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Updates to naima scripts #22

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Updates to naima scripts #22

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81d1617
Updates for python 3
henrikef Jun 7, 2021
e6e04a4
Note for fermi bottle users regarding emcee version conflict
henrikef Jun 7, 2021
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4 changes: 4 additions & 0 deletions Advanced_Topics/naima_examples/README.md
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Expand Up @@ -23,3 +23,7 @@ Recent-ish versions of matplotlib and astropy are needed.
`fitting_IC_spectrum.ipynb` is a very minimal example of how to fit parameters of an underlying electron population to VHE gamma-ray measurements.

All scripts are also provided as standalone python scripts that can be run outside of jupyter notebooks.

# For Fermibottle users

As of summer 2021, `naima 0.8.4` is installed as part of the fermit bottle. Unfortunately, there is a conflict in one of the depdencencies, `emcee`. Naima needs an older version: `emcee<3.0,>=2.2.0`, whereas `pint-pulsar 0.7` (also part of the fermi bottle) requires `emcee>=3.0`. If you just want to run the "exploring ..." scripts, this does not matter. If you want to run the `fitting_IC_spectrum` script or notebook, you will have to downgrade `emcee`. One way to do that is to run `pip install --upgrade naima`. This will install `naima 0.9.1` and `emcee 2.2.1`. Unfortunately, this might cause issues with `threeML` and `pint-pulsar`, both of which require newer versions of `emcee`. If you want to use `emcee` with either of those packages, you will have to create separate conda environments with the old and new versions of `naima`.
46 changes: 22 additions & 24 deletions Advanced_Topics/naima_examples/exploring_electron_spectra.ipynb
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6 changes: 3 additions & 3 deletions Advanced_Topics/naima_examples/exploring_electron_spectra.py
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Expand Up @@ -43,7 +43,7 @@
#naima models are phyical and accept/return astropy quantities.
#Try: electrons( 2.0 ) without a unit...
for E in [ 1*u.GeV, 1000*u.GeV, 1*u.TeV]:
print "dN/dE(", E, ") = ", electrons(E)
print( "dN/dE(", E, ") = ", electrons(E) )



Expand All @@ -66,8 +66,8 @@
synch.set_We(10**50 * u.erg)

#units check...
print "Flux dN/dE:", synch.flux([1]*u.keV, distance=2*u.kpc)
print "SED E^2dN/dE:", synch.sed([1]*u.keV, distance=2*u.kpc)
print( "Flux dN/dE:", synch.flux([1]*u.keV, distance=2*u.kpc) )
print( "SED E^2dN/dE:", synch.sed([1]*u.keV, distance=2*u.kpc) )


# In[47]:
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100 changes: 45 additions & 55 deletions Advanced_Topics/naima_examples/exploring_pion_decay_spectra.ipynb
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6 changes: 3 additions & 3 deletions Advanced_Topics/naima_examples/exploring_pion_decay_spectra.py
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Expand Up @@ -46,7 +46,7 @@
#naima models are phyical and accept/return astropy quantities.
#Try: protonsPL( 2.0 ) without a unit...
for E in [ 1*u.GeV, 1000*u.GeV, 1*u.TeV]:
print "dN/dE(", E, ") = ", protonsPL(E)
print( "dN/dE(", E, ") = ", protonsPL(E) )



Expand All @@ -68,8 +68,8 @@
pionsCutoff.set_Wp(10**50 * u.erg)

#units check...
print "Flux dN/dE:", pionsPL.flux([1]*u.TeV, distance=2*u.kpc)
print "SED E^2dN/dE:", pionsPL.sed([1]*u.TeV, distance=2*u.kpc)
print( "Flux dN/dE:", pionsPL.flux([1]*u.TeV, distance=2*u.kpc) )
print( "SED E^2dN/dE:", pionsPL.sed([1]*u.TeV, distance=2*u.kpc) )


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410 changes: 182 additions & 228 deletions Advanced_Topics/naima_examples/fitting_IC_spectrum.ipynb
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2 changes: 1 addition & 1 deletion Advanced_Topics/naima_examples/fitting_IC_spectrum.py
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Expand Up @@ -24,7 +24,7 @@

data = ascii.read("RXJ1713_HESS_2007.dat")

print data
print(data)


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