Informatique scientifique - ENS Lyon

GMT Generalities

Creation de cartes et de figures : GMT

4 Creation de cartes et de figures : GMTGeneralitiesSismicity mapHistogramSeafloor ageOceanic heat fluxHawaiian 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

first version in 1987

open source and platformindependent

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

0

2

4

6

0 2 4 6

0 2 4 6

870793

755690 800

800730

728

710780

804

855

830813

762

765 740 765760

790820

855

812 773

812

827 805

840

890

820

873875

873865 841

862 908

855850

882 910

940915

890

880

870

880

960

890

860

830

705

0 2 4 6

0 2 4 6

870793

755

710

697.5

780

800

781

729

760

804

855

830813

783.333

740

788.5

790820

855

820

827 805 835

890

873853

864862.5

915

871

908

960

896

940

890

870

880

890

860

800

850

0

2

4

6

0 2 4 6

750

800

850

900

0 2 4 6

800

850

900

950

1000

0 1 2 3 4 5 6 7 8 9 10

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.


0.00

0.25

0.50

0.75

1.00

Co

he

ren

cy2

100101102103

Wavelength (km)

Coherency2

10-1

100

101

102

103

104

Po

we

r (m

Ga

l2km

)

100101102103

Ship and Satellite Gravity

Input Power

Ship

Satellite

Histograms


SOUTH0.2

EASTWEST

NORTH

0 %

10 %

20 %

30 %

Fre

quency

-6000 -4000 -2000 0

Topography (m)

Two types of histograms

Vector fields and Contour mapswith labels


0 0

0.5

0.5

-2

-1

0

1

2

-2 -1 0 1 2

-0.2

-0.2

-0.2

-0.2

0

0

0.2

0.2

0.20.2

-2

-1

0

1

2

-2 -1 0 1 2

-0.4

-0.3

-0.2

-0.2

-0.1

-0.1

-0.1

0

0.1

0.1

0.1

0.2

0.2

0.3

0.4

-2

-1

0

1

2

-2 -1 0 1 2

-2

-1

0

1

2

-2 -1 0 1 2

z(x,y) = x * exp(-x2-y2)


GMT Generalities

PostScript Plotting

Color images from gridded or rawxyz data

0

1

0 1

0

1

0 1

0.0

0.5

1.0

Te

mp

era

ture

t =.0527

Multiple images

0

1

0 10

1

0 10

1

0 1

0

1

0 10

1

0 1

0.0

0.5

1.0

T

0.00

0.05

∆T

0

2

4

6

8

10

log

10η

(a) (b)

(c) (d) (e)

Text, labels, legend placement


GMT Generalities

PostScript Plotting - Base maps with coastlines, rivers,and borders


GMT Generalities

Is your GMT installed ?

Tape in the terminalpscoast

Path configuration - add to your ∼/.bashrc

#gmt variablesexport NETCDFHOME=/usr/libexport GMTHOME=/usr/lib/gmtexport PATH=$PATH:$GMTHOME/bin

source .bashrc


GMT Generalities

Figure Plotting

18 commands for plotting

psxy, psxyz, psbasemap, pscoast, pstext, · · ·

cmd [options] > myfigure.pstape cmd for help

Layering - calling several commands

cmd1 -K > myfigure.pscmd2 -O -K � myfigure.pscmd3 -O -K � myfigure.pscmd4 -O � myfigure.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.pspscoast -R-180/180/-89/89 -JW20c -Gblack -Bg30/g15 -P > test.ps

Useful trick

R=` minmax -I0.01/0.01 `


GMT Generalities

Configuration files

general: /path/to/gmt/gmtdefaults

personal: ∼/.gmtdefaults

gmtdefaults [-D | -L]

changing a parameter: gmtset (e.g. gmtset PAPER MEDIA A4+)


GMT Generalities

Plotting - finishing

Convert ps file to something more useful

ps2raster myfigure.ps (convertion to jpg)ps2raster -Tf myfigure.ps (convertion to pdf)


GMT Sismicity map




GMT Sismicity map

Seismicity the last 7 days

Get your data - USGSwget http://neic.usgs.gov/neis/gis/bulletin.asc -Oquakes.dat

I look at your data file (e.g. with more)I use minmax

Create your executable scriptI touch make map.shI chmod u+x make map.shI Start editing


GMT Sismicity map


Get ready - definitions

Tell that we are going to use bashI #!/bin/bash

Set GMT parametersI gmtset PAPER MEDIA A4+

Use variablesI input="quakes.dat"I psfile="map seismicity.ps"


GMT Sismicity map


First step - plot world map with continents: use pscoast

Choose your projection: -Jx0.1cdI x stands for linear projectionI 0.1c stands for scaling factor in cmI stands for using geographic coordinates

Choose your range: -R-180/180/-89/89

Choose your frame: -B60g30WSneI 60 stands for anotation each 60 degreeI g30 stands for grid line each 30 degreeI WSne stands for anotation on West/South/north/est

Tell to plot shorelines filled with lightgray: -W -Glightgray

Alltogether

pscoast -R-180/180/-89/89 -Jx0.1cd -B60g30WSne -Dc -Glightgray -W -P -K >

$psfile


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’I man awk

psxy -R -J -Gred -Wthin -Sc -O -K � $psfileI tape psxy for help

Redirecting output from awk as input for psxy

awk -F, ’{ print $4, $3, $5*0.02}’ $input psxy -R -J -Sc -Gred -Wthin -O -K �$psfile


GMT Sismicity map


Finally, plot your position - use echo and psxy

echo ”4.825 45.7426” psxy -R -J -Gblue -Wthin -Sa0.9c -O � $psfile

Don’t forget to close your ps file, no -K option!

Convert to pdf

ps2raster -Tf $psfile

Tell the world that your map is finished

echo map $psfile created

You are finished - run your script

./make map.sh

evince map seismicity.pdf


GMT Sismicity map


−180˚ −120˚ −60˚ 0˚ 60˚ 120˚ 180˚

−60˚

0˚

60˚


GMT Histogram




GMT Histogram

Histogram - use pshistogram

0

10

20

30

40

50

60

Nb o

f eart

hquaques

1 2 3 4 5 6 7

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 pshistogramI Range -Rxmin/xmax/ymin/ymaxI ProJection -JX20c/10cI Boundary -Ba1g1:"Magnitude":/a10f5:"Nb of

earthquaques":WSneI choose bin-Width -W?I -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 > $psfile

Don’t forget to replace question marks !M.Ulvrova, L.Pouilloux (ENS LYON) Informatique L3 Automne 2011 146 / 177

GMT Seafloor age




GMT Seafloor age

Seafloor age map

0 20 40 60 80 100 120 140 160 180 200 220 240 260

Seafloor Age [my]


GMT Seafloor age

Seafloor age map

Get your data from EarthByteuse wget or click strategy

I http://www.earthbyte.org/Resources/agegrid2008.htmlI download grids - ageI look at README to find out which data to download and download

them (a simple ASCII file - long, lat, age - is desirable).I unzip your file

F bunzip2F bzip2 -d

I examine your dataF the size (ls -l -h | grep age)F the range (minmax)

wget ftp://ftp.earthbyte.org/earthbyte/agegrid/2008/Grids/age.3.6.xyz.bz2

Data file is big - extract each 10th lineI $ awk ’0==NR % 10’ mydatafile.xyz > mydatafile.xyz.coarse


GMT Seafloor age

Seafloor age map - Let’s start

Create your executable scriptI touch make map seafloorage.shI chmod u+x make map seafloorage.shI Start editing

General rules to keep in mind when writing a scriptI comment all you are writing

F hash tag #

I define variablesF psfile=’map age seafloor.ps’


GMT Seafloor age

Seafloor age map - Get ready - definitions

Tell that we are going to use bashI #!/bin/bash -eI Note the -e option for handling errors


Define input and output variblesI input="myinputfile.xyz.coarse"I psfile="map age seafloor.ps"


GMT Seafloor age

Seafloor age map - Step by step

Converting an ASCII table to grd file formatI xyz2grd

Reading a grdfile and making a color palette fileI grd2cpt

Creating colored image from a 2-D grd fileI grdimage

Plotting land-masses, water-masses, coastlines, borders, and riversI pscoast

Creating colorscale for your mapI psscale


GMT Seafloor age

Seafloor age map

xyz2grd

Mandatory parametersI xyzfile - File holding (x,y,z) valuesI -G - Define name of the binary output grdfileI -I - Define grid spacingI -R - Specify the region of interest

OptionsI -fg - Geographic formating for i/o

xyz2grd $inputdata -R-180/180/-90/90 -I10m/10m -fg -Gage.grd


GMT Seafloor age

Seafloor age map

grd2cpt

Mandatory parametersI grdfile - Grd binary file created with xyz2grd

OptionsI -C - Select the color tableI -I - Inverse the sense of color progressionI -Z - Create a continuous color palette

All must be redirected to cpt file

grd2cpt age.grd -Crainbow -Z -I > age.cpt


GMT Seafloor age

Seafloor age map

grdimage

Mandatory parametersI grdfile - Grd binary file created with xyz2grdI -C - Color palette table created with grd2cptI -J - Select the map projection - Mollweide -JW

OptionsI -P - Select Portrait plotting modeI -K - Keep open the PostScript fileI -Y - Shift origin of plot

All must be redirected to PostScript file

grdimage age.grd -R -JW20c -Cage.cpt -Ya3c -P -K > $psfile


GMT Seafloor age

Seafloor age map

pscoast

Mandatory parametersI -J - Select the map projectionI -R - Specify the region of interest

OptionsI -B - Set map boundary tickmark intervalsI -G - Color filling for continentsI -P - Select Portrait plotting modeI -O - OverlayI -K - Keep open the PostScript file


pscoast -R -J -Bg30/g15 -Gblack -P -O -K � $psfile


GMT Seafloor age

Seafloor age map

psscale

Mandatory parametersI -D - Define the position of the center/top and the dimensions of the

scale

OptionsI -B - Set anotation, tick and gridline interval for the colorbarI -C - Define cptfile that is used for the color paletteI -O - Overlay


It’s the last step ⇒ no -K option !

psscale -D10c/-0.5c/20c/0.2ch -B20:”Seafloor Age [my]”: -Cage.cpt -O � $psfile


GMT Seafloor age

Seafloor age map - Finishing

Converting your PostScript file into a pdf file

ps2raster -A -Tf $psfile

Tell the world that your map was created

echo $psfile created

Cleaning

rm -f *.ps

Run your script

./make map seafloorage.sh


GMT Seafloor age

Seafloor age map - coarse data

0 20 40 60 80 100 120 140 160 180 200 220 240 260 280

Seafloor Age [my]


GMT Seafloor age

Seafloor age map - full data cover

0 20 40 60 80 100 120 140 160 180 200 220 240 260

Seafloor Age [my]


GMT Oceanic heat flux





Oceanic heat flow

Let’s compute and plot the oceanic heat flow

The heat flux q

q =490√

a

I a is the age of the seafloor in Myr for a ≤ 100MyI Comes from the theory of half space coolingI For larger ages q is constant and equal to q = 47 mWm−2



Oceanic heat flow - Step by step

Compute your data - all operations are performed on your grd fileI grdmath

Use a color palette fileI Will be downloaded

Creating colored image from a 2-D grd fileI grdimage

Plotting land-masses, water-masses, coastlines, borders, and riversI pscoast

Creating colorscale for your mapI psscale



Let’s start

Create your executable scriptI touch make hf.shI chmod u+x make hf.shI Start editing

Tell that we are going to use bashI #!/bin/bash -e


Use variablesI psfile="map heat flux.ps"



Oceanic heat flow

grdmath

490√a

= 490

(√(1

a

))

DivisionI 1 age.grd DIV

Square rootI SQRT

MultiplicationI 490 MUL

Is equal to your new grd fileI = flux.grd

grdmath 1 age.grd DIV SQRT 490 MUL = flux.grd



Oceanic heat flow

Download a color palette file - flux.cpt

wget goo.gl/CpvN4

grdimage flux.grd -R-180/180/-90/90 -JW20c -Cflux.cpt -Ya3c -P -K> $psfile

pscoast -R -J -Bg30/g15 -Dc -Gblack -P -O -K � $psfile

psscale -D10c/-0.5c/20c/0.2ch -C -L -B:”Heat flux [mWm@+-2@+]”: -Cflux.cpt -O � $psfile



Oceanic heat flow - Finishing

Convert to pdf




Run your script and look at results

./make hf.sh

evince map heat flux.pdf



Oceanic heat flow

47 60 80 100 120 140 220 320 5000

Heat flux [mW m−2]


GMT Hawaiian ridge




GMT Hawaiian ridge

3D mesh plot of Hawaiian topography - GMT example

Making complicated imageswith GMT - Let’s plot 2 layerperspective plot

I First layer - shows a contourmap of the marine geoid

I Second layer - shows 3D meshplot of the topography

I Also, show the position of theHawaiian islands

I Also, show an arrow pointingnorth

I Finally, add some text

0

0

4

4

4

8

8

12

12

−164˚

−162˚

−160˚

−158˚

−156˚

−154˚

−152˚

−150˚

18˚

20˚

22˚

24˚

N

−4

−2

02

4

Topo (

km

)

Hawaiian Ridge


GMT Hawaiian ridge

Hawaiian ridge - Step by step

Show contours of the geoidI grdcontour

Show Hawaiian isladsI pscoast

Show topography in 3DI grdview

Add title for your figureI pstext

0

0

4

4

4

8

8

12

12

−164˚

−162˚

−160˚

−158˚

−156˚

−154˚

−152˚

−150˚

18˚

20˚

22˚

24˚

N

−4

−2

02

4

Topo (

km

)

Hawaiian Ridge


GMT Hawaiian ridge

Let’s start

Get your data and extract themI wget http://goo.gl/aq1neI tar -xzf nameofyourdatafile.tar.gz

Create your executable scriptI touch make topo.shI chmod u+x make topo.sh

Start editingI #!/bin/bash -eI gmtset PAPER MEDIA A4+I psfile="map topo.ps"


GMT Hawaiian ridge

Hawaiian ridge

grdcontour

Mandatory parametersI grdfileI -C1 - Contours to be drawn - fixed contour intervalI -Jm1c - Projection - Mercator

OptionsI -E60/30 - Set azimuth and elevation of viewpointI -R195/210/18/25 - Set min/max coordinates of data regionI -A4 - Anotation for each fourth contour lineI -X2.5c -Y2.5c - X and Y shift of origin of plotI -P - Portrait page orientationI -K - Keep open


grdcontour HI geoid4.nc -Jm1c -E60/30 -R195/210/18/25 -C1 -A4 -G10c-K -P -X2.5c -Y2.5c > $psfile


GMT Hawaiian ridge

Hawaiian ridge

pscoast - Plot Hawaiian islands

You already know . . .

Don’t forget to set your viewpoint

Add a north-pointing map roseI -T-151/19.5/2.5c

pscoast -J -R -E60/30 -B2/2NEsw -Gblack -O -K -T-151/19.5/2.5c � $psfile


GMT Hawaiian ridge

Hawaiian ridge

grdview - Plot topography

Mandatory parametersI topofileI -J - ProjectionI -Jz0.8636c - Set projection in vertical directionI -Czero.cpt - Color palette table

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

Palette table - zero.cpt

echo ’-10 255 0 255’ > zero.cptecho ’ 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 � $psfile


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� $psfile

Convert to pdf




Run your script and look at results

./make topo.sh

evince map topo.pdf


GMT Hawaiian ridge

00

4

4

4

8

8

1212

−164˚

−162˚

−160˚

−158˚

−156˚

−154˚

−152˚

−150˚

18˚

20˚

22˚

24˚

N

−4

−2

02

4

Topo (

km

)

Hawaiian Ridge


Informatique scientifique - ENS Lyon

Documents

Transcript of Informatique scientifique - ENS Lyon