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 and prepare the data

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

Keep one spectrum and select the useful region:

X = dataset[0, 70.0:]

Apply a fast SNIP baseline correction:

X1 = X.snip()

prefs = scp.preferences
prefs.figure.figsize = (8, 4)
_ = X1.plot()

Despike with the default method

The despike method has two key parameters: size (Savitzky-Golay filter width) and delta (detection threshold in standard deviation units):

X2 = scp.despike(X1, size=11, delta=5)
_ = X1.plot()
_ = X2.plot(clear=False, ls="-", c="r")

Despike with the Whitaker method

X3 = scp.despike(X1, size=11, delta=5, method="whitaker")
_ = X1.plot()
_ = X3.plot(clear=False, ls="-", c="r")

The importance of parameter tuning

Poorly chosen parameters may remove valid peaks:

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

Uncomment the following line to display all figures when running the script directly with Python.

# scp.show()