MT-PGA

This github repository contains the exact code used for the reference below.

Reference

If you plan to use this code to generate results for a scientific document, thanks for referencing the following publication:

"Principal Geodesic Analysis of Merge Trees (and Persistence Diagrams)"
Mathieu Pont, Jules Vidal, Julien Tierny
IEEE Transactions on Visualization and Computer Graphics, 2022.

Paper

Installation Note

Tested on Ubuntu 20.04.5 LTS.

Install the dependencies

sudo apt-get install cmake-qt-gui libboost-system-dev libpython3.8-dev libxt-dev libxcursor-dev libopengl-dev
sudo apt-get install qt5-default qttools5-dev libqt5x11extras5-dev libqt5svg5-dev qtxmlpatterns5-dev-tools 
sudo apt-get install python3-sklearn 
sudo apt-get install libsqlite3-dev 
sudo apt-get install gawk

Install cmake 3.21 (Optional)

To install TTK (one of the next step), you will need cmake 3.21 or higher. If your OS does not allow to install automatically the latest version of cmake (like Ubuntu 20) you can install it with the following commands:
(while being in the parent directory of where this repository (MT-PGA) is)
(replace the 4 in make -j4 by the number of available cores on your system)
(if you do not want to install libssl-dev you can add -DCMAKE_USE_OPENSSL=OFF at the end of the command configure)

sudo apt-get install libssl-dev 
wget http://www.cmake.org/files/v3.21/cmake-3.21.6.tar.gz
tar xf cmake-3.21.6.tar.gz
cd cmake-3.21.6
./configure --prefix="./install/"
make -j4
make -j4 install

In all the following steps, please replace the command cmake by the binary PATHTO/cmake-3.21.6/install/bin/cmake (replace PATHTO by the absolute path to the cmake-3.21.6 folder). For example, while being in the cmake-3.21.6 folder, you can do:

cmake=`pwd`/install/bin/cmake

And replace cmake by $cmake in the following commands.

Install Paraview

First, go in the parent directory of where this repository (MT-PGA) is and run the following commands:
(replace the 4 in make -j4 by the number of available cores on your system)

git clone https://github.com/topology-tool-kit/ttk-paraview.git
cd ttk-paraview
git checkout 5.10.0
mkdir build && cd build
cmake -DCMAKE_BUILD_TYPE=Release -DPARAVIEW_USE_PYTHON=ON -DPARAVIEW_INSTALL_DEVELOPMENT_FILES=ON -DCMAKE_INSTALL_PREFIX=../install ..
make -j4
make -j4 install

Some warnings are expected when using the make command, they should not cause any problems.

Install TTK

Go in the ttk-dev2 directory then run the following commands:
(replace the 4 in make -j4 by the number of available cores on your system)

mkdir build && cd build
paraviewPath=`pwd`/../../../ttk-paraview/install/lib/cmake/paraview-5.9
cmake -DCMAKE_INSTALL_PREFIX=../install -DParaView_DIR=$paraviewPath ..
make -j4
make -j4 install

Stay in the build directory and set the environment variables: (replace 3.8 in python3.8 by your version of python)

TTK_PREFIX=`pwd`/../install
export PV_PLUGIN_PATH=$TTK_PREFIX/bin/plugins/TopologyToolKit
export LD_LIBRARY_PATH=$TTK_PREFIX/lib:$LD_LIBRARY_PATH
export PYTHONPATH=$TTK_PREFIX/lib/python3.8/site-packages

Get the results

Go in the root directory of this repository and extract the data:

tar xvJf data.tar.xz

table 1

To reproduce the results of the time table in the paper, please go in the scripts directory and enter the following commands:

for f in *.sh; do chmod u+x $f; done

Run the experiments (it will take a LONG time) and print table:
(replace N with the number of available cores on your system)
To decrease computation time you can set the optionnal parameter ptMult to a value greater than 1. It will have the effect to multiply the persistence thresholds by ptMult and hence decreasing the computation time (for example, replace [ptMult] by 7, default value is 1). However, the computation time will not decrease the same way for each dataset since the number of pairs removed si not linearly correlated with the persistence threshold. Moreover, when increasing the persistence threshold, the speedup will be lower.

./automata2.sh N [ptMult]
./timeTable.sh