Madagascar development blog

Sunday, June 21. 2009

Line lengths in Madagascar

Having a known maximum source code line length is a very useful thing. This way, code fragments can be automatically included into other kinds of media without breaking formatting rules. Coding standards for most large, established software projects (either open-source or proprietary) explicitly mention line length.

However, what is a good line length limit? The 80-character limit is very widespread, but how does it compare to what peoples have naturally been writing? To find out, I used a little Python script (adm/line_len_hist.py) to count line lengths for various types of files in the Madagascar code base. Pictures follow below, for all source code files (including SConstruct files) and the most prevalent file types. To my surprise, the 80-character threshold is quite relevant, and it might be worth having it as an explicit coding style suggestion on the wiki, to help new contributors!

Posted by Nick Vlad in Systems at 08:03 | Comment (1) | Trackbacks (0)

Wednesday, June 10. 2009

madagascar-0.9.8

A new stable release of madagascar is yet another step toward the first non-beta version (madagascar-1.0). It features new reproducible papers and many other improvements. The cumulative number of downloads for all stable versions has reached 5,500.

Posted by Sergey Fomel in Celebration at 00:52 | Comments (0) | Trackbacks (0)

Saturday, June 6. 2009

pens++

oglpen is a new "pen" contributed by Vladimir Bashkardin. It displays Vplot files using OpenGL and GLUT and can serve as a replacement for xtpen.

vpconvert is a script for converting Vplot files to other formats (EPS, PS, PDF, PPM, TIFF, JPEG, PNG, GIF, MPEG, AVI, SVG). You can use it for converting one file

bash$ vpconvert file.vpl file.jpg

or a collection of files

bash$ vpconvert format=tiff Fig/*.vpl

Posted by Sergey Fomel in Programs at 12:40 | Comments (0) | Trackbacks (0)

Sunday, April 26. 2009

Reproducible research

Madagascar is mentioned in Reproducible Research in Signal Processing - What, why, and how, a new paper by Patrick Vandewalle, Jelena Kovacevic, and Martin Vetterli, which appears in the latest issue of the IEEE Signal Processing Magazine and makes a strong case for reproducible research.

Posted by Sergey Fomel in Links at 09:26 | Comments (0) | Trackbacks (0)

Tuesday, April 14. 2009

Stacking using local correlation

A new paper is added to the collection of reproducible documents:

Stacking seismic data using local correlation

Posted by Sergey Fomel in Documentation at 16:01 | Comments (3) | Trackbacks (0)

Monday, March 23. 2009

pens++

Meet gdpen, a new "pen" program. gdpen converts vplot files to PNG or JPEG, or GIF graphics formats (including animated GIFs). Use it like this:

gdpen < file.vpl > file.png

gdpen type=jpeg < file.vpl > file.jpg

gdpen type=gif < file.vpl > file.gif

Other usual options are available.

gdpen requires the GD library at the compilation time.

Several other "pens" are under development:

cairopen - for outputting standard vector-graphics formats

svgpen - for outputting SVG directly

pdfpen - for outputting PDF directly

gtkpen/oglpen - for displaying plots on a screen (as a replacement for xtpen)

Posted by Sergey Fomel in Programs at 10:30 | Comments (0) | Trackbacks (0)

Sunday, March 15. 2009

How do I convert an image file to an RSF file?

One option is sfjpg2byte. It requires the JPEG library to be present at the compilation time.



< lena.jpg sfjpg2byte | sfdd type=float > lena.rsf

Another option (suggested by Vladimir Bashkardin) is to use the convert utility from ImageMagick.



< lena.jpg convert - lena.gray

echo in=lena.gray data_format=native_uchar n1=512 n2=512 | sfdd type=float > lena.rsf



< lena.jpg convert - lena.rgb

echo in=lena.rgb data_format=native_uchar n1=3 n2=512 n3=512 | sfdd type=float > lena.rsf

Posted by Sergey Fomel in FAQ at 10:52 | Comments (0) | Trackbacks (0)

Google Summer of Code

Michael Tobis has submitted a Madagascar application to the Google Summer of Code. Check out the ideas page.

Posted by Sergey Fomel in Celebration at 09:43 | Comments (0) | Trackbacks (0)

Madagascar group on LinkedIn

The greatest strength of open source software is the community of users and developers, with fast, two-way lateral communication that enables quick learning and rapid feedback cycles. Communication between users is improved when they know each other's backgrounds better.

To help users to better know each other, a Madagascar group was created on the LinkedIn professional networking site. Those of you who are members of LinkedIn, or are interested in becoming members, are welcome to join and to invite other Madagascar users. To keep away the ubiquitous spammers, admission to the group is subject to approval, but this will be granted as soon as possible to anybody who looks like a "real person".

LinkedIn offers forum capabilities as well, but please note that this is not an attempt to shift communication from existing channels (mailing lists, wiki, Sourceforge bug/feature request trackers/etc). On the contrary, since social networking sites generally try to "lock-in" users, and are not open to non-users, I would strongly recommend not using their discussion forums, but just using LinkedIn's connection features to get to know each other better.

Please note that this is not an endorsement of either social networking sites in general or LinkedIn in particular. It's just something entirely voluntary that some people find useful. For those of you who are not familiar with what LinkedIn is, a description can be found on Wikipedia.

Posted by Nick Vlad in Celebration at 08:25 | Comments (0) | Trackbacks (0)

Friday, March 13. 2009

Fractal heterogeneities and scattering attenuation

A new paper is added to the collection of reproducible documents:

Fractal heterogeneities in sonic logs and low-frequency scattering attenuation

Posted by Jules Browaeys in Documentation at 08:35 | Comments (0) | Trackbacks (0)

Sunday, March 1. 2009

Madagascar school at Delft

The madagascar event of the year is the School on Reproducible Computational Geophysics, which will be hosted by the Delft University of Technology on June 12-13, right after the EAGE meeting in Amsterdam. Attendance is free but registration is required. To register, send a free-form email to rsfschool@gmail.com.

Posted by Sergey Fomel in Celebration at 17:15 | Comments (0) | Trackbacks (0)

Thursday, February 26. 2009

Tutorial on wavefield seismic imaging

The February 2009 issue of The Leading Edge contains a tutorial Overview and classification of wavefield seismic imaging methods by Paul Sava and Steve Hill, with examples created in Madagascar. See Paul Sava's Wavefield Seismic Imaging page for more information.

Posted by Sergey Fomel in Documentation at 12:37 | Comments (0) | Trackbacks (0)

Sunday, February 8. 2009

What are the most popular programs in Madagascar?

In reverse order, the 10 most popular programs in Madagascar are:

10. sftransp Transpose two axes in a dataset (used in 83 projects)

9. sfadd Add, multiply, or divide RSF datasets (used in 92 projects)

8. sfgraph Graph plot (used in 99 projects)

7. sfspike Generate simple data: spikes, boxes, planes, constants (used in 109 projects)

6. sfcat Concatenate datasets (used in 110 projects)

5. sfput Input parameters into a header (used in 118 projects)

4. sfmath Mathematical operations on data files (used in 143 projects)

3. sfdd Convert between different formats (used in 163 projects)

2. sfwindow Window a portion of a dataset (used in 216 projects)

1. sfgrey Generate raster plot (used in 260 projects)

More documentation on these and other programs - in Guide to Madagascar programs.

The three most popular programs in the "generic" category (signal processing programs applicable to any kind of data) are sffft1 (Fast Fourier Transform along the first axis), sfnoise (Add random noise to the data), and sfsmooth (Multi-dimensional triangle smoothing).

The three most popular programs in the "seismic" category (signal processing programs applicable to seismic data) are sfmutter (Muting), sfricker1 (Convolution with a Ricker wavelet), and sfsegyread (Convert a SEG-Y or SU dataset to RSF).

Here is a simple Python script that extracts the popularity information:

#!/usr/bin/env python
from rsfdoc import progs
import rsfprog

def nuses(p):
    'how many times a program is used'
    n=0
    uses = progs[p].uses
    for book in uses.keys():
        for chapter in uses[book].keys():
            n = n + len(uses[book][chapter])
    return n

programs = progs.keys()
programs.sort(lambda x,y: nuses(y)-nuses(x))

for prog in programs:
    print '%s is used in %d projects' % (prog,nuses(prog))