xpectrass 0.0.4

FTIR/ToF-SIMS Spectral Analysis Suite - Preprocessing toolkit for spectral classification

xpectrass

Xpectrass - From preprocessing to Machine Learning for Spectral Data

A comprehensive Python toolkit for FTIR spectral data preprocessing, analysis, and machine learning classification.

Overview

Xpectrass provides an end-to-end pipeline for FTIR spectra classification, from raw spectral data to machine learning predictions with model explainability. The library is built around two main classes:

• FTIRdataprocessing: Comprehensive preprocessing pipeline with evaluation-first approach
• FTIRdataanalysis: Statistical analysis, dimensionality reduction, and machine learning

Key Features

🔬 Preprocessing Pipeline

• Evaluation-First Philosophy: Automatically find the best preprocessing parameters for your data
• 9 Preprocessing Steps with multiple methods for each step
• 50+ Baseline Correction algorithms via pybaselines (airpls, asls, arpls, etc.)
• 7 Denoising Methods (Savitzky-Golay, wavelet, median, Gaussian, etc.)
• 17+ Normalization Methods (SNV, vector, min-max, area, peak, PQN, entropy)
• Atmospheric Correction (CO₂/H₂O removal and interpolation)
• Spectral Derivatives (1st, 2nd, gap derivatives with smoothing)
• Real-time Visualization at every preprocessing step

📊 Analysis & Visualization

• Dimensionality Reduction: PCA, t-SNE, UMAP, PLS-DA, OPLS-DA
• Statistical Analysis: ANOVA, correlation analysis, coefficient of variation
• Clustering: K-means, hierarchical clustering with dendrograms
• Interactive Plots: Mean spectra, heatmaps, overlay plots, and more

🤖 Machine Learning

• 20+ Classification Models: Random Forest, XGBoost, LightGBM, SVM, Neural Networks, etc.
• Automated Evaluation: Cross-validation, confusion matrices, performance metrics
• Hyperparameter Tuning: Automatic optimization of top-performing models
• Model Explainability: SHAP analysis for feature importance
• Comparison Visualizations: Family comparison, efficiency analysis, overfitting detection

📦 Bundled Datasets

• 6 Pre-loaded FTIR Plastic Datasets from published studies (2018-2024)
• Ready-to-use examples for testing and learning
• Datasets: Jung 2018, Kedzierski 2019, Frond 2021, Villegas-Camacho 2024

Installation

From PyPI (when published)

pip install xpectrass

From Source

git clone https://github.com/kazilab/xpectrass.git
cd xpectrass
pip install -e .

With Development Dependencies

pip install -e ".[dev]"

Quick Start

Option 1: Use Bundled Datasets

Xpectrass comes with 6 pre-loaded FTIR plastic datasets:

from xpectrass import FTIRdataprocessing
from xpectrass.data import load_jung_2018, get_data_info

# See available datasets
print(get_data_info())

# Load a dataset
df = load_jung_2018()

# Remove duplicate spectra
df = df.drop_duplicates(subset=['sample_id'])
print(f"Loaded {len(df)} spectra")

# Start preprocessing
ftir = FTIRdataprocessing(df, label_column="type")

Option 2: Load Your Own Data

from xpectrass import FTIRdataprocessing
from xpectrass.utils import process_batch_files
import glob
import pandas as pd

# Load single CSV file
df = pd.read_csv("ftir_data.csv", index_col=0)

# Or load multiple files
files = glob.glob('data/plastics/*.csv')
df = process_batch_files(files)

print(f"Loaded {len(df)} spectra with {len(df.columns)-1} wavenumbers")

Data Format:

• Rows: Individual spectra
• Columns: One label column + wavenumber columns (e.g., "400.0", "401.0", ...)
• Index: Sample names or IDs

Example CSV structure:

sample_id,type,400.0,401.0,402.0,...,4000.0
HDPE_001,HDPE,0.123,0.125,0.128,...,0.045
PP_001,PP,0.098,0.102,0.105,...,0.038

Basic Preprocessing Workflow

Step-by-Step Approach

from xpectrass import FTIRdataprocessing

# Initialize
ftir = FTIRdataprocessing(
    df,
    label_column="type",  # Name of your label column
    wn_min=400,           # Minimum wavenumber
    wn_max=4000           # Maximum wavenumber
)

# Step 1: Convert to absorbance (if data is in transmittance)
ftir.convert(mode="to_absorbance", plot=True)

# Step 2: Evaluate and apply denoising
ftir.find_denoising_method(n_samples=50, plot=True)
ftir.denoise_spect(method="savgol", window_length=15)

# Step 3: Evaluate and apply baseline correction
ftir.find_baseline_method(n_samples=50, plot=True)
ftir.plot_rfzn_nar_snr(metric_name="SNR")  # Visualize evaluation metrics
ftir.correct_baseline(method="asls", plot=False)

# Step 4: Remove atmospheric interference (CO₂, H₂O)
ftir.exclude_interpolate(method="spline", plot=True)

# Step 5: Evaluate and apply normalization
ftir.find_normalization_method()
ftir.normalize(method="snv")

# Step 6: Compare all processing stages
ftir.plot_multiple_spec()

# Get processed data
processed_df = ftir.df_norm

Quick Run with Defaults

For rapid prototyping:

ftir = FTIRdataprocessing(df, label_column="type")

# Run entire pipeline with default settings
ftir.run()

# Get final processed data
processed_df = ftir.df_norm

Basic Analysis Workflow

After preprocessing, use FTIRdataanalysis for visualization and machine learning:

from xpectrass import FTIRdataanalysis

LABEL_COLUMN = "type"
MIN_SAMPLE_NUMBER_FOR_GROUP = 10
# remove small groups from processed data
processed_df = processed_df.dropna(subset=[LABEL_COLUMN])
group_counts=processed_df[LABEL_COLUMN].value_counts()
valid_groups = group_counts[group_counts >= MIN_SAMPLE_NUMBER_FOR_GROUP].index
processed_df = processed_df[processed_df[LABEL_COLUMN].isin(valid_groups)]

# Initialize analysis
analysis = FTIRdataanalysis(processed_df, label_column=LABEL_COLUMN)

# Visualize mean spectra by class
analysis.plot_mean_spectra()

# Plot spectral heatmap
analysis.plot_heatmap()

# Dimensionality reduction
analysis.plot_pca()
analysis.plot_tsne()
analysis.plot_umap()

# Statistical analysis
analysis.perform_anova()
analysis.plot_correlation()

Machine Learning

# Prepare data for ML
analysis.ml_prepare_data()

# Run all classification models
results = analysis.run_all_models()
print(results.sort_values('test_f1', ascending=False))

# Tune top performing models
tuned_results = analysis.model_parameter_tuning()

# Explain model predictions with SHAP
analysis.explain_by_shap()
analysis.local_shap_plot()

Main Features

Preprocessing Methods

Category	Methods Available
Baseline Correction	50+ methods: airpls, asls, arpls, poly, mor, rubberband, snip, etc.
Denoising	Savitzky-Golay, wavelet, median, Gaussian, bilateral, Wiener, FFT
Normalization	SNV, vector, min-max, area, peak, PQN, entropy-weighted
Atmospheric Correction	CO₂/H₂O region exclusion and spline/linear interpolation
Scatter Correction	MSC, EMSC, SNV+detrend
Spectral Derivatives	1st, 2nd, gap derivatives with Savitzky-Golay smoothing
Data Validation	Completeness checks, range validation, outlier detection
Region Selection	13 predefined FTIR regions for plastic analysis

Analysis Capabilities

Category	Methods
Visualization	Mean spectra, overlay plots, heatmaps, coefficient of variation
Dimensionality Reduction	PCA, t-SNE, UMAP, PLS-DA, OPLS-DA with loadings plots
Clustering	K-means (with elbow plot), hierarchical (with dendrogram)
Statistics	ANOVA (wavenumber-wise), correlation matrices

Machine Learning Models

20+ Classification Algorithms:

• Ensemble: Random Forest, Extra Trees, AdaBoost, Gradient Boosting
• Boosting: XGBoost, LightGBM (multiple configurations)
• SVM: Linear, RBF, Polynomial kernels
• Linear: Logistic Regression, Ridge, SGD
• Neighbors: K-Nearest Neighbors (multiple K values)
• Neural Networks: Multi-Layer Perceptron (multiple architectures)
• Naive Bayes: Gaussian, Multinomial
• Discriminant Analysis: LDA, QDA

Bundled Datasets

Load pre-processed FTIR datasets for immediate use:

from xpectrass.data import (
    load_jung_2018,
    load_kedzierski_2019,
    load_frond_2021,
    load_villegas_camacho_2024_c4,
    load_all_datasets,
    get_data_info
)

# Load a specific dataset
df = load_jung_2018()

# View all available datasets
info = get_data_info()
print(info)

# Load all datasets
all_data = load_all_datasets()

Available Datasets:

• Jung et al. 2018 (~500 spectra, multiple polymer types)
• Kedzierski et al. 2019 (2 variants, ~300 spectra each)
• Frond et al. 2021 (~400 spectra)
• Villegas-Camacho et al. 2024 (C4 and C8 fractions, ~600 each)

Loading Your Own Data

from xpectrass.utils import process_batch_files
import glob

# Load multiple CSV files
files = glob.glob('data/plastics/*.csv')
df = process_batch_files(files)

# Load single file
import pandas as pd
df = pd.read_csv("my_ftir_data.csv", index_col=0)

Expected Data Format:

• Rows: Individual spectra
• Columns: One label column + wavenumber columns (e.g., "400.0", "401.0", ...)
• Index: Sample identifiers

Documentation

Full documentation is available at xpectrass.readthedocs.io.

User Guide Sections:

• Getting Started
• Preprocessing Pipeline
• Data Loading
• Analysis & Visualization
• Machine Learning
• API Reference

Building Documentation Locally

cd docs
pip install -r requirements.txt
sphinx-build -b html . _build/html

Requirements

Core Dependencies

• Python ≥ 3.8
• NumPy ≥ 1.20.0
• SciPy ≥ 1.7.0
• Pandas ≥ 1.3.0
• Polars ≥ 0.15.0

Signal Processing

• PyBaselines ≥ 1.0.0
• PyWavelets ≥ 1.1.0

Visualization

• Matplotlib ≥ 3.4.0
• Seaborn ≥ 0.11.0

Machine Learning

• scikit-learn ≥ 1.0.0
• XGBoost ≥ 1.5.0
• LightGBM ≥ 3.3.0
• UMAP-learn ≥ 0.5.0
• SHAP ≥ 0.41.0

Utilities

• tqdm ≥ 4.60.0
• joblib ≥ 1.0.0

Project Structure

xpectrass/
├── __init__.py           # Main package exports
├── main.py               # FTIRdataprocessing & FTIRdataanalysis classes
├── data/                 # Bundled FTIR datasets
│   └── __init__.py
└── utils/                # Preprocessing & analysis utilities
    ├── baseline.py       # 50+ baseline correction methods
    ├── denoise.py        # 7 denoising methods
    ├── normalization.py  # 7+ normalization methods
    ├── atmospheric.py    # CO₂/H₂O correction
    ├── derivatives.py    # Spectral derivatives
    ├── scatter_correction.py  # MSC, EMSC, SNV
    ├── region_selection.py    # FTIR region handling
    ├── data_validation.py     # Data quality checks
    ├── ml.py                  # Machine learning models
    ├── plotting*.py           # Visualization functions
    └── ...

Philosophy

Evaluation-First Approach

Xpectrass uses an evaluation-first philosophy: instead of guessing preprocessing parameters, the library provides built-in evaluation methods to find the optimal settings for your specific data.

# Evaluate all baseline methods
ftir.find_baseline_method(n_samples=50, plot=True)
ftir.plot_rfzn_nar_snr()  # Visualize metrics

# Apply the best method
ftir.correct_baseline(method="asls")

State Management

The FTIRdataprocessing class maintains state through the entire pipeline, storing intermediate results for easy access and comparison:

ftir.df              # Original data
ftir.converted_df    # After conversion
ftir.df_atm         # After atmospheric correction
ftir.df_corr        # After baseline correction
ftir.df_denoised    # After denoising
ftir.df_norm        # After normalization
ftir.df_deriv       # After derivatives

Use Cases

• Plastic Classification: Identify polymer types from FTIR spectra
• Quality Control: Detect contamination or degradation in materials
• Environmental Analysis: Classify microplastics in environmental samples
• Material Science: Characterize polymer blends and composites
• Method Development: Compare preprocessing and classification strategies

License

This project is licensed under the MIT License - see the LICENSE file for details.

Citation

If you use this software in your research, please cite:

@software{xpectrass,
  author = {Data Analysis Team @KaziLab.se},
  title = {Xpectrass - From preprocessing to Machine Learning for Spectral Data},
  year = {2026},
  url = {https://github.com/kazilab/xpectrass}
}

Contributing

Contributions are welcome! Please feel free to submit issues, fork the repository, and create pull requests.

Development Setup

git clone https://github.com/kazilab/xpectrass.git
cd xpectrass
pip install -e ".[dev]"

Running Tests

pytest

Contact

• Email: [e-mail]
• GitHub: github.com/kazilab/xpectrass
• Documentation: xpectrass.readthedocs.io
• Issues: github.com/kazilab/xpectrass/issues

Acknowledgments

Built with ❤️ by the Data Analysis Team @KaziLab.se

Version History

v0.0.4 (Current)

• Fixed documentation
• Bug fixes and stability improvements

v0.0.3 (Current)

• Removed CatBoost dependency for simpler installation
• Bug fixes and stability improvements

v0.0.2

• Complete documentation overhaul
• Added FTIRdataprocessing and FTIRdataanalysis classes
• 6 bundled FTIR datasets
• 20+ machine learning models with SHAP explainability
• Comprehensive evaluation methods for all preprocessing steps
• Advanced visualization and statistical analysis tools

v0.0.1

• Initial release
• Basic preprocessing utilities