A machine learning pipeline for detecting and annotating birds in aerial imagery.

BOEM/
├── boem_conf/                         # Hydra configuration
│   ├── boem_config.yaml               # Top-level defaults
│   ├── classification_model/
│   │   ├── finetune.yaml              # DeepForest classifier settings
│   │   ├── hierarchical.yaml          # H-CAST classifier settings
│   │   └── USGS.yaml                  # Legacy classification config
│   ├── server/
│   │   └── serenity.yaml              # Label Studio server creds
│   ├── Detection/                     # (reserved)
│   ├── Images/                        # (reserved)
│   └── with/                          # (reserved)
│
├── src/                               # Pipeline source
│   ├── active_learning.py             # Pool prediction, selection, human review
│   ├── classification.py              # DeepForest crop classification train/ft
│   ├── detection.py                   # DeepForest detection train/infer
│   ├── hierarchical.py                # H-CAST wrapper + inference adapter
│   ├── label_studio.py                # LS auth, SFTP upload, task import/export
│   ├── pipeline.py                    # Orchestrates detection + classification
│   ├── pipeline_evaluation.py         # Eval metrics and summaries
│   ├── data_ingestion.py              # Data loading utilities
│   ├── data_processing.py             # Crop writing and preprocessing
│   ├── visualization.py               # Crop visualization, video helpers
│   ├── sagemaker_gt.py                # Optional SageMaker Ground Truth pipeline
│   ├── propagate.py                   # Result propagation utilities
│   ├── cluster.py                     # Clustering helpers
│   └── utils.py                       # Shared helpers
│
├── tamu_hcast/                        # H-CAST module (third-party)
│   ├── cast_models/                   # CAST model definitions
│   ├── deit/                          # Training/eval scripts and datasets
│   ├── data/                          # Dataset metadata
│   └── README.md
│
├── tests/                             # Pytest suite
│   ├── test_active_learning.py
│   ├── test_classification.py
│   ├── test_data_ingestion.py
│   ├── test_data_processing.py
│   ├── test_detection.py
│   ├── test_pipeline.py
│   ├── test_pipeline_evaluation.py
│   ├── test_propagate.py
│   └── test_visualization.py
│
├── main.py                            # Entry point (Hydra)
├── pyproject.toml                     # uv project metadata and deps
├── environment.yml                    # Legacy conda env (deprecated)
├── README.md                          # This file
└── scripts, utilities, and notebooks (various)

• data_ingestion.py: Handles data loading and initial preparation
• data_processing.py: Implements data preprocessing and transformations
• model_training.py: Contains model training logic
• pipeline_evaluation.py: Evaluates pipeline performance and model metrics
• model_deployment.py: Manages model deployment
• monitoring.py: Provides monitoring and logging capabilities
• reporting.py: Generates reports for pipeline results
• annotation/: Contains annotation-related functionality
  • pipeline.py: Implements the annotation pipeline

Contains test files corresponding to each component in src/. Uses pytest for testing.

Contains YAML configuration files managed by Hydra:

• config.yaml: Main configuration file defining pipeline parameters

For non-interactive Globus uploads:

1. Register a "Confidential" application at Globus Developers Console
2. Add to your .env file:

GLOBUS_CLIENT_ID=your_client_id_here
GLOBUS_CLIENT_SECRET=your_client_secret_here
GLOBUS_SOURCE_COLLECTION_ID=your_source_collection_id
GLOBUS_DEST_COLLECTION_ID=your_dest_collection_id  # Optional, defaults to UMESC-UF Pipeline

1. Clone the repository:

git clone https://github.com/your-username/project-name.git
cd project-name

2. Install Python deps with uv (PyPI packages only):

uv venv -p 3.10
uv pip install -e .

3. Install PyTorch (CUDA 12.1) and torchvision from NVIDIA wheels:

uv pip install torch==2.1.2 torchvision==0.16.2 --index-url https://download.pytorch.org/whl/cu121

4. Install DGL matching your CUDA/PyTorch:

uv pip install dgl -f https://data.dgl.ai/wheels/torch-2.1/cu121/repo.html

Notes:

• If using CPU-only, install CPU wheels instead of cu121. See PyTorch and DGL docs.
• H-CAST requires timm==0.4.12 and OpenCV, already included in pyproject.toml.

Using the Serenity container:

./run_ml_workflow.sh your-branch-name

Or directly with Python:

python main.py

Hydra configs live under boem_conf/. The top-level defaults are in boem_conf/boem_config.yaml.

• Switch classification backend:
  • DeepForest (default):
    • classification_model.backend: deepforest
  • Hierarchical (H-CAST):
    • classification_model.backend: hierarchical
    • classification_model.checkpoint: /path/to/best_checkpoint.pth (optional; auto-discovers under tamu_hcast/)

Override at runtime:

python main.py classification_model=hierarchical

The pipeline can automatically upload images, import preannotations, and fetch completed annotations from Label Studio.

Prereqs:

• Get your Label Studio API key and save it to .label_studio.config at repo root in the format:

  api_key=YOUR_API_KEY
  

• Configure Label Studio in Hydra (boem_conf/boem_config.yaml):
  • label_studio.url: server URL (e.g., https://labelstudio.naturecast.org/)
  • label_studio.folder_name: remote folder path (server-side) where images are uploaded via SFTP
  • label_studio.instances.{train,validation,review}.project_name: Label Studio project titles to target
  • label_studio.instances.{train,validation,review}.csv_dir: where downloaded annotations CSVs are written
  • SFTP credentials (server group) for uploads: user, host, key_filename

Run:

python main.py

What happens:

• The pipeline connects to Label Studio using LABEL_STUDIO_API_KEY (set automatically from .label_studio.config).
• New predictions are uploaded via SFTP to folder_name/input, then imported as tasks with bounding box + taxonomy preannotations.
• Completed tasks are downloaded to per-flight CSVs under the configured csv_dir folders, then removed from Label Studio to avoid duplication.
• Images marked as completed are archived server-side.

Manual overrides:

• To disable checking Label Studio, set check_annotations: false in boem_conf/boem_config.yaml.

pytest tests/

The pipeline uses Hydra for configuration management. Main configuration options are defined in conf/config.yaml.

Example configuration:

data:
  input_dir: "path/to/input"
  output_dir: "path/to/output"

model:
  type: "classification"
  parameters:
    learning_rate: 0.001
    batch_size: 32

pipeline:
  steps:
    - data_ingestion
    - data_processing
    - model_training
    - evaluation

Please read CONTRIBUTING.md for details on our code of conduct and the process for submitting pull requests.

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

Key dependencies include:

• Hydra
• PyTorch
• NumPy
• Pandas
• Pytest

See requirements.txt for a complete list.

• Each component is a separate module in the src/ directory
• Tests mirror the source code structure in the tests/ directory
• Configuration is managed through Hydra
• Monitoring and logging are integrated throughout the pipeline using comet

• Tests are written using pytest
• Each component has its own test file
• Run tests with pytest tests/

1. Create a new module in src/
2. Add corresponding test file in tests/
3. Update configuration in conf/config.yaml
4. Update main.py to integrate the new component
5. Create a branch and push your changes to the remote repository
6. Create a pull request to merge your changes into the main branch