"""
Visualising spectra
==========================

`RamanSPy` provides a broad selection of visualisation tools for the visualisation of Raman spectra and groups of Raman spectra.

This is enabled through the :meth:`ramanspy.plot.spectra` method, which can automatically produce informative,
highly-customisable visualisations with minimal software readjustments.

.. note:: The :meth:`ramanspy.plot.spectra` method is ideal for the visualisation of a small number of spectra. If you need
          to plot more data, you may need to use the :meth:`ramanspy.plot.mean_spectra` method instead, which allows the
          visualisation of spectral distributions.
"""

# %%
# To showcase the wide variety of plots of spectra that can be produced with `RamanSPy`, we will use a small sample from the
# training dataset of the :ref:`Bacteria data` available in `RamanSPy`.
#
# For the scope of this example, we will only select 3 Raman spectra from 5 of the species provided.
import ramanspy

dir_ = r"../../../../data/bacteria_data"
X_train, y_train = ramanspy.datasets.bacteria("train", folder=dir_)

# %%
species_size = 2000

# defining the samples, 3 Raman spectra per species
species_1_sample = [X_train[0, :], X_train[1, :], X_train[2, :]]
species_2_sample = [X_train[1*species_size + 0, :], X_train[1*species_size + 1, :], X_train[1*species_size + 2, :]]
species_3_sample = [X_train[2*species_size + 0, :], X_train[2*species_size + 1, :], X_train[2*species_size + 2, :]]
species_4_sample = [X_train[3*species_size + 0, :], X_train[3*species_size + 1, :], X_train[3*species_size + 2, :]]
species_5_sample = [X_train[4*species_size + 0, :], X_train[4*species_size + 1, :], X_train[4*species_size + 2, :]]


# %%
# Then, we can use `RamanSPy` to  visualise spectra in 4 different types of plots.


# %%
# Separate plots
# -------------------
# The first type of plots supported by the :meth:`ramanspy.plot.spectra` method is where the spectra of each group is
# plotted in a separate plot.
#
# This can be achieved by using ``plot_type="separate"`` when calling the method (default behaviour).

# a single spectrum => treated as a single group containing 1 spectrum
ramanspy.plot.spectra(species_1_sample[0], label=["Replicate 1"], title='Bacteria species 1')

# %%

# a list of 3 spectra => treated as 3 separate groups, each containing a single spectrum
ramanspy.plot.spectra(species_1_sample, label=["Replicate 1", "Replicate 2", "Replicate 3"], title='Bacteria species 1')

# %%

# a list of 5 lists => treated as 5 separate groups, each containing the number of spectra in each sub-list, i.e. 3
ramanspy.plot.spectra([species_1_sample, species_2_sample, species_3_sample, species_4_sample, species_5_sample],
                      label=["Species 1", "Species 2", "Species 3", "Species 4", "Species 5"], title='Bacteria species')


# %%
# Single plots
# --------------
# If we want to compare the groups of spectra provided, we may wish to visualise them within the same plot.
#
# This can be achieved by setting ``plot_type="single"``.

# a list of 3 spectra => treated as 3 separate groups, each containing a single spectrum
ramanspy.plot.spectra(species_1_sample, label=["Replicate 1", "Replicate 2", "Replicate 3"], title='Bacteria species 1',
                      plot_type="single"
                      )

# %%

# a list of 5 lists => treated as 5 separate groups, each containing the number of spectra in each sub-list, i.e. 3
ramanspy.plot.spectra([species_1_sample, species_2_sample, species_3_sample, species_4_sample, species_5_sample],
                      label=["Species 1", "Species 2", "Species 3", "Species 4", "Species 5"], title='Bacteria species',
                      plot_type="single")

# %%
# Stacked plots
# -------------------
# Plotting spectra in the same plot usually ends up in plots which are too jammed. To make plots more compact and readable,
# users can stack individual plots on top of each other. In this way, it becomes easier to compare different graphs and
# inspect their behaviour.
#
# One can do that by setting ``plot type='stacked'``.

# a list of 3 spectra => treated as 3 separate groups, each containing a single spectrum
ramanspy.plot.spectra(species_1_sample, label=["Replicate 1", "Replicate 2", "Replicate 3"], title='Bacteria species 1',
                      plot_type="stacked")

# %%

# a list of 5 SpectralContainer instances => treated as 5 separate groups, each containing the number of spectra in each instance, i.e. 3
ramanspy.plot.spectra([species_1_sample, species_2_sample, species_3_sample, species_4_sample, species_5_sample],
                      label=["Species 1", "Species 2", "Species 3", "Species 4", "Species 5"], title='Bacteria species',
                      plot_type="stacked")

# %%
# Single stacked plots
# ---------------------
# We can also visualise the stacked plots within the same plot by setting ``plot_type='single stacked'``.

# a list of 3 spectra => treated as 3 separate groups, each containing a single spectrum
ramanspy.plot.spectra(species_1_sample, label=["Replicate 1", "Replicate 2", "Replicate 3"], title='Bacteria species 1',
                      plot_type="single stacked")

# %%

# a list of 5 SpectralContainer instances => treated as 5 separate groups, each containing the number of spectra in each instance, i.e. 3
ramanspy.plot.spectra([species_1_sample, species_2_sample, species_3_sample, species_4_sample, species_5_sample],
                      label=["Species 1", "Species 2", "Species 3", "Species 4", "Species 5"], title='Bacteria species',
                      plot_type="single stacked")