#!/usr/bin/env python
import astropy.units as u
import numpy as np
from astropy.io import ascii

import naima
from naima.models import ExponentialCutoffPowerLaw, InverseCompton, Synchrotron

## Read data

# We only consider every fifth X-ray spectral point to speed-up calculations for this example
# DO NOT do this for a final analysis!
soft_xray = ascii.read("RXJ1713_Suzaku-XIS.dat")[::5]
vhe = ascii.read("RXJ1713_HESS_2007.dat")

## Model definition


def ElectronSynIC(pars, data):

    # Match parameters to ECPL properties, and give them the appropriate units
    amplitude = 10 ** pars[0] / u.eV
    alpha = pars[1]
    e_cutoff = (10 ** pars[2]) * u.TeV
    B = pars[3] * u.uG

    # Initialize instances of the particle distribution and radiative models
    ECPL = ExponentialCutoffPowerLaw(amplitude, 10.0 * u.TeV, alpha, e_cutoff)
    # Compute IC on CMB and on a FIR component with values from GALPROP for the
    # position of RXJ1713
    IC = InverseCompton(
        ECPL,
        seed_photon_fields=[
            "CMB",
            ["FIR", 26.5 * u.K, 0.415 * u.eV / u.cm ** 3],
        ],
        Eemin=100 * u.GeV,
    )
    SYN = Synchrotron(ECPL, B=B)

    # compute flux at the energies given in data['energy']
    model = IC.flux(data, distance=1.0 * u.kpc) + SYN.flux(
        data, distance=1.0 * u.kpc
    )

    # The first array returned will be compared to the observed spectrum for
    # fitting. All subsequent objects will be stored in the sampler metadata
    # blobs.
    return model, IC.compute_We(Eemin=1 * u.TeV)


## Prior definition


def lnprior(pars):
    """
    Return probability of parameter values according to prior knowledge.
    Parameter limits should be done here through uniform prior ditributions
    """
    # Limit norm and B to be positive
    logprob = (
        naima.uniform_prior(pars[0], 0.0, np.inf)
        + naima.uniform_prior(pars[1], -1, 5)
        + naima.uniform_prior(pars[3], 0, np.inf)
    )

    return logprob


if __name__ == "__main__":

    ## Set initial parameters and labels
    # Estimate initial magnetic field and get value in uG
    B0 = 2 * naima.estimate_B(soft_xray, vhe).to("uG").value

    p0 = np.array((33, 2.5, np.log10(48.0), B0))
    labels = ["log10(norm)", "index", "log10(cutoff)", "B"]

    ## Run sampler
    sampler, pos = naima.run_sampler(
        data_table=[soft_xray, vhe],
        p0=p0,
        labels=labels,
        model=ElectronSynIC,
        prior=lnprior,
        nwalkers=32,
        nburn=100,
        nrun=20,
        threads=4,
        prefit=True,
        interactive=False,
    )

    ## Save run results to HDF5 file (can be read later with naima.read_run)
    naima.save_run("RXJ1713_SynIC", sampler)

    ## Diagnostic plots
    naima.save_diagnostic_plots(
        "RXJ1713_SynIC",
        sampler,
        sed=True,
        blob_labels=["Spectrum", "$W_e$($E_e>1$ TeV)"],
    )
    naima.save_results_table("RXJ1713_SynIC", sampler)
