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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 \
"]
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