Generic Mapping Tools (GMT)

The Basics plus Plotting in X-Y Space

Goal – make scientific

illustrations

“Generic” is generic to the earth sciences community

MapsColor/bw/shaded topography and

bathymetry, point data (earthquakes, seismic or gps stations, etc.), line data (faults, eq rupture zones, roads), vector fields w/ error ellipses, focal mechanisms

3D surfaceCross sections

What is GMTGMT is an open source collection of ~60 tools

for manipulating geographic and Cartesian data sets (including filtering, trend fitting, gridding, projecting, etc.)

What is GMT

Produces PostScript File (PS) illustrations ranging from simple x-y plots via contour maps to artificially illuminated surfaces and 3-D perspective views

What is GMT

GMT supports ~30 map projections and transformations and comes with support data such as GSHHS coastlines, rivers, and political boundaries

If it does not have a map projection you want: it is open source and UNIX. (i.e. you can do it yourself)

Design PhilosophyFollows 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.

Design Philosophy

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

(4) the programs can be chained together in shell scripts or with pipes, thereby creating a process tailored to do a user-specific task

Maintained by Paul Wessel and Walter Smith (now at the University of Hawaii and NOAA respectively)

The GMT homepage is: gmt.soest.hawaii.edu

GMT documentation Tutorial

Technical Reference and Cookbook (aka Manual)

both available on web (http://gmt.soest.hawaii.edu/) as HTML on line, PDF, PostScript

GMT documentationUNIX “man” pages – available on web

and also as standard man pages on local installation.

Entering GMT program/filter name all by itself, or certain errors in command specification (switches, not data) – dumps man page to standard error.

What does/can GMT do?Filtering 1-D and 2-D data

simple processing GMT is NOT a general Number

Cruncher output is reprocessed data

What does/can GMT do?Plotting 1-D and 2-D data

points, lines (symbols, fill, geologic symbols on faults, etc.)

vector fields2-D images – grayscale and color,

illumination3-D perspective of 2-D images histograms, rose diagramstextfocal mechanism beachballs

What does/can GMT do?Data preparation

gridding, resampling, conversionContouringdata base: extraction, mergecross sectionsprojection/map transformation (map sphere to plane)

output is reprocessed data

Bookkeeping and bunch of other stuff

GMT Output1-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.

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. Such text is written to the standard error stream

GMT OutputPostScript – The plotting programs all use the

PostScript page description language to define plots. These commands are stored as ASCII text.

If you are really ambitious, you can directly edit this file using vim…but in general, don’t.

Postscript is directly translated by line printers, Adobe Illustrator/Photoshop, ghostscript, ghostview.

I frequently use Illustrator to edit raw Postscript prior to using figures in papers, presentations, or posters

output is “PostScript” program– generally ascii text, but not too readable. (GMT files can get amazingly BIG)% Map boundaries%S 1050 1050 1050 0 360 arc SS 1050 1050 1074 0 360 arc SS 24 WS 1050 1050 1062 -135 -90 arc SS 1050 1050 1062 135 180 arc SS 1050 1050 1062 45 90 arc SS 1050 1050 1062 -45 0 arc SS 1050 1050 1062 -90 -90 arcn SS 2 WS [] 0 B%% End of basemap%S [] 0 B%%Trailer%%BoundingBox: 0 0 647 647% Reset translations and scale and call showpageS -295 -295 T 4.16667 4.16667 scale 0 Ashowpage

Installation/Maintenance • Done for us by Mitch – THANKS.• Somewhat complicated, not for average user but can be installed on laptops

• Setup – basic setup done for us (don’t have to define GMTHOME, path, etc. if use standard CERI .login and .cshrc files)

Installation/Maintenance• Some common data sets (GTOPO-30, ETOPO-5, Predicted bathy, etc.) are installed

• “.gmtdefaults” (generic, is .gmtdefaults4 for version 4) file in your home or working directory.• if you’ve copied something from the tutorial or gotten a script from

someone else and it comes out “funny”, the “default” settings may be the culprit.

Easiest way to get started

• Find system with GMT already set up• Get working program (shell script) from

someone else and modify (hack) it.• Lots examples in

• Tutorial• available on www• available from your friends

Sources of operational parameters/job control

• command line options/switches or program defaults

• carried over from execution of previous commands

• from your .gmtdefaults file • (first in working directory if exists, if ~exist, then in your

home directory if exists, finally, system/program defaults)

Sources of operational parameters/job control

Why a defaults file?

- too many parameters to require setting all explicitly (powerful)

- customize – can have different defaults in different directories

Basic GMT useMost GMT programs read input from

terminal (stdin) or files, and write output to terminal (stdout) (a few write to files).

To write output to files one can use UNIX redirection:

GMTprogram switches >! outputfileGMTprogram input-file switches >! outputfile

Basic GMT useSome GMT programs will accept

input-file names, pipes and input redirection in lieu of stdin

GMTprogram switches < input-file >> outputfile

Someprogram | GMTprogram1 | GMTprogram2 >> outputfile

Basic GMT useSome GMT programs will accept in-

line input – reads whatever follows -- up to character string XXX -- as input.

GMTprogram switches << END >> output-file

.1 .1

.2 .2

END

Basic GMT useCan also do with “command

substitution”:

GMTprogram switches << FIN >> output-file `someprogram swithches < input-file…`FIN

Some GMT programs require input-file names (usually if need more than one input file)

GMT and scriptsGMT commands, once installed, act much like

regular Unix commands.

Generally, the commands are enacted within a shell script so that they may be combined with other unix commands such as awk.

Bash and csh are the most commonly encountered in academia and passing down GMT scripts is how much seismology gets illustrated

Use Comments!Comments are very popular to ignore but if you

don’t comment your script, 2 years later you may not remember what you were doing.

The spaces and blank lines make your script readable. While it may take more paper if you print it, it only takes two bytes to make new line or a space.

Example 1: PLOTTING in X-Y Space

psbasemap: Create a basemap framepsxy: Plot symbols, polygons, and lines in 2-Dsample1d: Resampling of 1-D table data sets

1) We start by making the basemap frame for a linear x-y plot that should be 5 by 3 inches in size. The –J option selects the type of projection (there are 25 potential projections). X is linear projection.

psbasemap –JX5i/3i

2) We want it to go from 0 to 100 in x and from 0 to 10 in y. Specified by the REGION (-R) option, which (in the usual form) is

psbasemap -R0/100/0/10 –JX5i/3i

3) The plot should annotated every 20 in x and every 2 in y with annotation on the lower and right axes only. This is specified by the –B option (Border).

psbasemap -R0/100/0/10 –JX5i/3i \-Ba20g10/a2f1g2WSne

a is for annotation spacing, 20 for x and 2 for y

g is for grid spacing, 10 for x and 2 for y

f is for frame, controlling the minor tick spacing in y only

4) The plot should be on portrait oriented paper (default is landscape)

psbasemap -R0/100/0/10 –JX5i/3i -B10/2nSeW –P

5) Since we will be adding more GMT script, we need to indicate this using the –K switch

psbasemap -R0/100/0/10 –JX5i/3i -B10/2nSeW –K –P

6) We can also specify exactly where on the page to place the plot

psbasemap -R0/100/0/10 –JX5i/3i -B10/2nSeW \ –X2 –Y14 –K –P >! plot.ps

7) Create a dataset of numbers from 0 to 100, every 1 point, and use awk to calculate the square root of each pointsample1d -I1 << END |\nawk '{print $1, sqrt($1)}' > input.dat0100END

8a) Read in the new dataset and plot a line. Use the –O flag to specify that this will be overlain within the boundaries of the previous gmt commandpsxy input.dat –R –JX -K –O >> plot.ps

8b) Use the –W flag to specify the linepsxy input.dat –R –JX -W5t15_15 -K –O >> plot.ps

The –W command can be quite complicated. In this example, the first 5 represents line width, the t signifies a dashed line, the 15_15 specifies the dash and space width

More simply, -W1/0 is more common. This is a 1 pt solid line width in black. Or use –W5/255/0/0 which is a solid line, width of 5, color red.

9a) Overlay red triangles with green outlines on every 10 data points. -S flag specifies using symbols with the t representing a triangle. When the –S flag is used, -W becomes the line around the symbol. -G controls the color of the symbol.

sample1d input.dat -I10 |\psxy -R –JX -St0.2 -G255/0/0 -W5/0/255/0 -O >> plot.ps

9b) Where is the –K???

Because this is the last line of our script, the –K flag is left off.

sample1d input.dat -I10 |\psxy -R –JX -St0.2 -G255/0/0 -W5/0/255/0 -O >> plot.ps

Several common “gotchas” • no showpage (can see on screen, but does not print – actually prints a blank page) (have a –K in last GMT call)

• showpage in middle of file (forgot the –K somewhere) – only get part of file on screen or in final print or get ghostscript error message.

• Have header in middle of file (forgot –O somewhere), get ghostscript error message.

There are two other non-map-projected forms

1) Logarithmic - add l (lower case letter L) after scale of axis you want logarithmic

-JX4l/2

2) Power/exponential – add p and exponent after scale of axis you want

exponential (can scale axes individually)-JX4p0.5/2

GMT ColorsColor is specified using Red/Green/Blue (RGB),

HSV or Grayscale color

Grayscale: WHITE=255LTGRAY=192VLTGRAY=225EXTGRAY=250GRAY=128BLACK=0

RGB: RED=250/0/0DKRED=196/50/50BLUE=0/0/255

GREEN=0/255/0

YELLOW=255/255/50ORANGE=255/192/50PURPLE=255/50/255CYAN=50/255/255LTBLUE=192/192/250VLTBLUE=225/250/250LTRED=250/225/225PINK=255/225/255BROWN=160/64/32