Dockerfile

FROM nvidia/cuda:12.2.2-cudnn8-devel-ubuntu22.04 as base

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

# build ohifv3 viewer
FROM node:18.16.1-slim as builder
RUN apt-get update && apt-get install -y build-essential yarn git && rm -rf /var/lib/apt/lists/*
WORKDIR /code
RUN git clone https://github.com/Project-MONAI/MONAILabel.git .
WORKDIR /code/plugins/ohifv3
COPY build-ohfiv3.sh monai_label.js /code/plugins/ohifv3/
RUN ./build-ohfiv3.sh 

# 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
FROM base as final

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
COPY --from=builder --chown=user /code/plugins/ohifv3/Viewers/platform/app/dist/ /usr/share/nginx/html

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