Informations

This model is developed within the framework of the InExES project: "Coupling Internal and External Eye Simulation" (https://inexes.unige.ch/) which is financially supported by the Velux Stiftung in Zürich, Switzerland (https://veluxstiftung.ch/). The model is being written during a PhD project (of which the author is the candidate) at the University of Geneva (Switzerland) and it is still under development.

How to install InExES

WIP we recommend to wait the release version before cloning it

We suppose that InExES can work on every machine, but we only tried on a Mac, Linux Ubuntu 16.04 and Linux Mint 19.3

Prerequisite

Python 3.5 or newer

Install instructions

git clone https://github.com/mm-89/InExEs.git
pip3 install matplotlib
pip3 install trimesh
pip3 install Rtree
pip3 install shapely

Librairies problems

You may face some problems reguarding libraries installation. Where is some solutions.

• Cannot install Rtree on mac or Linux :

  • Mac : pip install "rtree>=0.8,<0.9"
  • Linux : sudo apt install python3-rtree or pip install Rtree

• Missing C lib on mac (just after the Rtree problem) :

  • brew install spatialindex

• Any missing librairies like scipy,shapely,networkx,piglet

  • pip3 install "librairie_name"

• No module name '_tkinter' :

  • sudo apt install python3-tk

Start the simulation

• python3 main.py

Docker user guide :

• First of all make sure to have docker setup on your computer

• Go on project folder

• BUILD : docker build -t python:simulation .

• RUN : docker run --name CONTAINER_NAME -ti python:simulation

• Copy the beta file from the container : sudo docker cp CONTAINER_NAME:/app/input/beta_"MESH_NAME"_"N_VALUE".txt DESTINATION_PATH

• Warnings about the beta file copy :

  • Be sure to know which N value and mesh name you're using. Exemple of complete beta file name : beta_head_2.txt
  • Destination path must be the complete path !

Speed up simulation process with conda :

• Install anaconda
• Create an conda environment : conda create --name ENV_NAME
• Active the conda environment : conda activate ENV_NAME
• Install pyembree and trimesh with conda : conda install -c conda-forge pyembree and conda install -c conda-forge trimesh
• Then you may need to install some others librairies, like matplotlib networkx pyglet scipy vtkplotter : pip install LIBRAIRY_NAME
• Launch the programm with : python3 main.py (make sure your conda env is activate)