CLI tool for calculating peak areas in spectral data (UV-Vis, absorbance) with baseline correction.
Reads raw spectrometer output files (CSV), identifies spectral data columns automatically, and calculates the baseline-corrected integral between two wavelength bounds using the trapezoidal rule. The baseline is a straight line connecting the two endpoints.
Features:
- Parses raw spectrometer CSV files with metadata headers
- Handles detector overflow values (
OVRFLW) gracefully - Processes multiple data columns in a single run
- Generates annotated plots showing the spectrum, baseline, and integrated area
- Reports results in a clean tabular format
python spec-int.py [input_file] [start_wavelength] [end_wavelength] [column_names]
Arguments:
| Argument | Default | Description |
|---|---|---|
input_file |
example.csv |
Path to the spectrometer CSV file |
start_wavelength |
400 |
Lower wavelength bound (nm) |
end_wavelength |
650 |
Upper wavelength bound (nm) |
column_names |
all |
Comma-separated column names, or all |
Examples:
# Integrate all columns from 400-650 nm using the example file
python spec-int.py
# Specify a file and wavelength range
python spec-int.py data.csv 370 650
# Process specific columns only
python spec-int.py data.csv 300 500 H1,H3,H5
# Explicitly process all columns
python spec-int.py data.csv 250 600 allThe tool expects CSV files as output by plate-reader spectrometers. It looks for a row containing Wavelength as the header, treats everything above it as metadata, and parses numerical data below it. Non-numeric values like OVRFLW are handled automatically.
Example structure:
Software Version,3.10.06
Date,2025-01-26
Wavelength,Sample1,Sample2,Sample3
250,0.532,0.411,0.298
255,0.587,0.445,0.312
...
- Console: A table of baseline-corrected integral values per column
- PNG plots: One per column, showing the spectrum with the integration region and baseline highlighted
- Python 3.7+
- numpy
- matplotlib
Install dependencies:
pip install numpy matplotlibMIT