Setting up

This repository holds the code for

Requirements

You need to have a working MATLAB installation.

dotenv

This repository uses a .env file, in which variables specific to the machine are stored. Add a .env file in the root directory of the project (i.e. the same directory in which the README is located), and define the following variables:

PROJECT_DIR=/path/to/this/directory/
DATA_DIR=/path/to/this/directory/data/ # in which data is stored
SRC_DIR=/path/to/src/directory # path to which you want to install additional packages (mine is /home/paul/src)

then install matlab-dotenv by running the following in a MATLAB shell:

eval(webread('https://raw.githubusercontent.com/roslovets/matlab-dotenv/main/installer/installweb.m'))

This now allows you to access any variables defined in .env as follows:

dotenv.read().SRC_DIR

fastdmf

This repository uses the fastdmf package. To install, run (starting from this directory):

source .env
cd $SRC_DIR
git clone https://gitlab.com/concog/fastdmf

And to install the dmf package:

cd fastdmf/matlab
mex COPTIMFLAGS="-O3" DMF.cpp

Then make sure to add this directory to your path in MATLAB:

addpath(fullfile(dotenv.read().SRC_DIR, 'fastdmf', 'matlab'))
savepath()

Statistics and Machine Learning Toolbox

To add Statistics and Machine Learning Toolbox to your MATLAB installation, open the add-on explorer and search for Statistics and Machine Learning Toolbox, click on the right search result, and click on Install (or Sign in to install if not already signed in).