FROM projectmonai/monai:latest

RUN pip install --no-cache-dir scikit-image

WORKDIR /app

# Bundle configs and scripts
COPY bundle/ct_binary_coronary_segmentation/configs/ ct_binary_coronary_segmentation/configs/
COPY bundle/ct_binary_coronary_segmentation/scripts/ ct_binary_coronary_segmentation/scripts/
COPY bundle/ct_segmental_coronary_segmentation/configs/ ct_segmental_coronary_segmentation/configs/
COPY bundle/ct_segmental_coronary_segmentation/scripts/ ct_segmental_coronary_segmentation/scripts/

# Model weights
COPY bundle/ct_binary_coronary_segmentation/models/ ct_binary_coronary_segmentation/models/
COPY bundle/ct_segmental_coronary_segmentation/models/ ct_segmental_coronary_segmentation/models/

# Pipeline script
COPY scripts/run_pipeline.py scripts/run_pipeline.py

ENTRYPOINT ["python", "scripts/run_pipeline.py"]
CMD ["--input", "/input", "--output", "/output"]