"""
Plot a spectrum
===============
This is an example showing how to plot a spectrum with the
:func:`mcalf.visualisation.plot_spectrum` function.
"""

#%%
# First we shall create a list of wavelengths, with a variable
# wavelength spacing.
# Next, we shall use the Voigt profile to generate spectral
# intensities at each of the wavelength points.
# Typically you would provide a spectrum obtained from observations.

import numpy as np
wavelengths = np.linspace(8541, 8543, 20)
wavelengths = np.delete(wavelengths, np.s_[1:6:2])
wavelengths = np.delete(wavelengths, np.s_[-6::2])

from mcalf.profiles.voigt import voigt
spectrum = voigt(wavelengths, -526, 8542, 0.1, 0.1, 1242)

#%%
# Next, we shall import :func:`mcalf.visualisation.plot_spectrum`.

from mcalf.visualisation import plot_spectrum

#%%
# We can now simply plot the spectrum.

plot_spectrum(wavelengths, spectrum)

#%%
# Notice how the spectrum above is normalised.
# The normalisation is applied by dividing through
# by the mean of the three rightmost points.
# To plot the raw spectrum,

plot_spectrum(wavelengths, spectrum, normalised=False)

#%%
# The line connecting the points provided in the ``spectrum``
# array above is smooth. This is due to spline interpolation
# being applied. Interpolation can be disabled, resulting
# in a straight line between each of the points.

plot_spectrum(wavelengths, spectrum, smooth=False)