| FROM estenhl/pyment-preprocessing:1.0.0 | |
| RUN mkdir -p /repos/pyment | |
| COPY scripts /repos/pyment/scripts | |
| COPY pyment /repos/pyment/pyment | |
| COPY pyproject.toml /repos/pyment/ | |
| COPY README.md /repos/pyment/ | |
| COPY LICENSE.md /repos/pyment/ | |
| RUN python -m venv /envs/pyment | |
| RUN /envs/pyment/bin/pip install --upgrade pip poetry-core build && \ | |
| cd /repos/pyment && \ | |
| /envs/pyment/bin/pip install --no-cache-dir . | |
| RUN mkdir -p /.pyment/weights && \ | |
| chmod -R 1777 /.pyment | |
| COPY checkpoints/pyment /.pyment/weights | |
| CMD ["/bin/sh", "-c", "\ | |
| mkdir -p /output/fastsurfer && \ | |
| /scripts/preprocess.sh \ | |
| --license /licenses/freesurfer.txt \ | |
| --python /envs/fastsurfer/bin/python \ | |
| /input /output/fastsurfer && \ | |
| /envs/pyment/bin/python /repos/pyment/scripts/predict_from_fastsurfer_folder.py \ | |
| /output/fastsurfer \ | |
| -d /output/predictions.csv \ | |
| "] | |