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