CODEBASE_INVENTORY.md

# Comprehensive Codebase Audit: Polymer Aging ML Platform

## Executive Summary

This audit provides a technical inventory of the dev-jas/polymer-aging-ml repository—a modular machine learning platform for polymer degradation classification using Raman and FTIR spectroscopy. The system features robust error handling, multi-format batch processing, and persistent performance tracking, making it suitable for research, education, and industrial applications.

## 🏗️ System Architecture

### Core Infrastructure

- **Streamlit-based web app** (`app.py`) as the main interface
- **PyTorch** for deep learning
- **Docker** for deployment
- **SQLite** (`outputs/performance_tracking.db`) for performance metrics
- **Plugin-based model registry** for extensibility

### Directory Structure

- **app.py**: Main Streamlit application
- **README.md**: Project documentation
- **Dockerfile**: Containerization (Python 3.13-slim)
- **requirements.txt**: Dependency management
- **models/**: Neural network architectures and registry
- **utils/**: Shared utilities (preprocessing, batch, results, performance, errors, confidence)
- **scripts/**: CLI tools for training, inference, data management
- **outputs/**: Model weights, inference results, performance DB
- **sample_data/**: Demo spectrum files
- **tests/**: Unit tests (PyTest)
- **datasets/**: Data storage
- **pages/**: Streamlit dashboard pages

## 🤖 Machine Learning Framework

### Model Registry

Factory pattern in `models/registry.py` enables dynamic model selection:

```python
_REGISTRY: Dict[str, Callable[[int], object]] = {
    "figure2": lambda L: Figure2CNN(input_length=L),
    "resnet": lambda L: ResNet1D(input_length=L),
    "resnet18vision": lambda L: ResNet18Vision(input_length=L)
}
```

### Neural Network Architectures

The platform supports three architectures, offering diverse options for spectral analysis:

**Figure2CNN (Baseline Model):**

- Architecture: 4 convolutional layers (1→16→32→64→128), 3 fully connected layers (256→128→2).
- Performance: 94.80% accuracy, 94.30% F1-score (Raman-only).
- Parameters: ~500K, supports dynamic input handling.

**ResNet1D (Advanced Model):**

- Architecture: 3 residual blocks with 1D skip connections.
- Performance: 96.20% accuracy, 95.90% F1-score.
- Parameters: ~100K, efficient via global average pooling.

**ResNet18Vision (Experimental):**

- Architecture: 1D-adapted ResNet-18 with 4 layers (2 blocks each).
- Status: Under evaluation, ~11M parameters.
- Opportunity: Expand validation for broader spectral applications.

## 🔧 Data Processing Infrastructure

### Preprocessing Pipeline

The system implements a **modular preprocessing pipeline** in `utils/preprocessing.py` with five configurable stages:
**1. Input Validation Framework:**

- File format verification (`.txt` files exclusively)
- Minimum data points validation (≥10 points required)
- Wavenumber range validation (0-10,000 cm⁻¹ for Raman spectroscopy)
- Monotonic sequence verification for spectral consistency
- NaN value detection and automatic rejection

**2. Core Processing Steps:**

- **Linear Resampling**: Uniform grid interpolation to 500 points using `scipy.interpolate.interp1d`
- **Baseline Correction**: Polynomial detrending (configurable degree, default=2)
- **Savitzky-Golay Smoothing**: Noise reduction (window=11, order=2, configurable)
- **Min-Max Normalization**: Scaling to range with constant-signal protection

### Batch Processing Framework

The `utils/multifile.py` module (12.5 kB) provides **enterprise-grade batch processing** capabilities:

- **Multi-File Upload**: Streamlit widget supporting simultaneous file selection
- **Error-Tolerant Processing**: Individual file failures don't interrupt batch operations
- **Progress Tracking**: Real-time processing status with callback mechanisms
- **Results Aggregation**: Comprehensive success/failure reporting with export options
- **Memory Management**: Automatic cleanup between file processing iterations

## 🖥️ User Interface Architecture

### Streamlit Application Design

The main application implements a **sophisticated two-column layout** with comprehensive state management:[^1_2]

**Left Column - Control Panel:**

- **Model Selection**: Dropdown with real-time performance metrics display
- **Input Modes**: Three processing modes (Single Upload, Batch Upload, Sample Data)
- **Status Indicators**: Color-coded feedback system for user guidance
- **Form Submission**: Validated input handling with disabled state management

**Right Column - Results Display:**

- **Tabbed Interface**: Details, Technical diagnostics, and Scientific explanation
- **Interactive Visualization**: Confidence progress bars with color coding
- **Spectrum Analysis**: Side-by-side raw vs. processed spectrum plotting
- **Technical Diagnostics**: Model metadata, processing times, and debug logs

### State Management System

The application employs **advanced session state management**:

- Persistent state across Streamlit reruns using `st.session_state`
- Intelligent caching with content-based hash keys for expensive operations
- Memory cleanup protocols after inference operations
- Version-controlled file uploader widgets to prevent state conflicts

## 🛠️ Utility Infrastructure

### Centralized Error Handling

The `utils/errors.py` module provides with **context-aware** logging and user-friendly error messages.

### Performance Tracking System

The `utils/performance_tracker.py` module provides a robust system for logging and analyzing performance metrics.

- **Database Logging**: Persists metrics to a SQLite database.
- **Automated Tracking**: Uses a context manager to automatically track inference time, preprocessing time, and memory usage.
- **Dashboarding**: Includes functions to generate performance visualizations and summary statistics for the UI.

### Enhanced Results Management

The `utils/results_manager.py` module enables comprehensive session and persistent results tracking.

- **In-Memory Storage**: Manages results for the current session.
- **Multi-Model Handling**: Aggregates results from multiple models for comparison.
- **Export Capabilities**: Exports results to CSV and JSON.
- **Statistical Analysis**: Calculates accuracy, confidence, and other metrics.

## 📜 Command-Line Interface

### Training Pipeline

The `scripts/train_model.py` module (6.27 kB) implements **robust model training**:

**Cross-Validation Framework:**

- 10-fold stratified cross-validation for unbiased evaluation
- Model registry integration supporting all architectures
- Configurable preprocessing via command-line flags
- Comprehensive JSON logging with confusion matrices

**Reproducibility Features:**

- Fixed random seeds (SEED=42) across all random number generators
- Deterministic CUDA operations when GPU available
- Standardized train/validation splitting methodology

### Data Utilities

**File Discovery System:**

- Recursive `.txt` file scanning with label extraction
- Filename-based labeling convention (`sta-*` = stable, `wea-*` = weathered)
- Dataset inventory generation with statistical summaries

### Dependency Management

The `requirements.txt` specifies **core dependencies without version pinning**:[^1_12]

- **Web Framework**: `streamlit` for interactive UI
- **Deep Learning**: `torch`, `torchvision` for model execution
- **Scientific Computing**: `numpy`, `scipy`, `scikit-learn` for data processing
- **Visualization**: `matplotlib` for spectrum plotting
- **API Framework**: `fastapi`, `uvicorn` for potential REST API expansion

## 🐳 Deployment Infrastructure

### Docker Configuration

The Dockerfile uses Python 3.13-slim for efficient containerization:

- Includes essential build tools and scientific libraries.
- Supports health checks for container wellness.
- **Roadmap**: Implement multi-stage builds and environment variables for streamlined deployments.

### Confidence Analysis System

The `utils/confidence.py` module provides **scientific confidence metrics**

**Softmax-Based Confidence:**

- Normalized probability distributions from model logits
- Three-tier confidence levels: HIGH (≥80%), MEDIUM (≥60%), LOW (<60%)
- Color-coded visual indicators with emoji representations
- Legacy compatibility with logit margin calculations

### Session Results Management

The `utils/results_manager.py` module (8.16 kB) enables **comprehensive session tracking**:

- **In-Memory Storage**: Session-wide results persistence
- **Export Capabilities**: CSV and JSON download with timestamp formatting
- **Statistical Analysis**: Automatic accuracy calculation when ground truth available
- **Data Integrity**: Results survive page refreshes within session boundaries

## 🧪 Testing Framework

### Test Infrastructure

The `tests/` directory implements **basic validation framework**:

- **PyTest Configuration**: Centralized test settings in `conftest.py`
- **Preprocessing Tests**: Core pipeline functionality validation in `test_preprocessing.py`
- **Limited Coverage**: Currently covers preprocessing functions only

**Testing Coming Soon:**

- Add model architecture unit tests
- Integration tests for UI components
- Performance benchmarking tests
- Improved error handling validation

## 🔍 Security \& Quality Assessment

### Input Validation Security

**Robust Validation Framework:**

- Strict file format enforcement preventing arbitrary file uploads
- Content verification with numeric data type checking
- Scientific range validation for spectroscopic data integrity
- Memory safety through automatic cleanup and garbage collection

### Code Quality Metrics

**Production Standards:**

- **Type Safety**: Comprehensive type hints throughout codebase using Python 3.8+ syntax
- **Documentation**: Inline docstrings following standard conventions
- **Error Boundaries**: Multi-level exception handling with graceful degradation
- **Logging**: Structured logging with appropriate severity levels

## 🚀 Extensibility Analysis

### Model Architecture Extensibility

The **registry pattern enables seamless model addition**:

1. **Implementation**: Create new model class with standardized interface
2. **Registration**: Add to `models/registry.py` with factory function
3. **Integration**: Automatic UI and CLI support without code changes
4. **Validation**: Consistent input/output shape requirements

### Processing Pipeline Modularity

**Configurable Architecture:**

- Boolean flags control individual preprocessing steps
- Easy integration of new preprocessing techniques
- Backward compatibility through parameter defaulting
- Single source of truth in `utils/preprocessing.py`

### Export \& Integration Capabilities

**Multi-Format Support:**

- CSV export for statistical analysis software
- JSON export for programmatic integration
- RESTful API potential through FastAPI foundation
- Batch processing enabling high-throughput scenarios

## 📊 Performance Characteristics

### Computational Efficiency

**Model Performance Metrics:**

| Model          | Parameters | Accuracy         | F1-Score         | Inference Time   |
| :------------- | :--------- | :--------------- | :--------------- | :--------------- |
| Figure2CNN     | ~500K      | 94.80%           | 94.30%           | <1s per spectrum |
| ResNet1D       | ~100K      | 96.20%           | 95.90%           | <1s per spectrum |
| ResNet18Vision | ~11M       | Under evaluation | Under evaluation | <2s per spectrum |

**System Response Times:**

- Single spectrum processing: <5 seconds end-to-end
- Batch processing: Linear scaling with file count
- Model loading: <3 seconds (cached after first load)
- UI responsiveness: Real-time updates with progress indicators

### Memory Management

**Optimization Strategies:**

- Explicit garbage collection after inference operations[^1_2]
- CUDA memory cleanup when GPU available
- Session state pruning for long-running sessions
- Caching with content-based invalidation

## 🔮 Strategic Development Roadmap

The project roadmap has been updated to reflect recent progress:

- [x] **FTIR Support**: Modular integration of FTIR spectroscopy is complete.
- [x] **Multi-Model Dashboard**: A model comparison tab has been implemented.
- [ ] **Image-based Inference**: Future work to include image-based polymer classification.
- [x] **Performance Tracking**: A performance tracking dashboard has been implemented.
- [ ] **Enterprise Integration**: Future work to include a RESTful API and more advanced database integration.

## 💼 Business Logic \& Scientific Workflow

### Classification Methodology

**Binary Classification Framework:**

- **Stable Polymers**: Well-preserved molecular structure suitable for recycling
- **Weathered Polymers**: Oxidized bonds requiring additional processing
- **Confidence Thresholds**: Scientific validation with visual indicators
- **Ground Truth Validation**: Filename-based labeling for accuracy assessment

### Scientific Applications

**Research Use Cases:**

- Material science polymer degradation studies
- Recycling viability assessment for circular economy
- Environmental microplastic weathering analysis
- Quality control in manufacturing processes
- Longevity prediction for material aging

### Data Workflow Architecture

```text
Input Validation → Spectrum Preprocessing → Model Inference →
Confidence Analysis → Results Visualization → Export Options
```

## 🏁 Audit Conclusion

This codebase represents a **well-architected, scientifically rigorous machine learning platform** with the following key characteristics:

**Technical Excellence:**

- Production-ready architecture with comprehensive error handling
- Modular design supporting extensibility and maintainability
- Scientific validation appropriate for spectroscopic data analysis
- Clean separation between research functionality and production deployment

**Scientific Rigor:**

- Proper preprocessing pipeline validated for Raman spectroscopy
- Multiple model architectures with performance benchmarking
- Confidence metrics appropriate for scientific decision-making
- Ground truth validation enabling accuracy assessment

**Operational Readiness:**

- Containerized deployment suitable for cloud platforms
- Batch processing capabilities for high-throughput scenarios
- Comprehensive export options for downstream analysis
- Session management supporting extended research workflows

**Development Quality:**

- Type-safe Python implementation with modern language features
- Comprehensive documentation supporting knowledge transfer
- Modular architecture enabling team development
- Testing framework foundation for continuous integration

The platform successfully bridges academic research and practical application, providing both accessible web interface capabilities and automation-friendly command-line tools. The extensible architecture and comprehensive documentation indicate strong software engineering practices suitable for both research institutions and industrial applications.

**Risk Assessment:** Low - The codebase demonstrates mature engineering practices with appropriate validation and error handling for production deployment.

**Recommendation:** This platform is ready for production deployment, representing a solid foundation for polymer classification research and industrial applications.

### EXTRA

```text
1. Setup & Configuration (Lines 1-105)
    Imports: Standard libraries (os, sys, time), data science (numpy, torch, matplotlib), and Streamlit.
    Local Imports: Pulls from your existing utils and models directories.
    Constants: Global, hardcoded configuration variables.
    KEEP_KEYS: Defines which session state keys persist on reset.
    TARGET_LEN: A static preprocessing value.
    SAMPLE_DATA_DIR, MODEL_WEIGHTS_DIR: Path configurations.
    MODEL_CONFIG: A dictionary defining model paths, classes, and metadata.
    LABEL_MAP: A dictionary for mapping class indices to human-readable names.
    Page Setup:
    st.set_page_config(): Sets the browser tab title, icon, and layout.
    st.markdown(<style>...): A large, embedded multi-line string containing all the custom CSS for the application.
2. Core Logic & Data Processing (Lines 108-250)
    Model Handling:
    load_state_dict(): Cached function to load model weights from a file.
    load_model(): Cached resource to initialize a model class and load its weights.
    run_inference(): The main ML prediction function. It takes resampled data, loads the appropriate model, runs inference, and returns the results.
    Data I/O & Preprocessing:
    label_file(): Extracts the ground truth label from a filename.
    get_sample_files(): Lists the available .txt files in the sample data directory.
    parse_spectrum_data(): The crucial function for reading, validating, and parsing raw text input into numerical numpy arrays.
    Visualization:
    create_spectrum_plot(): Generates the "Raw vs. Resampled" matplotlib plot and returns it as an image.
    Helpers:
    cleanup_memory(): A utility for garbage collection.
    get_confidence_description(): Maps a logit margin to a human-readable confidence level.
3. State Management & Callbacks (Lines 253-335)
    Initialization:
    init_session_state(): The cornerstone of the app's state, defining all the default values in st.session_state.
    Widget Callbacks:
    on_sample_change(): Triggered when the user selects a sample file.
    on_input_mode_change(): Triggered by the main st.radio widget.
    on_model_change(): Triggered when the user selects a new model.
    Reset/Clear Functions:
    reset_results(): A soft reset that only clears inference artifacts.
    reset_ephemeral_state(): The "master reset" that clears almost all session state and forces a file uploader refresh.
    clear_batch_results(): A focused function to clear only the results in col2.
4. UI Rendering Components (Lines 338-End)
    Generic Components:
    render_kv_grid(): A reusable helper to display a dictionary in a neat grid.
    render_model_meta(): Renders the model's accuracy and F1 score in the sidebar.
    Main Application Layout (main()):
    Sidebar: Contains the header, model selector (st.selectbox), model metadata, and the "About" expander.
    Column 1 (Input): Contains the main st.radio for mode selection and the conditional logic to display the single file uploader, batch uploader, or sample selector. It also holds the "Run Analysis" and "Reset All" buttons.
    Column 2 (Results): Contains all the logic for displaying either the batch results or the detailed, tabbed results for a single file (Details, Technical, Explanation).
```