Docker (#48)

* Added CMAKE BUILD TYPE flag for potential speed up as per CGAL compile message

* Added docker build instructions

* Updated reference to dockerhub image

.dockerignore

@@ -0,0 +1,5 @@
+build/
+output/
+examples/
+MATLAB/
+test/

Dockerfile

@@ -0,0 +1,45 @@
+FROM ubuntu:bionic
+
+# Mount volumes - these are in root to make it easier to type 
+# and to avoid confusion between those included in the Mesher directory
+
+VOLUME /output
+VOLUME /input
+
+RUN apt-get update \
+    && apt-get install -y \
+    build-essential \
+    cmake \
+    libcgal-dev \
+    libcgal-qt5-dev \
+    libglu1-mesa \
+    libglu1-mesa-dev \
+    libxi-dev \
+    libxmu-dev 
+
+# Copy repo and make dirs
+COPY . /Mesher
+
+WORKDIR /Mesher
+RUN mkdir build && mkdir output
+
+# remove test from cmake list 
+RUN sed -i 's/^\(add_subdirectory(test).*\)/#\1/g' CMakeLists.txt
+
+WORKDIR /Mesher/build
+RUN cmake .. && make
+WORKDIR /Mesher
+
+#RUN echo "BUILD DONE. CHECKING MESHER RUNS"
+#RUN ./bin/mesher -i inputs/input.inr -e inputs/Electrodes.txt -p inputs/params.txt
+
+RUN apt-get clean \
+    && rm -rf /var/lib/apt/lists/* /tmp/* /var/tmp/*
+
+ENTRYPOINT [ "./bin/mesher" ]
+# default run with example inputs inside the container to demonstrate its working
+CMD ["-i", "inputs/input.inr", "-e", "inputs/Electrodes.txt", "-p", "inputs/params.txt"]
+
+# To run the Mesher, you need to mount the volumes and then direct the mesher to look into the correct directories e.g.:
+# docker run --rm -v ~/Mesher/inputs2:/input -v ~/Mesher/output2:/output  mesher -i /input/input.inr -e /input/Electrodes.txt -p /input/params.txt -d /output/ -o testing
+

README.md

@@ -16,7 +16,6 @@ EIT-MESHER is C++ software, based on the CGAL library, which generates high qual
 
 Examples for using the EIT-MESHER outputs with common EIT and DOT solvers are given in [solvers examples](examples/solvers)
 
-
 ## Build instructions (tested on Ubuntu 16, 17, 18)
 
 * Install dependencies
@@ -71,6 +70,57 @@ Example:
 ```bash
 ./bin/mesher -i inputs/input.inr -e inputs/Electrodes.txt -p inputs/params.txt
 ```
+
 Produces the following mesh as viewed in paraview
 
 ![Brain Example](examples/brain/figures/brain_PV.png)
+
+## Docker instructions (for Ubuntu 19&20+)
+
+EIT-MESHER can be built in a container to install on newer linux installations. Windows users require WSL2 for docker to work.
+
+### Install container
+
+The docker container can be obtained using two different methods:
+
+* Build container from source (`mesher` is a name of your choice):
+
+```bash
+docker build -t mesher .
+```
+
+* Pull image directly from dockerhub without having to build
+
+```bash
+docker pull doctorjimbles/eit-mesher
+```
+
+### Running Mesher from container
+
+To test it is working run the container with no inputs, this will call the mesher with defaults which runs the single example included in the container:
+
+```bash
+docker run --rm mesher
+```
+
+The `--rm` flag removes the container after its done to prevent having lots of unnecessary container IDs.
+
+The mesher can then be called with the parameter arguments as normal **Note** these are files *inside* the container.
+
+```bash
+docker run --rm mesher -i inputs/input.inr -e inputs/Electrodes.txt -p inputs/params.txt
+```
+
+* Using your own data - mounting volumes
+
+The container has two volumes `/input` and `/output` which can be mounted to a directory on the host using the `-v` flag. So for example with the `MESHER` repository on the home dir:
+
+```bash
+docker run --rm -v ~/Mesher/inputs:/input -v ~/Mesher/output:/output  mesher
+```
+
+The mesher can then finally be called by combining the volume definitions and the parameters. **Note** The directories must be with respect to the container file structure
+
+```bash
+docker run --rm  -v ~/Mesher/inputs:/input -v ~/Mesher/output:/output  mesher -i /input/input.inr -e /input/Electrodes.txt -p /input/params.txt -d /output/ -o dockertest
+```