Dockerfile_BrainMaskTool

FROM ubuntu:22.04
LABEL authors="iejohnson"

# Set environment variables
ENV LANG C.UTF-8
ENV LC_ALL C.UTF-8
ENV PATH /opt/venv/bin:$PATH

# Disable Prompt During Packages Installation
ARG DEBIAN_FRONTEND=noninteractive

LABEL maintainer="iejohnson"
LABEL version="0.1"
LABEL description="This is the Dockerfile for the brainmask_tool"
LABEL toolname="brainmask_tool"
LABEL toolversion="0.1"
LABEL tooltype="medical"
LABEL input="Directory containing dicom files for a single study"
LABEL output="Directory with brain masks and PDF report as well as dicom Encapsulated PDFs"


RUN apt update

# Install necessary libraries
RUN apt-get install -y \
    python3.10 \
    python3-pip \
    python3.10-venv \
    libpango-1.0-0 \
    libharfbuzz0b \
    libpangoft2-1.0-0

RUN rm -rf /var/lib/apt/lists/* && \
    apt clean

# Create needed directories
RUN mkdir /app
RUN mkdir /input
RUN mkdir /output

# Set the working directory
WORKDIR /app


# Upgrade pip
RUN python3.10 -m pip install --upgrade pip

# Create a virtual environment and activate it
RUN python3.10 -m pip install --user virtualenv
RUN python3.10 -m venv /opt/venv
RUN . /opt/venv/bin/activate

# Copy requirements file
COPY requirements_medical_tool.txt .

# Install Python dependencies
RUN pip install -r requirements_medical_tool.txt

# Copy the rest of the code
COPY example_tool/brainmask_tool.py /app/brainmask_tool.py
COPY example_tool/cnn_transforms.py /app/cnn_transforms.py
COPY example_tool/pipeline_functions.py /app/pipeline_functions.py
COPY example_tool/pdf_report.py /app/pdf_report.py
COPY example_tool/brainmask_model.ckpt /app/brainmask_model.ckpt

# TODO Check the code below. Im not sure if this is what we actually want
# The desired functionality is to have a mounted directory for input and output files
# I want to be able to run the container with the input and output directories as arguments
# Then I want to be able to trigger the tool to run with an extra parameter that is the study_id
# The tool should then read the input files, process them and write the output files to the output directory
# Add an environment variable for the input directory

ENV PYTHONPATH $PYTHONPATH:/app

ENTRYPOINT ["python", "brainmask_tool.py"]