2. Introduction — GMT 6.4.0 documentation

# 2. Introduction

## 2.1. Historical overview

Most scientists are familiar with the sequence: raw data → processing → final illustration. In order to finalize papers for submission to scientific journals, prepare proposals, and create illustrations for various presentations, many scientists spend large amounts of time and money to create high-quality figures. This process can be tedious and is often done manually, since available commercial or in-house software usually can do only part of the job. To expedite this process we introduce the Generic Mapping Tools (GMT for short), which is a free [2] software package that can be used to manipulate columns of tabular data, time-series, and gridded data sets, and display these data in a variety of forms ranging from simple x–y plots to maps and color-coded, perspective, and shaded-relief illustrations. GMT uses the PostScript page description language [Adobe Systems Inc., 1990]. With PostScript, multiple plot files can easily be superimposed to create arbitrarily complex images in gray tones or full color. Line drawings, bitmapped images, and text can be easily combined in one illustration. PostScript plot files are device-independent: The same file can be printed at 300 dots per inch (dpi) on a cheap printer or converted to a high-resolution PNG image for online usage. GMT software is written as a set of command-line tools [3] and is totally self-contained and fully documented. The system is offered free of charge and is distributed over the Internet [Wessel and Smith, 1991; 1995; 1998; Wessel et al., 2013; Wessel et al., 2019]. The PostScript plots are easily converted to other formats, such as PDF or any raster image [4].

The original version 1.0 of GMT was released in the summer of 1988 when the authors were graduate students at Lamont-Doherty Earth Observatory of Columbia University. During our tenure as graduate students, LDEO changed its computing environment to a distributed network of UNIX workstations, and we wrote GMT to run in this environment. It became a success at LDEO, and soon spread to numerous other institutions in the US, Canada, Europe, and Japan. The current version benefits from the many suggestions contributed by users of the earlier versions, and now includes more than 100 tools, more than 30 projections, and many other new, more flexible features. GMT provides scientists with a variety of tools for data manipulation and display, including routines to sample, filter, compute spectral estimates, and determine trends in time series, grid or triangulate arbitrarily spaced data, perform mathematical operations (including filtering) on 2-D data sets both in the space and frequency domain, sample surfaces along arbitrary tracks or onto a new grid, calculate volumes, and find trend surfaces. The plotting programs will let the user make linear, log\(_{10}\), and \(x^a - y^b\) diagrams, polar and rectangular histograms, maps with filled continents and coastlines choosing from many common map projections, contour plots, mesh plots, monochrome or color images, and artificially illuminated shaded-relief and 3-D perspective illustrations.

GMT is written in the highly portable ANSI C programming language [Kernighan and Ritchie, 1988], is fully POSIX compliant [Lewine, 1991], and may be used with any hardware running some flavor of UNIX. In writing GMT, we have followed the modular design philosophy of UNIX: The raw data → processing → final illustration flow is broken down to a series of elementary steps; each step is accomplished by a separate GMT or UNIX tool. This modular approach brings several benefits: (1) only a few programs are needed, (2) each program is small and easy to update and maintain, (3) each step is independent of the previous step and the data type and can therefore be used in a variety of applications, and (4) the programs can be chained together in shell scripts or with pipes, thereby creating a process tailored to do a user-specific task. The decoupling of the data retrieval step from the subsequent massage and plotting is particularly important, since each institution will typically have its own data base formats. To use GMT with custom data bases, one has only to write a data extraction tool which will put out data in a form readable by GMT (discussed below). After writing the extractor, all other GMT modules will work as they are.

GMT is thoroughly documented and comes with a technical reference and cookbook which explains the purpose of the package and its many features, and provides numerous examples to help new users quickly become familiar with the operation and philosophy of the system. The cookbook contains the shell scripts that were used for each example. The online GMT Documentation is also home to the extensive technical reference for all programs. The programs also have individual manual pages which can be installed as part of the on-line documentation under the UNIX man utility. In addition, the programs offer friendly help messages which make them essentially self-teaching – if a user enters invalid or ambiguous command arguments, the program will print a warning to the screen with a synopsis of the valid arguments. All the documentation is available for web browsing and may be installed at the user’s site.

The processing and display routines within GMT are completely general and will handle any (x,y) or (x,y,z) data as input. For many purposes the (x,y) coordinates will be (longitude, latitude) but in most cases they could equally well be any other variables (e.g., wavelength, power spectral density). Since the GMT plot tools will map these (x,y) coordinates to positions on a plot or map using a variety of transformations (linear, log-log, and several map projections), they can be used with any data that are given by two or three coordinates. In order to simplify and standardize input and output, by default GMT uses two file formats only. Arbitrary sequences of (x,y) or (x,y,z) data are read from multi-column ASCII tables, i.e., each file consists of several records, in which each coordinate is confined to a separate column [5]. This format is straightforward and allows the user to perform almost any simple (or complicated) reformatting or processing task using GMT processing tools (and in a pinch standard UNIX utilities such as cut, paste, grep, sed and awk). Two-dimensional data that have been sampled on an equidistant grid are read and written by GMT in a binary grid file using the functions provided with the netCDF library (a free, public-domain software library available separately from UCAR, the University Corporation of Atmospheric Research [Treinish and Gough, 1987]). This XDR (External Data Representation) based format is architecture independent, which allows the user to transfer the binary data files from one computer system to another [6]. GMT contains programs that will read ASCII (x,y,z) files and produce grid files. One such program, surface, includes new modifications to the gridding algorithm developed by Smith and Wessel [1990] using continuous splines in tension. Optionally, GMT can also read various binary and netCDF tables, as well as a variety of grid formats via GDAL.

Most of the programs will produce some form of output, which falls into four categories. Several of the programs may produce more than one of these types of output:

- 1-D ASCII Tables — For example, a (x,y) series may be filtered and the filtered values output. ASCII output is written to the standard output stream.

- 2-D binary (netCDF or user-defined) grid files – Programs that grid ASCII (x,y,z) data or operate on existing grid files produce this type of output.

- PostScript – The plotting programs all use the PostScript page description language to define plots. These commands are stored as ASCII text and can be edited should you want to customize the plot beyond the options available in the programs themselves.

- Reports – Several GMT programs read input files and report statistics and other information. Nearly all programs have an optional “verbose” operation, which reports on the progress of computation. All programs feature usage messages, which prompt the user if incorrect commands have been given. Such text is written to the standard error stream and can therefore be separated from ASCII table output.

GMT is available over the Internet at no charge. To obtain a copy, go to the GMT home page and follow instructions. We also maintain user forums and a bug and feature tracking system on the same page.

GMT has served a multitude of scientists very well, and their responses have prompted us to develop these programs even further. It is our hope that the new version will satisfy these users and attract new users as well. We present this system to the community in order to promote sharing of research software among investigators in the US and abroad.

## 2.2. References

- Adobe Systems Inc., PostScript Language Reference Manual, 2nd edition, 764, Addison-Wesley, Reading, Massachusetts, 1990.

- Kernighan, B. W., and D. M. Ritchie, The C programming language, 2nd edition, 272, Prentice-Hall, Englewood Cliffs, New Jersey, 1988.

- Lewine, D., POSIX programmer’s guide, 1st edition, 607, O’Reilly & Associates, Sebastopol, California, 1991.

- Treinish, L. A., and M. L. Gough, A software package for the data-independent management of multidimensional data, EOS Trans. AGU, 68(28), 633–635, 1987. doi:10.1029/EO068i028p00633.

## 2.3. Modern and Classic Mode

For almost three decades, GMT scripts have looked remarkably similar. The options flags and the general workflow of adding overlays to existing PostScript files have remained unchanged, and thousands of GMT scripts written in c-shell, bash shell, DOS batch, and other environments exist and their maintainers expect them to run in the future. This requirement of backwards compatibility has to some extent stifled our drive to make GMT easier and safer to use. Having run dozens of classes introducing GMT to students and staff, and helped hundreds of practitioners via email or forums over the years, we have a pretty clear idea of what is difficult.

Given its almost limitless capabilities, GMT has always had a fairly steep learning curve. The hardest aspects that have percolated to the top of the “rookie error” list include

1. The GMT “cake-baking”: Handling the use of -O, -K, and -P to manage PostScript overlays.

2. The PostScript redirection: Creating a new file versus appending to an existing file.

3. Reusing the current region (-R) and projection (-J) in multi-step scripts by repeating -R -J everywhere.

4. Converting the PostScript plot to more desirable graphic formats, such as PDF.

While pondering these facts, we have also started to gain experience with the MATLAB and Octave toolboxes and the preliminary design of the Python package. We were noticing that the resulting scripts looked too much like the GMT shell command-line versions, setting users up for a continuation of the same rookie errors. The solution to this conundrum was to introduce different run modes: Starting with GMT 6 we introduce a new operating mode for GMT named modern. In contrast to the classic (and only) mode available in earlier versions 1-5, the modern mode was designed to eliminate some of the hardest aspects of learning and using GMT. Depending on how GMT is started it will either be running in classic or modern mode. Classic mode is the GMT scripting in use for decades and it will remain the default mode for command-line work. The modern mode invokes simpler rules that eliminate the possibility of the listed rookie errors and simplifies scripting considerably across all interfaces. It also imposes a structure and hence not every single classic script can be represented in modern mode. Consequently, modern mode is less flexible but much easier to use, and we expect it will serve the needs of almost all GMT users. We strongly encourage new users to use the modern mode.

To defeat the rookie errors listed above, here are the features of modern mode:

1. The -O, -K, and P options have been removed.

2. Modules no longer write PostScript to standard output that the users must manage. Instead, they write to hidden temporary files. Checking the status of these files is what allows GMT to know if PostScript should be appended or if we are starting a new plot.

3. The modern mode runs the entire workflow in a unique temporary directory, hence numerous scripts can execute simultaneously without interfering, and we can use the gmt.history information to automatically supply missing regions (-R) and projection (-J) arguments.

4. When the workflow ends, the hidden PostScript files are automatically completed and converted to the chosen graphics format [Default is PDF for command-line work].

5. Page size is now automatically set regardless of size and properly cropped.

Not only does the new rules remove the greatest obstacles to GMT learning, it greatly simplifies scripting by eliminating needless repetition of options and output filenames. The modern mode is activated and deactivated by the new commands gmt begin and gmt end, respectively. Since these are not part of the classic repertoire one cannot accidentally execute a classic mode script in modern mode (or vice versa). We will discuss these two commands later. Finally, there are some new features in GMT that are only accessible under modern mode, such as subplots, new ways to specify the map domain, map insets, perform automatic legend creation and placement, create simpler animations, and to get multiple output formats from the same plot.

The modern mode relies on know what session is being run. If your script is explicitly or inadvertently creating sub-shells under UNIX then the script could fail. If this is the case then you will need to add export GMT_SESSION_NAME=<some unique string> before gmt begin starts the script. This is most easily done by using the gmt --new-script option to print a shell template to the standard output.

## 2.4. Footnotes

[2]

See GNU Lesser General Public License (http://www.gnu.org/copyleft/gpl.html) for terms on redistribution and modifications.

[3]

The tools can be installed on a variety of platforms - UNIX and non-UNIX alike (see Chapter GMT on non-UNIX Platforms).

[4]

One public-domain RIP is ghostscript, available from https://www.ghostscript.com/.

[5]

Programs now also allow for fast, binary multicolumn file i/o.

[6]

While the netCDF format is the default, many other formats are also possible.