xpectrass

Contents

  • Getting Started
    • Prerequisites
    • Installation
      • From PyPI
      • From Source
    • Quick Start
      • Option 1: Use Bundled Datasets
      • Option 2: Load Your Own Data
    • Basic Preprocessing Workflow
      • Step-by-Step Approach
      • Quick Run with Defaults
    • Basic Analysis Workflow
    • Machine Learning
    • Key Methods Quick Reference
      • FTIRdataprocessing
      • FTIRdataanalysis
    • Getting Help
  • User Guide
    • Preprocessing Pipeline
      • Overview
      • Initialization Parameters
        • FTIRdataprocessing.init()
        • Default Regions
      • Processing Workflow
        • 1. Data Conversion
        • 2. Atmospheric Correction
        • 3. Baseline Correction
        • 4. Denoising
        • 5. Normalization
        • 6. Spectral Derivatives
        • 7. Visualization and Comparison
      • Accessing Processed Data
      • Complete Example
      • Quick Run Method
      • Advanced Features
        • Custom Baseline Parameters
        • Custom Denoising Parameters
        • Stratified Sampling for Evaluation
      • Tips and Best Practices
      • Next Steps
    • Data Loading
      • Bundled Datasets
        • Available Datasets
        • Loading Individual Datasets
        • Loading All Datasets
        • Loading Specific Datasets
        • Dataset Information
      • Loading Your Own Data
        • From Single CSV File
        • From Multiple CSV Files (Batch Loading)
        • From Directory Structure
        • From Excel Files
      • Data Format Requirements
        • Required Format
        • Valid Wavenumber Column Formats
      • Data Validation
        • Validation Checks
      • Combining Datasets
        • Combine Bundled Datasets
        • Combine with Interpolation
      • Data Preprocessing Before Analysis
      • Exporting Processed Data
      • Tips and Best Practices
      • Example: Complete Data Loading Workflow
      • Common Data Loading Patterns
        • Pattern 1: Load and Preprocess Bundled Data
        • Pattern 2: Load Multiple Files from Directory
        • Pattern 3: Load and Combine Multiple Datasets
      • Next Steps
    • Data Analysis and Visualization
      • Overview
      • Initialization Parameters
        • FTIRdataanalysis.init()
      • Spectral Visualization
        • Plot Mean Spectra by Class
        • Plot Overlay of Mean Spectra
        • Plot Spectral Heatmap
        • Plot Coefficient of Variation
      • Statistical Analysis
        • ANOVA Analysis
        • Correlation Matrix
      • Dimensionality Reduction
        • Principal Component Analysis (PCA)
        • t-SNE (t-Distributed Stochastic Neighbor Embedding)
        • UMAP (Uniform Manifold Approximation and Projection)
        • PLS-DA (Partial Least Squares Discriminant Analysis)
        • OPLS-DA (Orthogonal PLS-DA)
      • Clustering Analysis
        • K-means Clustering
        • Hierarchical Clustering
      • Complete Analysis Example
      • Saving Figures
      • Tips and Best Practices
      • Next Steps
    • Machine Learning
      • Overview
      • Data Preparation
        • Train/Test Split
      • Available Models
        • View All Models
        • Model Categories
      • Running Models
        • Run a Single Model
        • Run All Models
        • View Top Models
      • Model Comparison Visualization
        • Model Comparison Plot
        • Family Comparison Plot
        • Efficiency Analysis Plot
        • Overfitting Analysis Plot
      • Hyperparameter Tuning
        • Tune Top Models
      • Model Interpretation
        • SHAP Explainability
        • Local SHAP Interpretation
        • Feature Importance by Wavenumber
      • Complete Machine Learning Workflow
      • Cross-Dataset Validation
      • Tips and Best Practices
        • Data Preparation
        • Model Selection
        • Hyperparameter Tuning
        • Model Interpretation
        • Performance Metrics
      • Common Issues and Solutions
        • Issue: Poor Model Performance
        • Issue: Overfitting
        • Issue: Slow Training
        • Issue: SHAP Takes Too Long
      • Model Export and Deployment
        • Save Trained Model
        • Load and Use Model
      • Next Steps
    • Data Validation
      • Overview
      • Functions
        • validate_spectra
        • detect_outlier_spectra
        • check_wavenumber_consistency
      • Example Output
      • Best Practices
    • Baseline Correction
      • Overview
        • Using FTIRdataprocessing Class (Recommended)
        • Using Utility Functions Directly
      • Available Methods
        • Whittaker-Based Methods
        • Polynomial-Based Methods
        • Morphological Methods
        • Spline-Based Methods
        • Custom Methods
      • Function Reference
        • baseline_correction
      • Evaluation
        • Metrics
      • Visualization
      • Recommendations for Plastics
      • Example
    • Denoising
      • Overview
        • Using FTIRdataprocessing Class (Recommended)
        • Using Utility Functions Directly
      • Available Methods
      • Method Details
        • Savitzky-Golay (Recommended)
        • Wavelet Denoising
        • Median Filter
        • Gaussian Filter
        • Moving Average
        • Whittaker Smoother
        • Low-Pass Filter
      • Evaluation
        • SNR Estimation
        • Batch Evaluation
      • Visualization
      • Recommendations
      • Example
    • Normalization
      • Overview
        • Using FTIRdataprocessing Class (Recommended)
        • Using Utility Functions Directly
      • Available Methods
      • Method Details
        • Standard Normal Variate (SNV) - Recommended
        • Vector Normalization (L2)
        • Min-Max Normalization
        • Area Normalization
        • Peak Normalization
      • Scaling Methods for PCA/PLS
        • Mean Centering
        • Auto-Scaling
        • Pareto Scaling
      • Detrending
      • Batch Operations
        • Normalize Multiple Spectra
        • DataFrame Operations
      • Comparison
      • Recommendations
      • Example
    • Atmospheric Correction
      • Overview
      • Interference Regions
      • Methods
      • Custom Regions
      • Detection
      • When to Use
    • Spectral Derivatives
      • Overview
      • Benefits
        • First Derivative
        • Second Derivative
      • Functions
        • spectral_derivative
        • first_derivative
        • second_derivative
        • gap_derivative
      • Parameter Guidelines
        • Window Length
        • Polynomial Order
      • Noise Considerations
      • Batch Processing
      • Visualization
      • Example
    • Scatter Correction
      • Overview
      • Methods
        • MSC (Multiplicative Scatter Correction)
        • EMSC (Extended MSC)
        • SNV
        • SNV + Detrend
      • Batch DataFrame Correction
      • Single Spectrum MSC Diagnostics
      • Quick Quality Check
    • Region Selection
      • Overview
      • Predefined Regions
        • Main Regions
        • Functional Groups
        • Plastic-Specific
        • Atmospheric
      • Functions
        • select_region
        • exclude_regions
        • exclude_atmospheric
      • NumPy Functions
      • Analysis
      • Helper Functions
      • Example: Classification Regions
    • Overview
    • Quick Start
      • Basic Preprocessing Workflow
      • Basic Analysis Workflow
    • Preprocessing Pipeline Order
    • Key Features
      • Evaluation-First Approach
      • Bundled Datasets
      • Comprehensive Machine Learning
    • Main Classes
      • FTIRdataprocessing
      • FTIRdataanalysis
  • API Reference
    • preprocessing_pipeline
      • Classes
        • FTIRPreprocessor
        • PreprocessingConfig
      • Functions
        • create_preprocessor
        • get_preset_config
    • Utils Module
      • data_validation
        • Data Validation Module for FTIR Spectral Preprocessing
        • validate_spectra()
        • detect_outlier_spectra()
        • check_wavenumber_consistency()
        • validate_spectra
        • detect_outlier_spectra
      • baseline
        • Baseline Correction Module for FTIR Spectral Preprocessing
        • baseline_correction()
        • apply_baseline_correction()
        • baseline_method_names()
        • plot_baseline_correction_metric_boxes()
        • plot_baseline_correction_metric_boxes_masked()
        • evaluate_baseline_correction_methods()
        • find_best_baseline_method()
        • baseline_correction
        • baseline_method_names
      • denoise
        • Denoising Module for FTIR Spectral Preprocessing
        • denoise()
        • denoise_method_names()
        • apply_denoising()
        • estimate_snr()
        • evaluate_denoising_methods_safe()
        • evaluate_denoising_methods()
        • plot_denoising_evaluation()
        • plot_denoising_evaluation_summary()
        • find_best_denoising_method()
        • plot_denoising_comparison()
        • denoise
      • normalization
        • Normalization Module for FTIR Spectral Preprocessing
        • normalize()
        • normalize_method_names()
        • normalize_df()
        • mean_center()
        • auto_scale()
        • pareto_scale()
        • detrend()
        • snv_detrend()
        • normalize_curvature_weighted()
        • normalize_peak_envelope()
        • normalize_entropy_weighted()
        • normalize_total_variation()
        • normalize_spectral_moments()
        • normalize_adaptive_regional()
        • normalize_derivative_ratio()
        • normalize_signal_to_baseline()
        • normalize_robust_snv()
        • normalize_pqn()
        • normalize_novel()
        • novel_normalize_method_names()
        • normalize
        • mean_center
        • auto_scale
      • atmospheric
        • Atmospheric Correction Module for FTIR Spectral Preprocessing
        • atmospheric_correction_spectrum()
        • identify_atmospheric_features()
        • exclude_and_interpolate_spectrum()
        • atmospheric_correction()
        • exclude_and_interpolate_regions()
        • atmospheric_correction
      • derivatives
        • Spectral Derivatives Module for FTIR Preprocessing
        • spectral_derivative()
        • first_derivative()
        • second_derivative()
        • gap_derivative()
        • derivative_with_smoothing()
        • derivative_batch()
        • plot_derivatives()
        • spectral_derivative
        • first_derivative / second_derivative
      • scatter_correction
        • Scatter Correction Module for FTIR Spectral Preprocessing
        • scatter_correction()
        • scatter_method_names()
        • apply_scatter_correction()
        • msc_single()
        • scatter_correction
      • region_selection
        • Region Selection Module for FTIR Spectral Preprocessing
        • get_region_names()
        • get_region_range()
        • select_region()
        • exclude_regions()
        • exclude_atmospheric()
        • select_region_np()
        • select_regions_np()
        • analyze_regions()
        • get_wavenumbers()
        • get_spectra_matrix()
        • select_region
        • exclude_regions
        • FTIR_REGIONS
      • file_management
        • process_batch_files()
        • import_data()
        • import_data_pd()
        • import_data_pl()
        • process_batch_files
        • import_data
    • Module Overview
    • Quick Import Guide
  • Examples
    • Example 1: Notebook-Style Method Selection
    • Example 2 Atmospheric + Normalization Workflow
    • Example 3: Derivatives + Multi-Dataset Combination
    • Example 4: Notebook-Style Data Analysis Class
  • Xpectrass for Bioinformatics
    • Why this matters in bioinformatics
    • A practical workflow
    • Example: from spectra to model comparison
    • Bioinformatics use cases
    • Explainability and auditability
    • Practical considerations
    • Conclusion
  • Acknowledgements
  • Changelog
    • Latest Release: v0.0.4 (2026-02-12)
      • Major Features
      • Improvements
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