Informatique Scientifique GMT For Web

GMT Generalities
Creation de cartes et de gures : GMT

4
Generalities
Sismicity map
Histogram
Seaoor age
Oceanic heat ux
Hawaiian ridge
M.Ulvrova, L.Pouilloux (ENS LYON) Informatique L3 Automne 2011 123 / 177
GMT Generalities
The Generic Mapping Tools
http://gmt.soest.hawaii.edu/
GMT Generalities
GMT - What is it? Why to use it?
GMT : Generic Mapping Tool
developed by Paul Wessel (UH)
and Walter Smith (NOAA) +
voluntaries
rst version in 1987
open source and platform
independent
data processing and manipulation (base sur UNIX tools awk,grep,sed,
etc.)
PostScript visualization
contains more than 60 individual programs
GMT Generalities
GMT users
2005: 10000+ 2011: 15000+
GMT Generalities
Data processing et manipulation
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2009 Oct 07 12:21:37 Example 14 in Cookbook
Filtering data
Gridding xyz data
Arbitrary math operations
Cut/paste grids
Data interpolation
Data extrapolation
GMT Generalities
PostScript Plotting
2D: Plots of points, lines etc.
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Ship and Satellite Gravity
Input Power
Ship
Satellite
Histograms
SOUTH
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10 %
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Topography (m)
Two types of histograms
Vector elds and Contour maps
with labels
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GMT Generalities
PostScript Plotting
Color images from gridded or raw
xyz data
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Text, labels, legend placement
GMT Generalities
PostScript Plotting - Base maps with coastlines, rivers,
and borders
GMT Generalities
Is your GMT installed ?
Tape in the terminal
pscoast
Path conguration - add to your /.bashrc
#gmt variables
export NETCDFHOME=/usr/lib
export GMTHOME=/usr/lib/gmt
export PATH=$PATH:$GMTHOME/bin
source .bashrc
GMT Generalities
Figure Plotting
18 commands for plotting
psxy, psxyz, psbasemap, pscoast, pstext,
cmd [options] > mygure.ps
tape cmd for help
Layering - calling several commands
cmd1 -K > mygure.ps
cmd2 -O -K mygure.ps
cmd3 -O -K mygure.ps
cmd4 -O mygure.ps
K: continue (keep)
O: overlay
GMT Generalities
GMT cake
GMT Generalities
Plotting - continuation
Usual compulsory parameters
-R Region Rw/e/s/n
-J proJection linear/logarithmic, polar, cylindrical, Mollweide,
-B Bound. annot.
pscoast -R-180/180/-89/89 -JW20c -Gblack -P > test.ps
pscoast -R-180/180/-89/89 -JW20c -Gblack -Bg30/g15 -P > test.ps
Useful trick
R=` minmax -I0.01/0.01 `
GMT Generalities
Conguration les
general: /path/to/gmt/gmtdefaults
personal: /.gmtdefaults
gmtdefaults [-D | -L]
changing a parameter: gmtset (e.g. gmtset PAPER MEDIA A4+)
GMT Generalities
Plotting - nishing
Convert ps le to something more useful
ps2raster mygure.ps (convertion to jpg)
ps2raster -Tf mygure.ps (convertion to pdf)
GMT Sismicity map
4
Generalities
Sismicity map
Histogram
Seaoor age
Oceanic heat ux
Hawaiian ridge
GMT Sismicity map
Seismicity the last 7 days
Get your data - USGS
wget http://neic.usgs.gov/neis/gis/bulletin.asc -O
quakes.dat
look at your data le (e.g. with more)
use minmax
Create your executable script
touch make map.sh
chmod u+x make map.sh
Start editing
GMT Sismicity map
Get ready - denitions
Tell that we are going to use bash
#!/bin/bash
Set GMT parameters
gmtset PAPER MEDIA A4+

Use variables
input="quakes.dat"
psfile="map seismicity.ps"
GMT Sismicity map
First step - plot world map with continents: use pscoast
Choose your projection: -Jx0.1cd
x stands for linear projection
0.1c stands for scaling factor in cm
stands for using geographic coordinates

Choose your range: -R-180/180/-89/89
Choose your frame: -B60g30WSne
60 stands for anotation each 60 degree
g30 stands for grid line each 30 degree
WSne stands for anotation on West/South/north/est

Tell to plot shorelines lled with lightgray: -W -Glightgray
Alltogether
pscoast -R-180/180/-89/89 -Jx0.1cd -B60g30WSne -Dc -Glightgray -W -P -K >
$psle
GMT Sismicity map
Processing and plotting data with awk and psxy
awk -F, IF NR>1 {print $4, $3, $5*0.02} $input sed s/,/./g
man awk
psxy -R -J -Gred -Wthin -Sc -O -K $psle
tape psxy for help

Redirecting output from awk as input for psxy
awk -F, { print $4, $3, $5*0.02} $input psxy -R -J -Sc -Gred -Wthin -O -K
$psle
GMT Sismicity map
Finally, plot your position - use echo and psxy
echo 4.825 45.7426 psxy -R -J -Gblue -Wthin -Sa0.9c -O $psle
Dont forget to close your ps le, no -K option!
Convert to pdf
ps2raster -Tf $psle
Tell the world that your map is nished
echo map $psle created
You are nished - run your script
./make map.sh
evince map seismicity.pdf
GMT Sismicity map
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GMT Histogram
4
Generalities
Sismicity map
Histogram
Seaoor age
Oceanic heat ux
Hawaiian ridge
GMT Histogram
Histogram - use pshistogram
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Magnitude
GMT Histogram
Histogram
Prepare your data: awk -F, IF NR>1 {print $?} $inputdata
Examine them: use minmax
Use them as an input for gmt program pshistogram: use pipe
Find parameters for pshistogram
Range -Rxmin/xmax/ymin/ymax
ProJection -JX20c/10c
Boundary -Ba1g1:"Magnitude":/a10f5:"Nb of
earthquaques":WSne
choose bin-Width -W?
-Ggray -Lthin -P
Alltogether
awk -F, IF NR>1 {print $?}$inputdata pshistogram
-Ba1g1:Magnitude:/a10f5:Nb of earthquaques:WSne -R?/?/?/? -JX20c/10c
-Ggray -Lthin -W? -P > $psle
Dont forget to replace question marks !
GMT Seaoor age
4
Generalities
Sismicity map
Histogram
Seaoor age
Oceanic heat ux
Hawaiian ridge
GMT Seaoor age
Seaoor age map
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Seafloor Age [my]
GMT Seaoor age
Seaoor age map
Get your data from EarthByte
use wget or click strategy
http://www.earthbyte.org/Resources/agegrid2008.html
download grids - age
look at README to nd out which data to download and download

them (a simple ASCII le - long, lat, age - is desirable).
unzip your le
bunzip2
bzip2 -d
examine your data
the size (ls -l -h | grep age)
the range (minmax)

wget ftp://ftp.earthbyte.org/earthbyte/agegrid/2008/Grids/age.3.6.xyz.bz2
Data le is big - extract each 10
th
line
$ awk 0==NR % 10 mydatale.xyz > mydatale.xyz.coarse

GMT Seaoor age
Seaoor age map - Lets start
touch make map seafloorage.sh
chmod u+x make map seafloorage.sh
Start editing
General rules to keep in mind when writing a script
comment all you are writing
hash tag #
dene variables
psle=map age seaoor.ps

GMT Seaoor age
Seaoor age map - Get ready - denitions
#!/bin/bash -e
Note the -e option for handling errors

Set GMT parameters

Dene input and output varibles
input="myinputfile.xyz.coarse"
psfile="map age seafloor.ps"

GMT Seaoor age
Seaoor age map - Step by step
Converting an ASCII table to grd le format
xyz2grd
Reading a grdle and making a color palette le
grd2cpt
Creating colored image from a 2-D grd le
grdimage
Plotting land-masses, water-masses, coastlines, borders, and rivers
pscoast
Creating colorscale for your map
psscale
GMT Seaoor age
Seaoor age map
xyz2grd
Mandatory parameters
xyzfile - File holding (x,y,z) values
-G - Dene name of the binary output grdle
-I - Dene grid spacing
-R - Specify the region of interest

Options
-fg - Geographic formating for i/o

xyz2grd $inputdata -R-180/180/-90/90 -I10m/10m -fg -Gage.grd
GMT Seaoor age
Seaoor age map
grd2cpt
grdfile - Grd binary le created with xyz2grd

Options
-C - Select the color table
-I - Inverse the sense of color progression
-Z - Create a continuous color palette

All must be redirected to cpt le
grd2cpt age.grd -Crainbow -Z -I > age.cpt
GMT Seaoor age
Seaoor age map
grdimage
grdfile - Grd binary le created with xyz2grd
-C - Color palette table created with grd2cpt
-J - Select the map projection - Mollweide -JW

Options
-P - Select Portrait plotting mode
-K - Keep open the PostScript le
-Y - Shift origin of plot

All must be redirected to PostScript le
grdimage age.grd -R -JW20c -Cage.cpt -Ya3c -P -K > $psle
GMT Seaoor age
Seaoor age map
pscoast
-J - Select the map projection
-R - Specify the region of interest

Options
-B - Set map boundary tickmark intervals
-G - Color lling for continents
-P - Select Portrait plotting mode
-O - Overlay
-K - Keep open the PostScript le

pscoast -R -J -Bg30/g15 -Gblack -P -O -K $psle
GMT Seaoor age
Seaoor age map
psscale
-D - Dene the position of the center/top and the dimensions of the

scale
Options
-B - Set anotation, tick and gridline interval for the colorbar
-C - Dene cptle that is used for the color palette
-O - Overlay
Its the last step no -K option !
psscale -D10c/-0.5c/20c/0.2ch -B20:Seaoor Age [my]: -Cage.cpt -O $psle
GMT Seaoor age
Seaoor age map - Finishing
Converting your PostScript le into a pdf le
ps2raster -A -Tf $psle
Tell the world that your map was created
echo $psle created
Cleaning
rm -f *.ps
Run your script
./make map seaoorage.sh
GMT Seaoor age
Seaoor age map - coarse data
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Seafloor Age [my]
GMT Seaoor age
Seaoor age map - full data cover
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Seafloor Age [my]
GMT Oceanic heat ux
4
Generalities
Sismicity map
Histogram
Seaoor age
Oceanic heat ux
Hawaiian ridge
GMT Oceanic heat ux
Oceanic heat ow
Lets compute and plot the oceanic heat ow
The heat ux q
q =
490
a is the age of the seaoor in Myr for a 100My
Comes from the theory of half space cooling
For larger ages q is constant and equal to q = 47 mWm

2
GMT Oceanic heat ux
Oceanic heat ow - Step by step
Compute your data - all operations are performed on your grd le
grdmath
Use a color palette le
Will be downloaded
Creating colored image from a 2-D grd le
grdimage
Plotting land-masses, water-masses, coastlines, borders, and rivers
pscoast
Creating colorscale for your map
psscale
GMT Oceanic heat ux
Lets start
touch make hf.sh
chmod u+x make hf.sh
Start editing
#!/bin/bash -e
Set GMT parameters

Use variables
psfile="map heat flux.ps"

GMT Oceanic heat ux
Oceanic heat ow
grdmath
490
a
= 490
1
a
Division
1 age.grd DIV
Square root
SQRT
Multiplication
490 MUL
Is equal to your new grd le
= flux.grd
grdmath 1 age.grd DIV SQRT 490 MUL = ux.grd
GMT Oceanic heat ux
Oceanic heat ow
Download a color palette le - ux.cpt
wget goo.gl/CpvN4
grdimage ux.grd -R-180/180/-90/90 -JW20c -Cux.cpt -Ya3c -P -K
> $psle
pscoast -R -J -Bg30/g15 -Dc -Gblack -P -O -K $psle
psscale -D10c/-0.5c/20c/0.2ch -C -L -B:Heat ux [mW
m@+-2@+]: -Cux.cpt -O $psle
GMT Oceanic heat ux
Oceanic heat ow - Finishing
Convert to pdf
ps2raster -Tf $psle
Run your script and look at results
./make hf.sh
evince map heat ux.pdf
GMT Oceanic heat ux
Oceanic heat ow
47 60 80 100 120 140 220 320 5000
Heat flux [mW m
2
]
GMT Hawaiian ridge
4
Generalities
Sismicity map
Histogram
Seaoor age
Oceanic heat ux
Hawaiian ridge
GMT Hawaiian ridge
3D mesh plot of Hawaiian topography - GMT example
Making complicated images
with GMT - Lets plot 2 layer
perspective plot
First layer - shows a contour

map of the marine geoid
Second layer - shows 3D mesh

plot of the topography
Also, show the position of the

Hawaiian islands
Also, show an arrow pointing

north
Finally, add some text

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Hawaiian Ridge
GMT Hawaiian ridge
Hawaiian ridge - Step by step
Show contours of the geoid
grdcontour
Show Hawaiian islads
pscoast
Show topography in 3D
grdview
Add title for your gure
pstext
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Hawaiian Ridge
GMT Hawaiian ridge
Lets start
Get your data and extract them
wget http://goo.gl/aq1ne
tar -xzf nameofyourdatale.tar.gz

touch make topo.sh
chmod u+x make topo.sh

Start editing
#!/bin/bash -e
psfile="map topo.ps"
GMT Hawaiian ridge
Hawaiian ridge
grdcontour
grdle
-C1 - Contours to be drawn - xed contour interval
-Jm1c - Projection - Mercator

Options
-E60/30 - Set azimuth and elevation of viewpoint
-R195/210/18/25 - Set min/max coordinates of data region
-A4 - Anotation for each fourth contour line
-X2.5c -Y2.5c - X and Y shift of origin of plot
-P - Portrait page orientation
-K - Keep open
grdcontour HI geoid4.nc -Jm1c -E60/30 -R195/210/18/25 -C1 -A4 -G10c
-K -P -X2.5c -Y2.5c > $psle
GMT Hawaiian ridge
Hawaiian ridge
pscoast - Plot Hawaiian islands
You already know . . .
Dont forget to set your viewpoint
Add a north-pointing map rose
-T-151/19.5/2.5c
pscoast -J -R -E60/30 -B2/2NEsw -Gblack -O -K -T-151/19.5/2.5c $psle
GMT Hawaiian ridge
Hawaiian ridge
grdview - Plot topography
topole
-J - Projection
-Jz0.8636c - Set projection in vertical direction
-Czero.cpt - Color palette table

Options
-R195/210/18/25/-6/4 - Set min/max coordinates of data region

Palette table - zero.cpt
echo -10 255 0 255 > zero.cpt
echo 0 100 10 100 zero.cpt
grdview HI topo4.nc -J -Jz0.8636c -Czero.cpt -E60/30 -R195/210/18/25/-6/4
-N-6/lightgray -Qsm -O -K -B2/2/2:Topo (km):neswZ -Y5c $psle
GMT Hawaiian ridge
Hawaiian ridge - Finishing
pstext - Adding title
echo 5 8 40 0.0 6 BC Hawaiian Ridge pstext -R0/10/0/10 -Jx1.5c -O
$psle
Convert to pdf
ps2raster -Tf $psle
Run your script and look at results
./make topo.sh
evince map topo.pdf
GMT Hawaiian ridge
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Hawaiian Ridge

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GMT Generalities

Creation de cartes et de gures : GMT

look at your data le (e.g. with more)

touch make map.sh

chmod u+x make map.sh

gmtset PAPER MEDIA A4+

x stands for linear projection

0.1c stands for scaling factor in cm

stands for using geographic coordinates

60 stands for anotation each 60 degree

g30 stands for grid line each 30 degree

WSne stands for anotation on West/South/north/est

tape psxy for help

choose bin-Width -W?

download grids - age

look at README to nd out which data to download and download

examine your data

the size (ls -l -h | grep age)

the range (minmax)

$ awk 0==NR % 10 mydatale.xyz > mydatale.xyz.coarse

touch make map seafloorage.sh

chmod u+x make map seafloorage.sh

comment all you are writing

psle=map age seaoor.ps

Note the -e option for handling errors

gmtset PAPER MEDIA A4+

psfile="map age seafloor.ps"

xyzfile - File holding (x,y,z) values

-G - Dene name of the binary output grdle

-I - Dene grid spacing

-R - Specify the region of interest

-fg - Geographic formating for i/o

grdfile - Grd binary le created with xyz2grd

-C - Select the color table

-I - Inverse the sense of color progression

-Z - Create a continuous color palette

grdfile - Grd binary le created with xyz2grd

-C - Color palette table created with grd2cpt

-J - Select the map projection - Mollweide -JW

-P - Select Portrait plotting mode

-K - Keep open the PostScript le

-Y - Shift origin of plot

-J - Select the map projection

-R - Specify the region of interest

-B - Set map boundary tickmark intervals

-G - Color lling for continents

-P - Select Portrait plotting mode

-K - Keep open the PostScript le

-D - Dene the position of the center/top and the dimensions of the

-B - Set anotation, tick and gridline interval for the colorbar

-C - Dene cptle that is used for the color palette

a is the age of the seaoor in Myr for a 100My

Comes from the theory of half space cooling

For larger ages q is constant and equal to q = 47 mWm

touch make hf.sh

chmod u+x make hf.sh

gmtset PAPER MEDIA A4+

psfile="map heat flux.ps"

First layer - shows a contour

Second layer - shows 3D mesh

Also, show the position of the

Also, show an arrow pointing

Finally, add some text