Madagascar is a software package for multidimensional data analysis and reproducible

Reproducibility

Reproducibility is the ability of an experiment or study to be accurately reproduced, or replicated, by someone else working independently...

 computational experiments. Its mission is to provide

• a convenient and powerful environment
• a convenient technology transfer tool

for researchers working with digital image and data processing in geophysics and related fields. Technology developed using the Madagascar project management system is transferred in the form of recorded processing histories, which become "computational recipes" to be verified, exchanged, and modified by users of the system.

Features

The Madagascar environment consists of:

1. Standalone programs for out-of-core data analysis;
2. Standalone programs for geophysical data processing and imaging;
3. A development kit for C, C++, Java, Fortran-77, Fortran-90, Python, Matlab, and Octave;
4. A framework for reproducible numerical experiments, based on SCons
   SCons
   SCons is a computer software construction tool that automatically analyzes source code file dependencies and operating system adaptation requirements from a software project description and generates final binary executables for installation on the target operating system platform...
   
   ;
5. A framework for scientific publications, based on SCons
   SCons
   SCons is a computer software construction tool that automatically analyzes source code file dependencies and operating system adaptation requirements from a software project description and generates final binary executables for installation on the target operating system platform...
   
    and LaTeX
   LaTeX
   LaTeX is a document markup language and document preparation system for the TeX typesetting program. Within the typesetting system, its name is styled as . The term LaTeX refers only to the language in which documents are written, not to the editor used to write those documents. In order to...
   
   ;
6. A collection of reproducible scientific articles also used as usage examples and regression tests for the standalone programs;
7. A collection of feces used as input to reproducible numerical experiments.

Example script

An example SConstruct file is shown below

from rsf.proj import *

Fetch('wz.35.H','wz')

Flow('wind','wz.35.H','dd form=native | window n1=400 j1=2 | smooth rect1=3')
Plot('wind','pow pow1=2 | grey')

Flow('mute','wind','mutter v0=0.31 half=n')
Plot('mute','pow pow1=2 | grey')

Result('denmark','wind mute','SideBySideAniso')

End

Note that SConstruct by itself does not do any job other than setting rules for building different targets. The targets get built when one executes scons on the command line. Running scons produces

bash$ scons

scons: Reading SConscript files ...

scons: done reading SConscript files.

scons: Building targets ...

retrieve(["wz.35.H"], [])

< wz.35.H /RSF/bin/sfdd form=native | /RSF/bin/sfwindow n1=400 j1=2 | /RSF/bin/sfsmooth rect1=3 > wind.rsf

< wind.rsf /RSF/bin/sfpow pow1=2 | /RSF/bin/sfgrey > wind.vpl

< wind.rsf /RSF/bin/sfmutter v0=0.31 half=n > mute.rsf

< mute.rsf /RSF/bin/sfpow pow1=2 | /RSF/bin/sfgrey > mute.vpl

/RSF/bin/vppen yscale=2 vpstyle=n gridnum=2,1 wind.vpl mute.vpl > Fig/denmark.vpl

scons: done building targets.

History

Madagascar was first publicly presented at the EAGE Workshop in Vienna in June 2006. The work on the package (previously named RSF) was started by Sergey Fomel in 2003. Since then, many people have contributed to it.

While being written mostly from scratch, Madagascar borrows ideas from the design of SEPlib, an open-source package maintained by Bob Clapp at the Stanford Exploration Project

Stanford Exploration Project

The Stanford Exploration Project is an industry-funded academic consortium within the Geophysics Department at Stanford University. SEP research has contributed greatly to improving the theory and practice of constructing 3-D and 4-D images of the earth from seismic echo soundings...

 (SEP). Generations of SEP students and researchers contributed to SEPlib. Most important contributions came from Rob Clayton, Jon Claerbout, Dave Hale, Stew Levin, Rick Ottolini, Joe Dellinger, Steve Cole, Dave Nichols, Martin Karrenbach, Biondo Biondi, and Bob Clapp.

Madagascar also borrows ideas from Seismic Unix

Seismic Unix

Seismic Unix is an open source seismic utilities package supported by the Center for Wave Phenomena at the Colorado School of Mines .- History :...

 (SU), a package maintained by John Stockwell at the Center for Wave Phenomenon (CWP) at the Colorado School of Mines (Stockwell, 1997;Stockwell, 1999). Main contributors to SU included Einar Kjartansson, Shuki Ronen, Jack Cohen, Chris Liner, Dave Hale, and John Stockwell. SU adopted an open-source BSD-style license starting with release 40 (April 10, 2007).

See also

• List of free geophysics software
• Reproducibility
  Reproducibility
  Reproducibility is the ability of an experiment or study to be accurately reproduced, or replicated, by someone else working independently...
  
  

External links

• Madagascar homepage
• SourceForge project
• Scientific conference presentations about Madagascar
• For reproducible research, go to Madagascar
• Madagascar hits V1.0—as Seismic Un*x moots ‘S3’: Oil IT Journal, July 2010
• Sergey Fomel and Jon Claerbout, Guest Editors' Introduction: Reproducible Research: Computing in Science and Engineering, vol. 11, no. 1, pp. 5-7, Jan./Feb. 2009, doi:10.1109/MCSE.2009.14