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FROM nvidia/cuda:12.2.2-cudnn8-devel-ubuntu22.04 | |
ENV DEBIAN_FRONTEND=noninteractive \ | |
TZ=America/Los_Angeles | |
USER root | |
RUN apt-get update && apt-get install -y \ | |
git \ | |
make build-essential libssl-dev zlib1g-dev \ | |
libbz2-dev libreadline-dev libsqlite3-dev wget curl llvm \ | |
libncursesw5-dev xz-utils tk-dev libxml2-dev libxmlsec1-dev libffi-dev liblzma-dev git-lfs \ | |
cmake-curses-gui cmake libinsighttoolkit4-dev libfftw3-dev libvtk7-dev \ | |
ffmpeg libsm6 libxext6 cmake libgl1-mesa-glx lsof \ | |
orthanc orthanc-dicomweb vim \ | |
nginx \ | |
&& rm -rf /var/lib/apt/lists/* \ | |
&& git lfs install | |
# install plastimatch | |
RUN git clone https://gitlab.com/plastimatch/plastimatch && cd plastimatch && mkdir build && cd build && cmake .. && make -j$(nproc) && make install | |
WORKDIR /code | |
COPY ./requirements.txt /code/requirements.txt | |
# User | |
RUN useradd -m -u 1000 user | |
ENV HOME=/home/user \ | |
PATH=/home/user/.local/bin:$PATH | |
USER user | |
# Pyenv | |
RUN curl https://pyenv.run | bash | |
ENV PATH=$HOME/.pyenv/shims:$HOME/.pyenv/bin:$PATH | |
ARG PYTHON_VERSION=3.10.13 | |
# Python | |
RUN pyenv install $PYTHON_VERSION && \ | |
pyenv global $PYTHON_VERSION && \ | |
pyenv rehash && \ | |
pip install --no-cache-dir --upgrade pip setuptools wheel && \ | |
pip install --no-cache-dir \ | |
datasets \ | |
huggingface-hub "protobuf<4" "click<8.1" | |
RUN pip install --no-cache-dir --upgrade -r /code/requirements.txt | |
# Set the working directory to /data if USE_PERSISTENT_DATA is set, otherwise set to $HOME/app | |
WORKDIR $HOME/app | |
ENV HOME=/home/user \ | |
PATH=/home/user/.local/bin:$PATH \ | |
PYTHONPATH=$HOME/app \ | |
PYTHONUNBUFFERED=1 | |
RUN monailabel apps --name radiology --download --output apps | |
RUN monailabel datasets --download --name Task09_Spleen --output datasets | |
# RUN monailabel datasets --download --name Task01_BrainTumour --output datasets | |
# RUN monailabel datasets --download --name Task09_Spleen --output . | |
# RUN plastimatch convert --patient-id patient1 --input Task09_Spleen/imagesTs/spleen_1.nii.gz --output-dicom dicom_output | |
# monailabel start_server --app apps/radiology --studies http://127.0.0.1:8042/dicom-web --conf models deepedit | |
# CMD ["monailabel", "start_server", "--app", "apps/radiology", "--studies", "http://0.0.0.0:8042/dicom-web", "--conf" , "models", "deepedit"] | |
# CMD ["monailabel", "start_server", "--app", "apps/radiology", "--studies", "datasets/Task01_BrainTumour/imagesTr", "--conf" , "models", "deepedit"] | |
# /etc/orthanc/orthanc.json -> "RemoteAccessAllowed": false, -> "RemoteAccessAllowed": true, | |
# RUN sed -i 's/"RemoteAccessAllowed" : false,/"RemoteAccessAllowed" : true,/g' /etc/orthanc/orthanc.json | |
USER root | |
RUN mkdir -p /var/cache/orthanc /var/log/orthanc /var/lib/orthanc && \ | |
chown -R user:user /var/cache/orthanc /var/log/orthanc /usr/share/orthanc/ /var/lib/orthanc /etc/orthanc && \ | |
mkdir -p /var/cache/nginx /var/log/nginx /var/lib/nginx && \ | |
touch /var/run/nginx.pid && \ | |
chown -R user:user /var/cache/nginx /var/log/nginx /var/lib/nginx /var/run/nginx.pid | |
COPY --chown=user orthanc.json /etc/orthanc/orthanc.json | |
COPY --chown=user nginx.conf /etc/nginx/sites-available/default | |
USER user | |
COPY --chown=user run.sh . | |
CMD ["sh", "run.sh"] | |
# monailabel start_server --app apps/radiology --studies datasets/Task01_BrainTumour/imagesTr --conf models deepedit |