This is a fixed-text formatted version of a Jupyter notebook.

Spectral models in Gammapy

Introduction

This notebook explains how to use the functions and classes in gammapy.spectrum.models in order to work with spectral models.

The following clases will be used:

Setup

Same procedure as in every script …

In [1]:
%matplotlib inline
import matplotlib.pyplot as plt
In [2]:
import numpy as np
import astropy.units as u
from gammapy.spectrum import models
from gammapy.utils.modeling import Parameter, ParameterList

Create a model

To create a spectral model, instantiate an object of the spectral model class you’re interested in.

In [3]:
pwl = models.PowerLaw()
print(pwl)
PowerLaw

Parameters:

           name     value   error       unit      min max frozen
        --------- --------- ----- --------------- --- --- ------
            index 2.000e+00   nan                 nan nan  False
        amplitude 1.000e-12   nan 1 / (cm2 s TeV) nan nan  False
        reference 1.000e+00   nan             TeV nan nan   True

This will use default values for the model parameters, which is rarely what you want.

Usually you will want to specify the parameters on object creation. One way to do this is to pass astropy.utils.Quantity objects like this:

In [4]:
pwl = models.PowerLaw(
    index=2.3 * u.Unit(''),
    amplitude=1e-12 * u.Unit('cm-2 s-1 TeV-1'),
    reference=1 * u.TeV,
)
print(pwl)
PowerLaw

Parameters:

           name     value   error       unit      min max frozen
        --------- --------- ----- --------------- --- --- ------
            index 2.300e+00   nan                 nan nan  False
        amplitude 1.000e-12   nan 1 / (cm2 s TeV) nan nan  False
        reference 1.000e+00   nan             TeV nan nan   True

As you see, some of the parameters have default min and values as well as a frozen flag. This is only relevant in the context of spectral fitting and thus covered in spectrum_analysis.ipynb. Also, the parameter errors are not set. This will be covered later in this tutorial.

Get and set model parameters

The model parameters are stored as ParameterList on the spectal model. Each model parameter is Parameter instance. It has a value and a unit attribute, as well as a quantity property for convenience.

In [5]:
print(pwl.parameters)

print(pwl.parameters['index'])
pwl.parameters['index'].value=2.6
print(pwl.parameters['index'])

print(pwl.parameters['amplitude'])
pwl.parameters['amplitude'].quantity = 2e-12 * u.Unit('m-2 TeV-1 s-1')
print(pwl.parameters['amplitude'])
ParameterList
Parameter(name='index', value=2.3, unit='', min=nan, max=nan, frozen=False)
Parameter(name='amplitude', value=1e-12, unit='1 / (cm2 s TeV)', min=nan, max=nan, frozen=False)
Parameter(name='reference', value=1.0, unit='TeV', min=nan, max=nan, frozen=True)

Covariance:
None
Parameter(name='index', value=2.3, unit='', min=nan, max=nan, frozen=False)
Parameter(name='index', value=2.6, unit='', min=nan, max=nan, frozen=False)
Parameter(name='amplitude', value=1e-12, unit='1 / (cm2 s TeV)', min=nan, max=nan, frozen=False)
Parameter(name='amplitude', value=2e-12, unit='1 / (m2 s TeV)', min=nan, max=nan, frozen=False)

List available models

All spectral models in gammapy are subclasses of SpectralModel. The list of available models is shown below.

In [6]:
models.SpectralModel.__subclasses__()
Out[6]:
[gammapy.spectrum.models.ExponentialCutoffPowerLaw,
 gammapy.spectrum.models.CompoundSpectralModel,
 gammapy.spectrum.models.PowerLaw2,
 gammapy.spectrum.models.PowerLaw,
 gammapy.spectrum.models.ConstantModel,
 gammapy.spectrum.models.TableModel,
 gammapy.spectrum.models.PLSuperExpCutoff3FGL,
 gammapy.spectrum.models.AbsorbedSpectralModel,
 gammapy.spectrum.models.ExponentialCutoffPowerLaw3FGL,
 gammapy.spectrum.models.LogParabola,
 gammapy.spectrum.crab.MeyerCrabModel]

Plotting

In order to plot a model you can use the plot function. It expects an energy range as argument. You can also chose flux and energy units as well as an energy power for the plot

In [7]:
energy_range = [0.1, 10] * u.TeV
pwl.plot(energy_range, energy_power=2, energy_unit='GeV')
Out[7]:
<matplotlib.axes._subplots.AxesSubplot at 0x7f26cc68d6d8>
../_images/notebooks_spectrum_models_16_1.png

Parameter errors

Parameters are stored internally as covariance matrix. There are, however, convenience methods to set individual parameter errors on ParameterList.

In [8]:
errors = dict(
    index = 0.2 * u.Unit(''),
    amplitude = 0.1 * pwl.parameters['amplitude'].quantity
)
pwl.parameters.set_parameter_errors(errors)
print(pwl)
PowerLaw

Parameters:

           name     value     error        unit      min max frozen
        --------- --------- --------- -------------- --- --- ------
            index 2.600e+00 2.000e-01                nan nan  False
        amplitude 2.000e-12 2.000e-13 1 / (m2 s TeV) nan nan  False
        reference 1.000e+00 0.000e+00            TeV nan nan   True

Covariance:

        name/name index amplitude
        --------- ----- ---------
            index  0.04       0.0
        amplitude   0.0     4e-26

You can access the parameter errors like this

In [9]:
print(pwl.parameters.covariance)
print(pwl.parameters.error('index'))
[[  4.00000000e-02   0.00000000e+00   0.00000000e+00]
 [  0.00000000e+00   4.00000000e-26   0.00000000e+00]
 [  0.00000000e+00   0.00000000e+00   0.00000000e+00]]
0.2

You can plot the butterfly using the plot_error method.

In [10]:
ax = pwl.plot_error(energy_range, color='blue', alpha=0.2)
pwl.plot(energy_range, ax=ax, color='blue')
Out[10]:
<matplotlib.axes._subplots.AxesSubplot at 0x7f26cc2c3ba8>
../_images/notebooks_spectrum_models_22_1.png

Integral fluxes

You’ve probably asked yourself already, if it’s possible to integrated models. Yes, it is. Where analytical solutions are available, these are used by default. Otherwise, a numerical integration is performed.

In [11]:
integral = pwl.integral(emin=1 * u.TeV, emax= 10*u.TeV)
print(integral)
1.2186014196061302e-12 1 / (m2 s)

User-defined model

Now we’ll see how you can define a custom model. To do that you need to subclass SpectralModel. All SpectralModel subclasses need to have an __init__ function, which sets up the ParameterList of the model and a static function called evaluate where the mathematical expression for the model is defined.

As an example we will use a PowerLaw plus a Gaussian (with fixed width).

In [12]:
class UserModel(models.SpectralModel):
    def __init__(self, index, amplitude, reference, mean, width):
        self.parameters = ParameterList([
                Parameter('index', index, parmin=0),
                Parameter('amplitude', amplitude, parmin=0),
                Parameter('reference', reference, frozen=True),
                Parameter('mean', mean, parmin=0),
                Parameter('width', width, parmin=0, frozen=True)
            ])
    @staticmethod
    def evaluate(energy, index, amplitude, reference, mean, width):
        pwl = models.PowerLaw.evaluate(energy=energy, index=index, amplitude=amplitude, reference=reference)
        gauss = amplitude * np.exp(-1 *(energy - mean) ** 2/( 2 * width ** 2))
        return pwl + gauss
In [13]:
model = UserModel(
    index=2 * u.Unit(''),
    amplitude=1e-12 * u.Unit('cm-2 s-1 TeV-1'),
    reference=1 * u.TeV,
    mean=5 * u.TeV,
    width=0.2 * u.TeV,
)
print(model)
UserModel

Parameters:

           name     value   error       unit      min max frozen
        --------- --------- ----- --------------- --- --- ------
            index 2.000e+00   nan                 nan nan  False
        amplitude 1.000e-12   nan 1 / (cm2 s TeV) nan nan  False
        reference 1.000e+00   nan             TeV nan nan   True
             mean 5.000e+00   nan             TeV nan nan  False
            width 2.000e-01   nan             TeV nan nan   True
In [14]:
energy_range = [1, 10] * u.TeV

fig, ax = plt.subplots(1)
model.plot(ax=ax, energy_range=energy_range)
Out[14]:
<matplotlib.axes._subplots.AxesSubplot at 0x7f26cc12ed68>
../_images/notebooks_spectrum_models_28_1.png

What’s next?

In this tutorial we learnd how to work with spectral models. Go to gammapy.spectrum to see what else you can do with gammapy.spectrum.