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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
$PLACE_OF_VENV
is where you decide to put your environment on your
harddrive (e.g. $HOME/my_venv
).
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)
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!
Updated