Software Spotlight/ Chunmiao Zheng, Software Editor

SGeMS: A Free and Versatile Tool for Three-

Dimensional Geostatistical Applications
reviewed by Marco Bianchi1 and Chunmiao Zheng2

Introduction Stanford University, and it is considered an evolution of

Most of the data used in ground water studies vary
spatially, such as hydraulic conductivity, contaminant
concentration, and aquifer thickness. The analysis of spa-
tial data and more specifically the estimation of values at
unsampled locations from a discrete number of measure-
ments at specific locations are an essential part of most
hydrogeologic investigations. Geostatistical techniques
such as kriging and stochastic simulation are widely used
to accomplish these tasks.
The marketplace offers a wide selection of software
packages for geostatistical applications. Some of these pack-
ages are limited to two-dimensional data sets, some are quite
expensive, while others lack the necessary theoretical rigor.
A very popular collection of geostatistical programs is
GSLIB developed by two well-known experts in the field of
geostatistics (Deutsch and Journel 1998). GSLIB is an open
source and can be incorporated into other programs or
expanded to new geostatistical applications. These advan-
tages made GSLIB a must-have for both professionals and
researchers involved in geostatistical data analysis. Un-
fortunately, GSLIB does not have an easy-to-use graphical
user interface (GUI) for input and output operations. The
preparation of input files and compilation of the source
codes can in fact be difficult and tedious, especially if
the user is not familiar with the FORTRAN programming
language. This disadvantage can now be overcome by the
Stanford Geostatistical Modeling Software (SGeMS), which
is freely available on the Internet.
SGeMS was developed by Nicholas Remy with con-
tributions from Alexandre Boucher, Jianbing Wu, and Ting
Li in the Department of Energy Resources Engineering at
1Department of Geological Sciences, University of Alabama,
Tuscaloosa, AL 35487; (205) 348-3015; fax: (205) 348-0818;
mbianchi@bama.ua.edu
2Corresponding author: Department of Geological Sciences,
University of Alabama, Tuscaloosa, AL 35487; (205) 348-0579;
fax: (205) 348-0818; czheng@ua.edu
Copyright 2008 The Author(s)
Journal compilation 2008 National Ground Water Association.
doi: 10.1111/j.1745-6584.2008.00522.x
8 Vol. 47, No. 1GROUND WATERJanuaryFebruary 2009
GSLIB. The geostatistical algorithms implemented in
SGeMS are taken from the Geostatistics Template Library
(GSTL) (Remy 2001), which is a C11 library containing
an extensive set of geostatistical tools. This library is de-
signed to be easily extended and readily integrated into
software packages. SGeMS is an example of integrating
GSTL into a user-friendly software tool with a GUI.
How We Tested
Version 2.0 of the SGeMS software was tested on a
laptop computer with a 2.6 GHz Intel
Pentium 4 CPU
and 512 MB RAM under Microsoft Windows XP and an-
other laptop computer with 2.0 GHz Pentium M CPU and
2 GB RAM running Microsoft Windows Vista. The main
installation program (8.5 MB) was downloaded from the
software authors Web site, and the installation went
smoothly and quickly without any problems. Different
types of installation (compact, standard, complete, and
custom) can be performed. The compact installation with-
out source codes requires 18.7 MB of hard disk space,
while the complete installation with source codes, doc-
umentation, and the GSTL library uses about 35.8 MB.
During the evaluation period, no conflicts between
SGeMS and other software applications were experi-
enced. The reviewers tested the software by working with
real-world three-dimensional (3D) data sets.
What We Found
Documentation and Technical Support
An SGeMS users manual in PDF format can be
downloaded from the authors Web site where an online
tutorial for writing commands and scripts, an online devel-
opers reference, and an online tutorial for creating a new
geostatistics plug-ins are also available. The users manual
provides a general overview of the software capabilities; a
description of the GUI; a simple tutorial to guide through
the steps of importing data, performing ordinary kriging,
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and displaying the results; and a description of some of
the geostatistical estimation and simulation algorithms
available in SGeMS. Since the users manual was written
in 2004 and refers to a previous version of the software,
some of the tools that are present in the tested version of
SGeMS are not described in the manual. However, by the
end of 2008, a new users guide will be available (Remy
et al. 2008). At the time this review was written, the re-
viewers had no access to the new users guide, but the
books preorder information indicates that it will provide a
step-by-step guide to using SGeMS geostatistical tools, a
complete explanation of the underlying theory, and a dis-
cussion of how to complete automatic tasks using the em-
bedded scripting language and how to develop new
algorithms and integrate them into SGeMS.
To receive technical support, the user can subscribe to
a mailing list through the authors Web site. The mailing
list is intended for seeking help on using SGeMS, getting
information about new releases, or exchanging problems or
issues with the authors and other users. Another mailing
list is specifically dedicated to developers of new algo-
rithms or scripts. Once an e-mail message is submitted, it
is forwarded to all members of the mailing list. Requests
Figure 1. A screen capture of the SGeMS GUI showing the algorithm panel (on the left), display panel (right) and, command
panel (bottom).
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for technical help are also accessible from a forum-type
Web site at the following address: http://sourceforge.net/
mailarchive/forum.php?forum_name=sgems-users. The re-
viewers did not submit any technical questions, but from a
surfing of this Web site, it appears that the user can get a
prompt reply from the authors or other users within days.
GUI and Data Import and Management
The GUI of SGeMS is well designed (Figure 1).
The program window is divided into three main panels:
the algorithms panel, the display panel, and the com-
mand panel, each of which can be activated or deacti-
vated at the discretion of the user. Once a geostatistical
tool is selected from the algorithm panel, the user has to
input all the necessary parameters in order to run the
corresponding algorithm. Both reviewers found this task
straightforward, thanks to the intuitive design of the
GUI. The display panel is a true interactive 3D environ-
ment where it is possible to have full control of the
visualization through simple movements of the mouse.
The graphics can be adjusted by changing color maps
or by visualizing cross sections or portions of the 3D
volumes resulting from geostatistical estimation or
Vol. 47, No. 1GROUND WATERJanuaryFebruary 2009 9
simulation. From the command panel, the user can also
control the software by typing text commands rather
than using the GUI. It also displays a history of all com-
mands executed.
Data can be imported by using the menu option Ob-
jects / Load Object or by simply hitting CTRL-L on the
keyboard. Two data formats are supported by default: the
GSLIB format, which is an ASCII format, and the SGeMS
binary format. Details on the GSLIB format can be found
in Deutsch and Journel (1998). When importing data with
the GSLIB format, the user must specify if the data repre-
sent a point set, a normal grid, or a masked grid. A masked
grid is the kind of grid where only some of the cells are ac-
tive. The steps necessary for importing data sets are easy to
follow, but some knowledge of the GSLIB format is helpful.
Geostatistical Tools
With SgeMS, it is possible to perform a complete ge-
ostatistical analysis, including descriptive statistical anal-
ysis of univariate and bivariate data, variogram
estimation and modeling, variable estimation, and differ-
ent types of geostatistical modeling and postprocessing.
Descriptive statistical analysis of univariate data can be
performed by calculating summary statistics and plotting
Figure 2. A screen capture of the SGeMS GUI showing the controls for variogram modeling.
10 Vol. 47, No. 1GROUND WATERJanuaryFebruary 2009
histograms and cumulative histograms. Bivariate data can
be analyzed using scatter plots, q-q plots and p-p plots.
The parameters needed for variogram, cross-variogram,
and indicator-variogram calculation and modeling are very
similar to those used in the code GAMV of GSLIB. Assign-
ing the required parameters for the experimental variogram
computation is intuitive. These parameters include the num-
ber of lags, lag separation and tolerance, azimuth, dip angu-
lar tolerance, and bandwidth. Several directions can be
explored at the same time, making it easy to search for ani-
sotropy. Variogram, covariance function, and correlograms
can be calculated and plotted (Figure 2). The current ver-
sion of SGeMS allows the user to choose among four basic
variogram models and any positive linear combination.
These are the nugget effect, the exponential, the spherical,
and the Gaussian models. Once the appropriate model is se-
lected and adjusted to fit the experimental variogram, the
user can save a parameter file that summarizes all the char-
acteristics (i.e., type, sill, ranges) of the fitted variogram
model. This parameter file can be used during the estima-
tion or modeling phase.
Estimation tools include several types of kriging (sim-
ple kriging, ordinary kriging, universal kriging, and simple
kriging with locally varying mean), indicator kriging, and
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simple and ordinary cokriging. A 3D grid must be first de-
fined in order to perform the kriging interpolation. This
task can be done by selecting Objects / New grid from
the menu option or by simply hitting CTRL-N on the key-
board. In the grid creation dialog, the user must specify
the dimensions of the grid, the coordinates of the origin
(the lower left corner), and the dimensions of each grid
cell. For testing purposes, the reviewers estimated the dis-
tribution of a spatial variable in a 31 3 31 3 63 grid using
different types of kriging algorithms. All the algorithms
tested were stable and computationally efficient.
SGeMS provides a comprehensive selection of algo-
rithms for stochastic simulation. In particular, SGeMS
provides algorithms for both variogram-based stochastic
simulation (e.g., sequential Gaussian simulation) and
multiple-point simulation (e.g., single normal equation
simulation and filter-based simulation). The following
geostatistical simulations can be performed: sequential
Gaussian simulation, sequential indicator simulation, se-
quential Gaussian cosimulation, sequential indicator
cosimulation, direct sequential simulation, single normal
equation simulation, and filter-based simulation. All the
necessary parameters to run these algorithms can be
specified in the algorithm panel. The reviewers tested
only the algorithms for sequential Gaussian simulation
and sequential indicator simulation and, as for the kriging
algorithms, no problems were encountered.
Running the Software in Batch Mode and Expandability
Each of the operations performed in SGeMS by
mouse clicks can also be performed by typing lines of
commands in the command panel. The advantage is that
it is possible to include a list of commands in a script and
let the program execute them sequentially in batch mode.
This is particularly important if the user needs to repeat
the same task (e.g., ordinary kriging) multiple times with
different input parameters (e.g., search radius and/or
number of conditioning data). Scripts can be created us-
ing an editor that can be activated from the menu options.
To perform repetitive actions, SGeMS uses the Python
scripting language. More details and examples about
how to create scripts in SGeMS can be found at the follow-
ing Web address: http://sgems.sourceforge.net/doc/sgems_
scripts.html.
New geostatistical algorithms can be added to
SGeMS. These must be written in the form of generic
plug-ins in the C11 programming language. Plug-ins
can be compiled separately and then called from the main
program when needed. Two examples of incorporating
new geostatistical tools to SGeMS are presented in Li
and Caers (2008) and Wu et al. (2008). A tutorial for cre-
ating a SGeMS geostatistics plug-in can be found at the
following Web address: http://sgems.sourceforge.net/doc/
geostatistics_plugin_howto.html.
Output
The content in the display panel can be exported in
PNG, PS, BMP, and PPM files. The same formats are
available for exporting specific graphs such as histograms
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and variograms. Output data from estimation and simula-
tion algorithms can be saved in the same two formats as
used for importing data: the GSLIB ASCII format and
the SGeMS binary format.
What We Liked
SGeMS provides a comprehensive set of geostatisti-
cal tools wrapped in an easy-to-use GUI. The number of
geostatistical algorithms that are available is impressive.
These include both classical kriging algorithms, instru-
ments for multivariate kriging (co-kriging), indicator
kriging, and several types of stochastic simulation algo-
rithms. SGeMS is the only software available that pro-
vides algorithms for multiple-point statistics simulation.
The GUI is sufficiently intuitive to use and parame-
ters input operations are easy to follow. Moreover, the
software alerts the user with error messages whenever an
input parameter is not correctly entered. After running an
estimation or simulation algorithm, results are directly vi-
sualized in the display panel.
Another attractive feature is the possibility of writing
scripts and geostatistical plug-ins. Running the program
in batch mode can save a considerable amount of time es-
pecially if the user needs to repeat the same operation
many times as, for instance, during sensitivity analyses.
The fact that the software can be augmented by writing
geostatistical plug-ins makes it possible to customize and
update SGeMS easily. The mailing lists for technical sup-
port can also help both advanced and novice users to ex-
change experience and problems.
The reviewers also liked the fact that, even though
the GUI makes parameter input operations easy to follow,
the user still must know the theoretical basis of geostatis-
tics in order to use SGeMS effectively. For example,
some software packages allow the user to perform kriging
without calculating the variogram by using default pa-
rameters of doubtful practical and theoretical validity.
This is not the case with SGeMS. The user must have at
least a basic knowledge of geostatistical concepts to run
the geostatistical tools that are available.
What We Did Not Like
A noticeable limitation of the visualization panel is
that it is not possible to visualize Cartesian axes and label
data points or import any kind of base map in either raster
or vector formats. These features would have certainly
helped the user in localizing data and interpolating results
more easily on the display. It is also not possible to con-
trol some graphical aspects of output displays such as his-
tograms and variograms (e.g., colors, lines widths, fonts).
Because of these limitations, the graphical outputs pro-
duced by SGeMS may need to be processed with other
graphical softwares for publications and reports.
The downloadable users manual needs to be updated.
Many of the geostatistical tools currently available in ver-
sion 2.0 of SGeMS are not described and therefore they
cannot be used unless the user has an advanced knowledge
Vol. 47, No. 1GROUND WATERJanuaryFebruary 2009 11
of these geostatistical algorithms. It is a welcome develop-
ment that a new users manual in the form of a reference
book will become available by the end of 2008 that will
probably provide a more complete and up-to-date descrip-
tion of the features included in SGeMS. Nevertheless, the
reviewers hope a new downloadable manual will be made
available soon to keep the open source software up to date.
Overall
Once in while, one might discover a rare gem on the
Internet that is an absolute delight to have. SGeMS is
such a discovery for the reviewers. It is free and yet few,
if any, commercial or open source software can match its
capabilities. The number of geostatistical tools included
in SGeMS is very impressive. SGeMS combines an easy-
to-use GUI with a theoretical rigor and expandability that
will please both practitioners and researchers involved in
geostatistical data analysis from routine to very sophisti-
cated. According to the users manual, SGeMS was
designed with the twofold goal of providing a user-
friendly software tool with a wide range of geostatistical
algorithms and an evolving software package whose capa-
bilities can be conveniently augmented. The reviewers be-
lieve these goals have been fully accomplished.
Ranking
The reviewer ranked the softwares capability, reli-
ability, ease of use, and technical support on a scale of 1
(worst) to 5 (best). The following rankings are the aver-
age of the scores from both reviewers:
Capability: 4.7
Reliability: 4.5
Ease of use: 4.0
Technical support: 4.5
12 Vol. 47, No. 1GROUND WATERJanuaryFebruary 2009
How to Obtain the Software
SGeMSs installation file, source code, and users
manual can be downloaded freely from the authors Web
site at http://sgems.sourceforge.net/. The software is dis-
tributed under the GNU General Public License.
Our Mission
The goal of Software Spotlight is to help readers
identify well-written, intuitive, and useful software. Inde-
pendent reviewers from government, industry, and aca-
demia try out full working versions of software packages
and provide readers with a concise summary of their ex-
periences and opinions regarding the capability, stability,
and ease of use of these packages.
Software Editor Chunmiao Zheng can be reached
at the Department of Geological Sciences, University
of Alabama, Box 870338, Tuscaloosa, AL 35487;
czheng@ua.edu.
References
Deutsch, C.V., and A.G. Journel. 1998. GSLIB, Geostatistical
Software Library and Users Guide, 2nd ed. New York:
Oxford University Press.
Li, T., and J. Caers. 2008. Solving spatial inverse problems
using the probability perturbation method: An S-GEMS
implementation. Computers & Geosciences 34, 1127
1141.
Remy, N.N. 2001. GSTL: the geostatistical template library in
C++. M.S. thesis, Stanford University, Stanford, California.
Remy, N.N., J. Wu, and A. Boucher. 2008. Applied Geostatistics
with SGeMS: A Users Guide. Cambridge, UK: Cambridge
University Press.
Wu, J., A. Boucher, and T. Zhang. 2008. A SGeMS code for
pattern simulation of continuous and categorical variables:
FILTERSIM. Computers & Geosciences 34, no. 12: 1863
1876.
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