# ======================================================================================
# Copyright (©) 2014-2026 Laboratoire Catalyse et Spectrochimie (LCS), Caen, France.
# CeCILL-B FREE SOFTWARE LICENSE AGREEMENT
# See full LICENSE agreement in the root directory.
# ======================================================================================
# ruff: noqa
"""
Removing cosmic ray spikes from a Raman spectrum
================================================

In this example, we use the `despike` method to remove the noise from a Raman
spectrum.
"""

import spectrochempy as scp

# %%
# Load the data

dataset = scp.read("ramandata/labspec/serie190214-1.txt")

# %%
# Keep only one spectrum in this series
# and select the useful region

X = dataset[0, 70.0:]

# %%
# Baseline correction the data using the fast ~spectrochempy.snip` algorithm

X1 = X.snip()

# %%
# Plot the data

prefs = scp.preferences
prefs.figure.figsize = (8, 4)
X1.plot()
# %%
# Now let's use the `~spectrochempy.despike` method.
# Only two parameters needs to be tuned: the `size` of the filter
# (actually a Savitsky-Golay filter of order 2), and `delta`, the threshold for the
# detection of spikes (outliers).
# A spike is detected if its value is greater than `delta` times the standard deviation
# of the difference between the original and the smoothed data.

X2 = scp.despike(X1, size=11, delta=5)
X1.plot()
X2.plot(clear=False, ls="-", c="r")
# %%
# Another method, 'whitaker', is also available (see the documentation for details):
# %%
X3 = scp.despike(X1, size=11, delta=5, method="whitaker")
X1.plot()
X3.plot(clear=False, ls="-", c="r")
# %%
# Getting the desired results require the tuning of size and delta parameters.
# And sometimes may need to repeat the procedure on a previously filtered spectra.
#
# For example, if size or delta are badly chosen, valid peaks could be removed.
# So careful inspection of the results is crucial.

X4 = scp.despike(X1, size=21, delta=2)
X1.plot()
X4.plot(clear=False, ls="-", c="r")


# %%
# This ends the example ! The following line can be uncommented if no plot shows when
# running the .py script with python

# scp.show()

# sphinx_gallery_thumbnail_number = -1