W2-PD-Dict

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:

"Wasserstein Dictionaries of Persistence Diagrams"
Keanu Sisouk, Julie Delon, Julien Tierny
IEEE Transactions on Visualization and Computer Graphics, 2023.

Paper

The instructions below explain how to install the software and how to reproduce the Table 1 (fifth column) of the reference above.

Installation Note

Tested on Ubuntu 22.04.2 LTS.

Install the dependencies

sudo apt-get install cmake-qt-gui libboost-system-dev libpython3.10-dev libxt-dev libxcursor-dev libopengl-dev libgl1-mesa-dev
sudo apt install qtbase5-dev qtchooser qt5-qmake qtbase5-dev-tools qttools5-dev
sudo apt-get install libqt5x11extras5-dev libqt5svg5-dev qtxmlpatterns5-dev-tools
sudo apt install python3-sklearn
sudo apt install libsqlite3-dev
sudo apt install libeigen3-dev
sudo apt install gawk
sudo apt install git

Install Paraview

First, go in the root of this repository and run the following commands: (replace the 5 in make -j 5 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 -j 5
make install -j 5

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

Stay in the build directory and set the environment variables: (replace 3.10 in python3.10 by your version of python)

PV_PREFIX=`pwd`/../install
export PATH=$PATH:$PV_PREFIX/bin
export LD_LIBRARY_PATH=$PV_PREFIX/lib:$LD_LIBRARY_PATH
export PYTHONPATH=$PV_PREFIX/lib/python3.10/site-packages

Install TTK

Go in the ttk-newMethodCompression directory then run the following commands: (replace the 5 in make -j 5 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 -DEigen3_DIR=/usr/share/eigen3/cmake -DParaView_DIR=$paraviewPath ..
make -j 5
make install -j 5

Stay in the build directory and set the environment variables: (replace 3.10 in python3.10 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:$LD_LIBRARY_PATH
export PYTHONPATH=$PYTHONPATH:$TTK_PREFIX/lib/python3.10/site-packages

Get the result

The python files provided generate the running time results reported in Table 1 of the reference above.
Go in the root directory and then go in the dataAndScripts directory:

Table 1

There are two options, first to reproduce the fifth line of the fifth column you can run the following line:

python3 pythonScriptTestOneLine.py

To reproduce the whole fifth column you can run:

python3 pythonScriptParsingTest.py

Note that it can take some time to get the whole column (e.g ~30 minutes overall on 20 threads). Both of those scripts will ask you the number of threads allocated for the experiments when the following sentence appears Please chose the number of threads: type it and press enter. Some warnings and "errors" from Paraview are expected, they do not cause any problems. A time table will appear at the end in the terminal. The outputs of the experiments (the dictionaries and the weights) can be found in the generated Outputs directory in a vtm format for the former and in a csv format for the latter.