Package overview

2013-02-19T12:51:43Z

NanetteWashington1968: /* How to obtain Madagascar */

[[Image:Fotolia_5127720_XS.jpg|right|]]

The mission of the Madagascar project is to provide a '''shared research environment''' for computational data analysis in geophysics and related fields.

The Madagascar environment consists of:
# Standalone programs for out-of-core data analysis;
# Standalone programs for geophysical data processing and imaging;
# A development kit for C, C++, Java, Fortran-77, Fortran-90, Python, Matlab, and Octave;
# A framework for reproducible numerical experiments, based on [http://www.scons.org/ SCons];
# A framework for scientific publications, based on [http://www.scons.org/ SCons] and [http://en.wikipedia.org/wiki/LaTeX LaTeX];
# A collection of reproducible scientific articles also used as usage examples and regression tests for the standalone programs;
# A collection of datasets used as input to reproducible numerical experiments.

This guide serves as a brief introduction of different components and shows how they all fit together.

==How to obtain Madagascar==

See [[Download|download]] and [[Installation | installation instructions]]. Madagascar runs on Unix/Linux platforms, including MacOS X and Unix emulations under Miscrosoft Windows. It is such a perfect internet site! Nonetheless, is it real to find some term papers writing helper here? I am willing to buy [http://exclusivepapers.com college research paper]! Please give me your suggestions! Its installation requires, at a minimum, a working C compiler and Python.

==How to find your way around Madagascar==

Start by checking the [[Reproducible_Documents|list of reproducible papers]]. If any of these papers looks close to your interests, follow the links until you find a figure with a "wrench" button under it [[Image:configure.png]]. Click on the wrench, and it will open a computational recipe used for generating the figure (the <tt>SConstruct</tt> file).
<python>
from rsf.proj import *
Flow('rose',None,
'''
math n1=629 d1=0.01 o1=0 n2=40 d2=1 o2=5
output="x2*(8+sin(6*x1+x2/10))" |
rtoc |
math output="input*exp(I*x1)"
''')
Result('rose',
'graph title=Rose screenratio=1 wantaxis=n')
End()
</python>
You can copy this recipe to your computer or simply find it already existing in the "book" subtree under the Madagascar source directory. For example, the recipe at http://www.reproducibility.org/RSF/book/rsf/rsf/sfmath.html also exists in the file <tt>RSFSRC/book/rsf/rsf/sfmath/SConstruct</tt>. After copying or locating the appropriate <tt>SConstruct</tt> file,
run
<pre>
scons view
</pre>
on the command line to generate all the figures in the selected project and to display them on your screen. For example, try
<pre>
bash$ cd RSFSRC/book/rsf/rsf/sfmath
bash$ scons view
</pre>
where <tt>bash$</tt> stands for the Unix prompt and <tt>RSFSRC</tt> stands for the Madagascar source directory. The output should look like
<pre>
scons: Reading SConscript files ...
scons: done reading SConscript files.
scons: Building targets ...
/RSFROOT/bin/sfmath n1=629 d1=0.01 o1=0 n2=40 d2=1 o2=5 output="x2*(8+sin(6*x1+x2/10))" | /RSFROOT/bin/sfrtoc |
/RSFROOT/bin/sfmath output="input*exp(I*x1)" > rose.rsf
< rose.rsf /RSFROOT/bin/sfgraph title=Rose screenratio=1 wantaxis=n > Fig/rose.vpl
/RSFROOT/bin/sfpen Fig/rose.vpl
scons: done building targets.
</pre>
with a picture appearing on your screen.
[[Image:rose.png|frame|center]]
If there are several figures in the recipe, you can run
<pre>
scons figurename.view
</pre>
(e.g. <tt>scons rose.view</tt>) to display individual figures. To remove all files that <tt>scons view</tt> generated, run
<pre>
scons -c view
</pre>
If you want to know in advance what commands will be executed to generate the figures, try
<pre>
scons -n view
</pre>
You can output this command to a file
<pre>
scons -n -Q view > script.sh
</pre>
and use <tt>script.sh</tt> as a shell script. If you are to make modifications to the data processing recipe (changing parameters or trying new data), working with SCons is more powerful and convenient than running shell scripts.

A computational recipe puts together individual commands through Unix pipes and SCons rules. These commands act like Lego blocks for creating complex data analysis constructions. In the example above, three "blocks" are used: <tt>sfmath</tt>, <tt>sfrtoc</tt>, and <tt>sfgraph</tt>. To find out what a particular command is doing, you can follow the links from the bottom of the web page http://www.reproducibility.org/RSF/book/rsf/rsf/sfmath.html
Alternatively, run the command without arguments on the command line. Running
<pre>
bash$ sfrtoc
</pre>
produces something like
<pre>
NAME
sfrtoc
DESCRIPTION
Convert real data to complex (by adding zero imaginary part).
SYNOPSIS
sfrtoc < real.rsf > cmplx.rsf
COMMENTS
See also: sfcmplx
USED IN
bei/ft1/plane4
bei/ft1/autocor
bei/ft1/brad
[...]
SOURCE
user/main/rtoc.c
DOCUMENTATION
http://reproducibility.org/wiki/Guide_to_madagascar_programs#sfrtoc
</pre>

The <b>DOCUMENTATION</b> section provides a link to a more detailed documentation on the web. The most useful part is the <b>USED IN</b> section, which points to more examples of using the program. As an exercise, change directory to <tt>RSFSRC/book/bei/ft1/plane4</tt> or any other example directory, examine the <tt>SConstruct</tt> file, and run <tt>scons view</tt>. Alternatively, look at http://www.reproducibility.org/RSF/book/bei/ft1/plane4.html

Want to find a program by keywords? Try <tt>sfdoc -k</tt>.
<pre>
bash$ sfdoc -k complex
sfsort: Sort a float/complex vector by absolute values.
sfrtoc: Convert real data to complex (by adding zero imaginary part).
sfjacobi2: Find eigenvalues of a general complex matrix by Jacobi-like iteration.
sfboolcmp: Element-wise boolean comparison of values. For int/float/complex data-sets.
sfcmatmult: Simple matrix multiplication for complex matrices
sfimag: Extract real (sfreal) or imaginary (sfimag) part of a complex dataset.
sfthr: Threshold float/complex inputs given a constant/varying threshold level.
sfcpef: 1-D prediction-error filter estimation from complex data
sfroots: Find roots of a complex polynomial.
sfreal: Extract real (sfreal) or imaginary (sfimag) part of a complex dataset.
sfcmplx: Create a complex dataset from its real and imaginary parts.
sfsin: Simple operations with complex sinusoids
sfcdottest: Generic dot-product test for complex linear operators with adjoints
sfcconjgrad: Generic conjugate-gradient solver for linear inversion with complex data
</pre>

Individual components of the Madagascar environment are described in more details below.

==Madagascar components==

===Standalone programs===
The list of all standalone programs is available [http://www.reproducibility.org/RSF/ online]. Most programs act as filters on input data and can be chained through Unix pipes, i.e.:
<bash>
< data.rsf sfwindow n1=100 | sfbandpass fhi=60 > data2.rsf
</bash>
This approach follows the Unix philosophy, as formulated by Doug McIlroy, the inventor of Unix pipes (Salus, 1994<ref>Salus, P. H., 1994, A quarter-century of Unix: Addison-Wesley.</ref>):
#Write programs that do one thing and do it well.
#Write programs to work together.
#Write programs to handle text streams, because that is a universal interface.

Following the Unix convention, programs have brief <tt>man</tt> pages, which explain the program purpose and parameters. You can access this documentation by running a program without parameters. To search for a program by a keyword, use <tt>sfdoc -k <keyword></tt>.

The [[guide to madagascar programs]] provides more detailed documentation for selected programs while the [[task-centric program list]] attempts to categorize them. You can see the programs in actual use in the [[Reproducible Documents]].

===Data format===

For data, Madagascar uses the [[Guide to RSF file format| Regularly Sampled Format]] (RSF), which is based on the concept of hypercubes (n-D arrays, or regularly sampled functions of several variables), much like the SEPlib (its closest relative), DDS, or the regularly-sampled version of the Javaseis format (SVF). Up to 9 dimensions are supported. For 1D it is conceptually analogous to a time series, for 2D to a raster image, and for 3D to a [http://en.wikipedia.org/wiki/Voxel voxel volume]. The format (actually a [http://en.wikipedia.org/wiki/Meta meta]format) makes use of a ASCII file with metadata (information about the data), including a pointer (<tt>in=</tt> parameter) to the location of the file with the actual data values. Irregularly sampled data are currently handled as a pair of datasets, one containing data and the second containing the corresponding irregular geometry information. Programs for conversion to and from other formats such as SEG-Y and SU are provided.

For graphics, Madagascar currently uses the Vplot vector graphics format. Converters to other graphics formats (Postscript, PNG, GIF, JPEG) are also provided.

===Reproducible documents===

A reproducible document consists of LaTeX source combined with SCons rules required to fully build the documents. These rules are expressed in terms of SCons extensions that are provided as part of Madagascar.

This is the key to the reproducibility aspect of Madagascar. An introduction to reproducible Madagascar documents is at [[Reproducible_computational_experiments_using_SCons]] .

===Vplot graphics===

In contrast to most other Madagascar Components, graphics components produce Vplot data as output.

Vplot is a device independent graphics format that allows both vector and raster elements (as such,
it is comparable to Postscript). Vplot files are interpreted by a number of output devices. Its typical usage is for a visual display in X-windows. A list of them is [[Guide to madagascar programs#Plotting programs | provided on the wiki]].

Here is an example of a Madagascar pipe. In this case it takes a subsection of a file, low-pass
filters it, and saves the result

<bash>
< data.rsf sfwindow n1=100 | sfbandpass fhi=60 > data2.rsf
</bash>

In this more elaborate case, the final output is passed to a graphics program and plotted.

<bash>
< data.rsf sfwindow n1=100 | sfbandpass fhi=60 | sfcontour | xtpen
</bash>

More extensive examples are seen in [[Guide to madagascar programs]] . The novice reader should probably read the material below before proceeding to that page.

===Reproducibility and Project Management===

Madagascar uses and extends [http://www.scons.org/ SCons], an open-source
software construction package, to document and maintain data processing flows. Documented projects become
computational recipes that can be easily exchanged among Madagascar users.

SCons is a rule-based package in Python typically used as a build system analogous to <tt>make</tt>. Familiarity with any build system will
be helpful in understanding SCons. SCons statements, as python statements, are invoked in the sequence they are
written, but as such they only define rules. The rules are invoked in accordance with a dependency graph which
SCons builds based on those rules. Components regarded as "up-to-date" are not rebuilt.

SCons allows for user-contributed Builders (meta-rule categories) and Madagascar uses this capability extensively.
The idea is that building an output file based on a workflow chain is very much analogous to building a
software package based on a software tool chain. The calculation is seen simply as a build with dependencies.
This is a considerable benefit in developing alternative workflows using a given dataset. The system
maintains an awareness of already completed calculations. Without user intervention, redundant calculations
are avoided.

Madagascar calculations are thus expressed as SCons scripts (<tt>SConstruct</tt> files). SCons extensions follow SCons conventions in beginning
with an uppercase letter. The most common Madagascar extensions are <tt>Flow()</tt>, <tt>Result()</tt>, and <tt>End()</tt>. A <tt>Flow()</tt> invocation wraps Madagascar computational components. <tt>Result()</tt> is a version of <tt>Flow()</tt> with a graphical output. Finally an
End() actually invokes the default rules for multiple results.

Finally, Madagascar enables a collection of reproducible documents, organized in living books. Each
reproducible book contains a collection of Madagascar recipes (<tt>SConstruct</tt> files) used to generate book figures. The recipes
cover a variety of data processing and imaging tasks described in the books. Figures and recipes serve
dual purpose with respect to Madagascar maintenance. They provide demos for introducing new users to the
functionality of the package and, at the same time, [[Automatic Testing|regression tests]] for assuring the system stability
under change.

==Madagascar Trivia==

===Why the Name "Madagascar"?===

[http://www.reproducibility.org/rsflog/index.php?/archives/67-Madagascar.html Whimsy, really]. It seems easier to remember than the previous name "RSF", and it provides us interesting [http://www.reproducibility.org/rsflog/index.php?/archives/178-Ahay!.html mascots].

===License===

The Madagascar package is released in an open-source form under the standard [http://www.gnu.org/copyleft/gpl.html GNU GPL] license. In simple
words, there are no restrictions on the use of the software (including copying, modifying, selling, etc.)
However, there are restrictions on the software redistribution intended to prevent the package from losing
its open-source status. Users are encouraged to [[Contributing new programs to Madagascar|submit their modifications]] back to the original distribution for the benefit of the whole [[Package_overview#Community|community]].

===Community===

Madagascar seeks to be an open and active community. Mailing lists are maintained, and annual meetings take place. See
* [[Conferences]]
* [http://www.ahay.org/rsflog Development blog]
* [https://lists.sourceforge.net/lists/listinfo/rsf-user RSF-user mailing list]
* [https://lists.sourceforge.net/lists/listinfo/rsf-devel RSF-devel mailing list]
Your participation is welcome.

===History===

Madagascar was first publicly presented at the [[Conferences#Vienna_2006_.28EAGE.29|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. See [http://rsf.svn.sourceforge.net/viewvc/rsf/trunk/AUTHORS.txt?view=markup AUTHORS.txt] for an incomplete list.

While being written mostly from scratch, Madagascar borrows ideas from the design of [http://sepwww.stanford.ed/doku.php?id=sep:software:seplib SEPlib], a package maintained by Bob Clapp at the Stanford Exploration Project (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 [http://timna.mines.edu/cwpcodes/ Seismic Unix] (SU), an open-source package maintained by John Stockwell at the Center for Wave Phenomena (CWP) at the Colorado School of Mines (Stockwell, 1997<ref>Stockwell, J. W., 1997, Free software in education: A case study of CWP/SU: Seismic Unix: The Leading Edge, '''16''', 1045--1049.</ref>;Stockwell, 1999<ref>--------, 1999, The CWP/SU: Seismic Un*x package: Computers and Geosciences, '''25''', 415--419.</ref>). 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).

<references/>

Madagascar - User contributions [en]

Package overview