Atmospheric Correction

Atmospheric correction removes CO2 and H2O vapor interference from FTIR spectra.

Overview

In xpectrass, atmospheric correction is typically applied to full DataFrames (rows = samples, columns = wavenumbers).

from xpectrass.data import load_jung_2018
from xpectrass.utils import atmospheric_correction

df = load_jung_2018().head(50)

corrected_df = atmospheric_correction(
    data=df,
    method="interpolate",
    label_column="type",
    exclude_columns=["study", "sample_id", "environmental", "resolution"],
)

Interference Regions

Band	Wavenumber Range	Source
CO2	2300-2400 cm^-1	Asymmetric stretch
H2O bend	1350-1900 cm^-1	Bending mode
H2O stretch	3550-3900 cm^-1	Stretching modes

Methods

Valid methods for atmospheric_correction(..., method=...):

interpolate (default)
spline
reference
zero
exclude

# Spline interpolation
df_spline = atmospheric_correction(
    data=df,
    method="spline",
    label_column="type",
    exclude_columns=["study", "sample_id", "environmental", "resolution"],
)

# Set atmospheric regions to local baseline
df_zero = atmospheric_correction(
    data=df,
    method="zero",
    label_column="type",
    exclude_columns=["study", "sample_id", "environmental", "resolution"],
)

Custom Regions

Use co2_ranges and h2o_ranges (lists of tuples):

df_custom = atmospheric_correction(
    data=df,
    method="interpolate",
    co2_ranges=[(2280, 2420)],
    h2o_ranges=[(1400, 1850), (3600, 3850)],
    label_column="type",
    exclude_columns=["study", "sample_id", "environmental", "resolution"],
)

Detection

Check atmospheric interference on a single spectrum:

import numpy as np
from xpectrass.utils import identify_atmospheric_features

spectral_cols = [c for c in df.columns if c not in ["study", "sample_id", "type", "environmental", "resolution"]]
wavenumbers = np.array([float(c) for c in spectral_cols])
intensities = df.iloc[0][spectral_cols].to_numpy(dtype=float)

report = identify_atmospheric_features(intensities, wavenumbers)

if report["co2_detected"]:
    print("CO2 interference detected")
if report["h2o_detected"]:
    print("H2O interference detected")

When to Use

Measurement Mode	Recommendation
ATR	Often minimal correction needed
Transmission	Usually recommended
External reflection	Often helpful