VVVVVVVV           VVVVVVVV IIIIIIIIII DDDDDDDDDDDDD        EEEEEEEEEEEEEEEEEEEEEE            
            V::::::V           V::::::V I::::::::I D::::::::::::DDD     E::::::::::::::::::::E            
            V::::::V           V::::::V I::::::::I D:::::::::::::::DD   E::::::::::::::::::::E            
            V::::::V           V::::::V II::::::II DDD:::::DDDDD:::::D  EE::::::EEEEEEEEE::::E            
             V:::::V           V:::::V    I::::I     D:::::D    D:::::D   E:::::E       EEEEEE            
              V:::::V         V:::::V     I::::I     D:::::D     D:::::D  E:::::E                         
               V:::::V       V:::::V      I::::I     D:::::D     D:::::D  E::::::EEEEEEEEEE               
                V:::::V     V:::::V       I::::I     D:::::D     D:::::D  E:::::::::::::::E               
                 V:::::V   V:::::V        I::::I     D:::::D     D:::::D  E:::::::::::::::E               
                  V:::::V V:::::V         I::::I     D:::::D     D:::::D  E::::::EEEEEEEEEE               
                   V:::::V:::::V          I::::I     D:::::D     D:::::D  E:::::E                         
                    V:::::::::V           I::::I     D:::::D    D:::::D   E:::::E       EEEEEE            
                     V:::::::V          II::::::II DDD:::::DDDDD:::::D  EE::::::EEEEEEEE:::::E            
                      V:::::V           I::::::::I D:::::::::::::::DD   E::::::::::::::::::::E            
                       V:::V            I::::::::I D::::::::::::DDD     E::::::::::::::::::::E            
                        VVV             IIIIIIIIII DDDDDDDDDDDDD        EEEEEEEEEEEEEEEEEEEEEE            

VIDE, the Void IDentification and Examination toolkit is a widely used void finder. It has been used on both spectroscopic and photometric data, on simulations and mocks. VIDE is the French word for void, as historically the software was first developed by a group of researchers working at the Institut d'Astrophysique de Paris (IAP, Paris, France). The following page lists all papers based on VIDE: Papers using VIDE.

Citing VIDE

Please cite the following papers if you use the VIDE software for your work: arXiv:1406.1191 and arXiv:0712.3049, using the following suggested sentence:

This work uses voids identified with VIDE\footnote{\url{http://www.cosmicvoids.net}} (Sutter et al. 2014), which implements an enhanced version of ZOBOV (Neyrinck 2008) to construct voids with a watershed algorithm.

Note that if you use one of the public void catalogs, the catalog README will instruct you to reference the appropriate paper(s).

License/Copyright information

Copyright (C) 2010-2021 Guilhem Lavaux, 2011-2014 P.M. Sutter. This software is put under the GNU Public License. Please see LICENSE for further information.

Requirements

The package swig needs to be installed and available in the PATH (http://www.swig.org/). It is required by scipy and we have not decided to bundle it with VIDE at the moment.

Installation

Please note that this wiki and instructions refer to the latest python 3 version of VIDE. The python 2.7 version of VIDE is deprecated, but if needed, old instructions can be found here: Deprecated python 2.7 VIDE instructions.

It is generally advised to create a python3 virtual environment. This can be achieved as follows

python3 -m venv --system-site-packages $PLACE_OF_VENV
source $PLACE_OF_VENV/bin/activate

Note: on OSX there are some difficulties to use the native clang compiler. Please use a brew installed compiler like GCC.

brew install gcc
export CC=/usr/local/bin/gcc-10
export CXX=/usr/local/bin/g++-10

After this step you may start the build process

python3 setup.py build

It will take a lot of time. It may also download python packages that you miss on your system. On BigSur some of them fail to compile by default.

After installing the package with

python3 setup.py install

To test that the package is indeed installed you can execute

python3 -m void_pipeline

Usage: ./generateCatalog.py parameter_file.py

The VIDE tools are all packaged in the vide package, you can therefore

import vide

Notes for CONDA installation

VIDE can be installed using CONDA. If you use a conda installation, you have to be sure to use all the building tools that are consistent. On linux that means for example installing the conda packages gcc_linux-64 and gxx_linux-64. In addition to that it is recommended to define the environment variable LIBRARY_PATH=the_path_of_your_conda_environment_with_/lib. For example if your environment is in '/home/user/conda' you should define

export LIBRARY_PATH=/home/user/conda/lib

conda create --name VIDEenv --channel conda-forge python=3.7 scipy pandas matplotlib PySide2 cmake=3.17.0

You can then initiate the construction with

python3 setup.py build

Detailed Guide (Currently being updated)

Data Preparation & Running

Void Catalogs & Analysis

Version Summary

v1.0 - Initial Release v2.0 - Ported to python3, revisited build system

Credits

Originally developed by Guilhem Lavaux and P.M. Sutter, with contributions from Ben Wandelt, Nico Hamaus, Alice Pisani, Paul Zivick, and Qingqing Mao.

Main current maintainer: Guilhem Lavaux.

Based on ZOBOV developed by Mark Neyrinck. HOD code developed by Jeremy Tinker. SDF library developed by Mike Warren and John Salmon. fit_hod code provided by Francisco Villaescusa-Navarro. RAMSES module provided by Benjamin B. Thompson.

User guide originally written by P.M. Sutter and Alice Pisani, updated by Alice Pisani & Guilhem Lavaux.

Contributing to VIDE

We welcome comments, suggestions, and most importantly bug fixes. Write permissions will be granted on a case-by-case basis, although the pull request functionality is heavily encouraged. If you want to make a major contribution or addition, we suggest that you author a journal paper featuring the addition in an application. We will then request that users of the added functionality cite that paper in addition to the main VIDE paper.

Have fun!