameter("reference", reference, frozen=True)
self.ecut = Parameter("ecut", ecut)
super().__init__(
[self.index_1, self.index_2, self.amplitude, self.reference, self.ecut]
)
[docs] @staticmethod
def evaluate(energy, amplitude, reference, ecut, index_1, index_2):
"""Evaluate the model (static function)."""
pwl = amplitude * (energy / reference) ** (-index_1)
try:
cutoff = np.exp((reference / ecut) ** index_2 - (energy / ecut) ** index_2)
except AttributeError:
from uncertainties.unumpy import exp
cutoff = exp((reference / ecut) ** index_2 - (energy / ecut) ** index_2)
return pwl * cutoff
[docs]class LogParabola(SpectralModel):
r"""Spectral log parabola model.
.. math::
\phi(E) = \phi_0 \left( \frac{E}{E_0} \right) ^ {
- \alpha - \beta \log{ \left( \frac{E}{E_0} \right) }
}
Note that :math:`log` refers to the natural logarithm. This is consistent
with the `Fermi Science Tools
<https://fermi.gsfc.nasa.gov/ssc/data/analysis/scitools/source_models.html>`_
and `ctools
<http://cta.irap.omp.eu/ctools-devel/users/user_manual/getting_started/models.html#log-parabola>`_.
The `Sherpa <http://cxc.harvard.edu/sherpa/ahelp/logparabola.html_
package>`_ package, however, uses :math:`log_{10}`. If you have
parametrization based on :math:`log_{10}` you can use the
:func:`~gammapy.spectrum.models.LogParabola.from_log10` method.
Parameters
----------
amplitude : `~astropy.units.Quantity`
:math:`\phi_0`
reference : `~astropy.units.Quantity`
:math:`E_0`
alpha : `~astropy.units.Quantity`
:math:`\alpha`
beta : `~astropy.units.Quantity`
:math:`\beta`
Examples
--------
This is how to plot the default `LogParabola` model::
from astropy import units as u
from gammapy.spectrum.models import LogParabola
log_parabola = LogParabola()
log_parabola.plot(energy_range=[0.1, 100] * u.TeV)
plt.show()
"""
__slots__ = ["amplitude", "reference", "alpha", "beta"]
def __init__(
self, amplitude="1e-12 cm-2 s-1 TeV-1", reference="10 TeV", alpha=2, beta=1
):
self.amplitude = Parameter("amplitude", amplitude)
self.reference = Parameter("reference", reference, frozen=True)
self.alpha = Parameter("alpha", alpha)
self.beta = Parameter("beta", beta)
super().__init__([self.amplitude, self.reference, self.alpha, self.beta])
[docs] @classmethod
def from_log10(cls, amplitude, reference, alpha, beta):
"""Construct LogParabola from :math:`log_{10}` parametrization"""
beta_ = beta / np.log(10)
return cls(amplitude=amplitude, reference=reference, alpha=alpha, beta=beta_)
[docs] @staticmethod
def evaluate(energy, amplitude, reference, alpha, beta):
"""Evaluate the model (static function)."""
try:
xx = (energy / reference).to("")
exponent = -alpha - beta * np.log(xx)
except AttributeError:
from uncertainties.unumpy import log
xx = energy / reference
exponent = -alpha - beta * log(xx)
return amplitude * np.power(xx, exponent)
@property
def e_peak(self):
r"""Spectral energy distribution peak energy (`~astropy.units.Quantity`).
This is the peak in E^2 x dN/dE and is given by:
.. math::
E_{Peak} = E_{0} \exp{ (2 - \alpha) / (2 * \beta)}
"""
p = self.parameters
reference = p["reference"].quantity
alpha = p["alpha"].quantity
beta = p["beta"].quantity
return reference * np.exp((2 - alpha) / (2 * beta))
[docs]class TableModel(SpectralModel):
"""A model generated from a table of energy and value arrays.
the units returned will be the units of the values array provided at
initialization. The model will return values interpolated in
log-space, returning 0 for energies outside of the limits of the provided
energy array.
Class implementation follows closely what has been done in
`naima.models.TableModel`
Parameters
----------
energy : `~astropy.units.Quantity` array
Array of energies at which the model values are given
values : array
Array with the values of the model at energies ``energy``.
norm : float
Model scale that is multiplied to the supplied arrays. Defaults to 1.
values_scale : {'log', 'lin', 'sqrt'}
Interpolation scaling applied to values. If the values vary over many magnitudes
a 'log' scaling is recommended.
interp_kwargs : dict
Interpolation keyword arguments pass to `scipy.interpolate.interp1d`.
By default all values outside the interpolation range are set to zero.
If you want to apply linear extrapolation you can pass `interp_kwargs={'fill_value':
'extrapolate', 'kind': 'linear'}`
meta : dict, optional
Meta information, meta['filename'] will be used for serialization
"""
__slots__ = ["energy", "values", "norm", "meta", "_evaluate"]
def __init__(
self, energy, values, norm=1, values_scale="log", interp_kwargs=None, meta=None
):
self.norm = Parameter("norm", norm, unit="")
self.energy = energy
self.values = values
self.meta = dict() if meta is None else meta
interp_kwargs = interp_kwargs or {}
interp_kwargs.setdefault("values_scale", "log")
interp_kwargs.setdefault("points_scale", ("log",))
self._evaluate = ScaledRegularGridInterpolator(
points=(energy,), values=values, **interp_kwargs
)
super().__init__([self.norm])
[docs] @classmethod
def read_xspec_model(cls, filename, param, **kwargs):
"""Read XSPEC table model
The input is a table containing absorbed values from a XSPEC model as a
function of energy.
TODO: Format of the file should be described and discussed in
https://gamma-astro-data-formats.readthedocs.io/en/latest/index.html
Parameters
----------
filename : str
File containing the XSPEC model
param : float
Model parameter value
Examples
--------
Fill table from an EBL model (Franceschini, 2008)
>>> from gammapy.spectrum.models import TableModel
>>> filename = '$GAMMAPY_DATA/ebl/ebl_franceschini.fits.gz'
>>> table_model = TableModel.read_xspec_model(filename=filename, param=0.3)
"""
filename = str(make_path(filename))
# Check if parameter value is in range
table_param = Table.read(filename, hdu="PARAMETERS")
param_min = table_param["MINIMUM"]
param_max = table_param["MAXIMUM"]
if param < param_min or param > param_max:
err = "Parameter out of range, param={}, param_min={}, param_max={}".format(
param, param_min, param_max
)
raise ValueError(err)
# Get energy values
table_energy = Table.read(filename, hdu="ENERGIES")
energy_lo = table_energy["ENERG_LO"]
energy_hi = table_energy["ENERG_HI"]
# Hack while format is not fixed, energy values are in keV
energy_bounds = EnergyBounds.from_lower_and_upper_bounds(
lower=energy_lo, upper=energy_hi, unit=u.keV
)
energy = energy_bounds.log_centers
# Get spectrum values (no interpolation, take closest value for param)
table_spectra = Table.read(filename, hdu="SPECTRA")
idx = np.abs(table_spectra["PARAMVAL"] - param).argmin()
values = u.Quantity(table_spectra[idx][1], "", copy=False) # no dimension
kwargs.setdefault("values_scale", "lin")
return cls(energy=energy, values=values, **kwargs)
[docs] @classmethod
def read_fermi_isotropic_model(cls, filename, **kwargs):
"""Read Fermi isotropic diffuse model
see `LAT Background models <https://fermi.gsfc.nasa.gov/ssc/data/access/lat/BackgroundModels.html>`_
Parameters
----------
filename : str
filename
"""
filename = str(make_path(filename))
vals = np.loadtxt(filename)
energy = u.Quantity(vals[:, 0], "MeV", copy=False)
values = u.Quantity(vals[:, 1], "MeV-1 s-1 cm-2 sr-1", copy=False)
return cls(energy=energy, values=values, **kwargs)
[docs] def evaluate(self, energy, norm):
"""Evaluate the model (static function)."""
values = self._evaluate((energy,), clip=True)
return norm * values
class ScaleModel(SpectralModel):
"""Wrapper to scale another spectral model by a norm factor.
Parameters
----------
model : `SpectralModel`
Spectral model to wrap.
norm : float
Multiplicative norm factor for the model value.
"""
__slots__ = ["norm", "model"]
def __init__(self, model, norm=1):
self.norm = Parameter("norm", norm, unit="")
self.model = model
super().__init__([self.norm])
def evaluate(self, energy, norm):
return norm * self.model(energy)
[docs]class Absorption:
r"""Gamma-ray absorption models.
Parameters
----------
energy_lo, energy_hi : `~astropy.units.Quantity`
Lower and upper bin edges of energy axis
param_lo, param_hi : `~astropy.units.Quantity`
Lower and upper bin edges of parameter axis
data : `~astropy.units.Quantity`
Model value
Examples
--------
Create and plot EBL absorption models for a redshift of 0.5:
.. plot::
:include-source:
import matplotlib.pyplot as plt
import astropy.units as u
from gammapy.spectrum.models import Absorption
# Load tables for z=0.5
redshift = 0.5
dominguez = Absorption.read_builtin('dominguez').table_model(redshift)
franceschini = Absorption.read_builtin('franceschini').table_model(redshift)
finke = Absorption.read_builtin('finke').table_model(redshift)
# start customised plot
energy_range = [0.08, 3] * u.TeV
ax = plt.gca()
opts = dict(energy_range=energy_range, energy_unit='TeV', ax=ax, flux_unit='')
franceschini.plot(label='Franceschini 2008', **opts)
finke.plot(label='Finke 2010', **opts)
dominguez.plot(label='Dominguez 2011', **opts)
# tune plot
ax.set_ylabel(r'Absorption coefficient [$\exp{(-\tau(E))}$]')
ax.set_xlim(energy_range.value) # we get ride of units
ax.set_ylim([1.e-4, 2.])
ax.set_yscale('log')
ax.set_title('EBL models (z=' + str(redshift) + ')')
plt.grid(which='both')
plt.legend(loc='best') # legend
# show plot
plt.show()
"""
def __init__(
self, energy_lo, energy_hi, param_lo, param_hi, data, interp_kwargs=None
):
self.data = data
# set values log centers
self.energy = np.sqrt(energy_lo * energy_hi)
self.param = (param_hi + param_lo) / 2
interp_kwargs = interp_kwargs or {}
interp_kwargs.setdefault("points_scale", ("log", "lin"))
self._evaluate = ScaledRegularGridInterpolator(
points=(self.param, self.energy), values=data, **interp_kwargs
)
[docs] @classmethod
def read(cls, filename):
"""Build object from an XSPEC model.
Todo: Format of XSPEC binary files should be referenced at https://gamma-astro-data-formats.readthedocs.io/en/latest/
Parameters
----------
filename : str
File containing the model.
"""
# Create EBL data array
filename = str(make_path(filename))
table_param = Table.read(filename, hdu="PARAMETERS")
par_min = table_param["MINIMUM"]
par_max = table_param["MAXIMUM"]
par_array = table_param[0]["VALUE"]
par_delta = np.diff(par_array) * 0.5
param_lo, param_hi = par_array, par_array # initialisation
param_lo[0] = par_min - par_delta[0]
param_lo[1:] -= par_delta
param_hi[:-1] += par_delta
param_hi[-1] = par_max
# Get energy values
table_energy = Table.read(filename, hdu="ENERGIES")
energy_lo = u.Quantity(
table_energy["ENERG_LO"], "keV", copy=False
) # unit not stored in file
energy_hi = u.Quantity(
table_energy["ENERG_HI"], "keV", copy=False
) # unit not stored in file
# Get spectrum values
table_spectra = Table.read(filename, hdu="SPECTRA")
data = table_spectra["INTPSPEC"].data
return cls(
energy_lo=energy_lo,
energy_hi=energy_hi,
param_lo=param_lo,
param_hi=param_hi,
data=data,
)
[docs] @classmethod
def read_builtin(cls, name):
"""Read one of the built-in absorption models.
Parameters
----------
name : {'franceschini', 'dominguez', 'finke'}
name of one of the available model in gammapy-data
References
----------
.. [1] Franceschini et al., "Extragalactic optical-infrared background radiation, its time evolution and the cosmic photon-photon opacity",
`Link <http://adsabs.harvard.edu/abs/2008A%26A...487..837F>`__
.. [2] Dominguez et al., " Extragalactic background light inferred from AEGIS galaxy-SED-type fractions"
`Link <http://adsabs.harvard.edu/abs/2011MNRAS.410.2556D>`__
.. [3] Finke et al., "Modeling the Extragalactic Background Light from Stars and Dust"
`Link <http://adsabs.harvard.edu/abs/2010ApJ...712..238F>`__
"""
models = dict()
models["franceschini"] = "$GAMMAPY_DATA/ebl/ebl_franceschini.fits.gz"
models["dominguez"] = "$GAMMAPY_DATA/ebl/ebl_dominguez11.fits.gz"
models["finke"] = "$GAMMAPY_DATA/ebl/frd_abs.fits.gz"
return cls.read(models[name])
[docs] def table_model(self, parameter, unit="TeV"):
"""Table model for a given parameter (`~gammapy.spectrum.models.TableModel`).
Parameters
----------
parameter : float
Parameter value.
unit : str, (optional)
desired value for energy axis
"""
energy = self.energy.to(unit)
values = self.evaluate(energy=energy, parameter=parameter)
return TableModel(energy=energy, values=values, values_scale="lin")
[docs] def evaluate(self, energy, parameter):
"""Evaluate model for energy and parameter value."""
return self._evaluate((parameter, energy))
[docs]class AbsorbedSpectralModel(SpectralModel):
"""Spectral model with EBL absorption.
Parameters
----------
spectral_model : `~gammapy.spectrum.models.SpectralModel`
Spectral model.
absorption : `~gammapy.spectrum.models.Absorption`
Absorption model.
parameter : float
parameter value for absorption model
parameter_name : str, optional
parameter name
"""
__slots__ = ["spectral_model", "absorption", "parameter", "parameter_name"]
def __init__(
self, spectral_model, absorption, parameter, parameter_name="redshift"
):
self.spectral_model = spectral_model
self.absorption = absorption
self.parameter = parameter
self.parameter_name = parameter_name
min_ = self.absorption.param.min()
max_ = self.absorption.param.max()
par = Parameter(parameter_name, parameter, min=min_, max=max_, frozen=True)
parameters = spectral_model.parameters.parameters.copy()
parameters.append(par)
super().__init__(parameters)
[docs] def evaluate(self, energy, **kwargs):
"""Evaluate the model at a given energy."""
# assign redshift value and remove it from dictionnary
# since it does not belong to the spectral model
parameter = kwargs[self.parameter_name]
del kwargs[self.parameter_name]
flux = self.spectral_model.evaluate(energy=energy, **kwargs)
absorption = self.absorption.evaluate(energy=energy, parameter=parameter)
return flux * absorption
[docs]class NaimaModel(SpectralModel):
r"""A wrapper for Naima models
This class provides an interface with the models defined in the `~naima.models` module.
The model accepts as a positional argument a `Naima <https://naima.readthedocs.io/en/latest/>`_
radiative model instance, used to compute the non-thermal emission from populations of
relativistic electrons or protons due to interactions with the ISM or with radiation and magnetic fields.
One of the advantages provided by this class consists in the possibility of performing a maximum
likelihood spectral fit of the model's parameters directly on observations, as opposed to the MCMC
`fit to flux points <https://naima.readthedocs.io/en/latest/mcmc.html>`_ featured in
Naima. All the parameters defining the parent population of charged particles are stored as
`~gammapy.utils.modeling.Parameter` and left free by default. In case that the radiative model is `
~naima.radiative.Synchrotron`, the magnetic field strength may also be fitted. Parameters can be
freezed/unfreezed before the fit, and maximum/minimum values can be set to limit the parameters space to
the physically interesting region.
Parameters
----------
radiative_model : `~naima.models.BaseRadiative`
An instance of a radiative model defined in `~naima.models`
distance : `~astropy.units.Quantity`, optional
Distance to the source. If set to 0, the intrinsic differential
luminosity will be returned. Default is 1 kpc
seed : str or list of str, optional
Seed photon field(s) to be considered for the `radiative_model` flux computation,
in case of a `~naima.models.InverseCompton` model. It can be a subset of the
`seed_photon_fields` list defining the `radiative_model`. Default is the whole list
of photon fields
Examples
--------
Create and plot a spectral model that convolves an `ExponentialCutoffPowerLaw` electron distribution
with an `InverseCompton` radiative model, in the presence of multiple seed photon fields.
.. plot::
:include-source:
import naima
from gammapy.spectrum.models import NaimaModel
import astropy.units as u
import matplotlib.pyplot as plt
particle_distribution = naima.models.ExponentialCutoffPowerLaw(1e30 / u.eV, 10 * u.TeV, 3.0, 30 * u.TeV)
radiative_model = naima.radiative.InverseCompton(
particle_distribution,
seed_photon_fields=[
"CMB",
["FIR", 26.5 * u.K, 0.415 * u.eV / u.cm ** 3],
],
Eemin=100 * u.GeV,
)
model = NaimaModel(radiative_model, distance=1.5 * u.kpc)
opts = {
"energy_range" : [10 * u.GeV, 80 * u.TeV],
"energy_power" : 2,
"flux_unit" : "erg-1 cm-2 s-1",
}
# Plot the total inverse Compton emission
model.plot(label='IC (total)', **opts)
# Plot the separate contributions from each seed photon field
for seed, ls in zip(['CMB','FIR'], ['-','--']):
model = NaimaModel(radiative_model, seed=seed, distance=1.5 * u.kpc)
model.plot(label="IC ({})".format(seed), ls=ls, color="gray", **opts)
plt.legend(loc='best')
plt.show()
"""
# TODO: prevent users from setting new attributes after init
def __init__(self, radiative_model, distance=1.0 * u.kpc, seed=None):
import naima
self.radiative_model = radiative_model
self._particle_distribution = self.radiative_model.particle_distribution
self.distance = Parameter("distance", distance, frozen=True)
self.seed = seed
# This ensures the support of naima.models.TableModel
if isinstance(self._particle_distribution, naima.models.TableModel):
param_names = ["amplitude"]
else:
param_names = self._particle_distribution.param_names
parameters = []
for name in param_names:
value = getattr(self._particle_distribution, name)
setattr(self, name, Parameter(name, value))
parameters.append(getattr(self, name))
# In case of a synchrotron radiative model, append B to the fittable parameters
if "B" in self.radiative_model.param_names:
B = getattr(self.radiative_model, "B")
setattr(self, "B", Parameter("B", B))
parameters.append(getattr(self, "B"))
super().__init__(parameters)
[docs] def evaluate_error(self, energy):
# This method will need to be overridden here, since the radiative models in naima don't
# support the evaluation on energy values that is performed in the base class method
raise NotImplementedError(
"Error evaluation for naima models currently not supported."
)
[docs] def evaluate(self, energy, **kwargs):
"""Evaluate the model"""
for name, value in kwargs.items():
setattr(self._particle_distribution, name, value)
distance = self.distance.quantity
# Flattening the input energy list and later reshaping the flux list
# prevents some radiative models from displaying broadcasting problems.
if self.seed is None:
dnde = self.radiative_model.flux(energy.flatten(), distance=distance)
else:
dnde = self.radiative_model.flux(
energy.flatten(), seed=self.seed, distance=distance
)
dnde = dnde.reshape(energy.shape)
unit = 1 / (energy.unit * u.cm ** 2 * u.s)
return dnde.to(unit)