EFA analysis example

In this example, we perform the Evolving Factor Analysis

sphinx_gallery_thumbnail_number = 2

import os
import spectrochempy as scp

Upload and preprocess a dataset

datadir = scp.preferences.datadir
dataset = scp.read_omnic(os.path.join(datadir, "irdata", "nh4y-activation.spg"))

columns masking

dataset[:, 1230.0:920.0] = scp.MASKED  # do not forget to use float in slicing
dataset[:, 5997.0:5993.0] = scp.MASKED

difference spectra

dataset -= dataset[-1]
dataset.plot_stack()

<_Axes: xlabel='wavenumbers $\\mathrm{/\\ \\mathrm{cm}^{-1}}$', ylabel='absorbance $\\mathrm{/\\ \\mathrm{a.u.}}$'>

column masking for bad columns

dataset[10:12] = scp.MASKED

Evolving Factor Analysis

efa = scp.EFA(dataset)

Show results

npc = 4
c = efa.get_conc(npc)
c.T.plot()

# scp.show()  # Uncomment to show plot if needed (not necessary in jupyter notebook)

<_Axes: xlabel='acquisition timestamp (GMT) $\\mathrm{/\\ \\mathrm{s}}$', ylabel='relative concentration $\\mathrm{}$'>