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GMT and gridded data sets

• GMT can be used to calculate and display gridded data sets

• A gridded data set is an array of regularly spaced points in space

• You can think of it as a matrix (or as a spreadsheet):

– Rows and columns correspond to y and x axis (for instance latitude
and longitude)

– The value in each cell represents the measured quantify (for

instance elevation)

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GMT and gridded data sets

• Gridded data sets in GMT are stored in net-CDF format: a binary
format with a header followed by the data

• grdinfo allows you to check the contents of a GMT grid file

• Download etopo5.grd from the class web site and type grdinfo
etopo5.grd to get:
etopo5.grd: Title: TOPO world
etopo5.grd: Command: grdmath etopo5.grd 1000 x = etopo5km.grd
etopo5.grd: Remark:
etopo5.grd: Normal node registration used
etopo5.grd: grdfile format # 0
etopo5.grd: x_min: 0 x_max: 360 x_inc: 0.0833333 units: degree nx: 4321
etopo5.grd: y_min: -90 y_max: 90 y_inc: 0.0833333 units: degree ny: 2161
etopo5.grd: z_min: -10741 z_max: 7833 units: km
etopo5.grd: scale_factor: 1 add_offset: 0

• This file contains the world topography and bathymetry with a grid step
of 5 minutes (about 10 km)
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Contouring gridded data sets

• Gridded data sets can be displayed as contour maps
• For instance:
grdcontour etopo5.grd -R0/360/-70/70 -JM7i \
-C500 -P -B30 > etopo5_cont.ps

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Contouring gridded data sets

Other contouring options:

• Annotate contours with -A2000 (every 2000 unit)

• Add smoothing with -S4

• Tick highs and lows with -T

• Skip small features with -Q100 (skip if contour defined by less than
100 points)

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Contouring gridded data sets

Customize your contours:
• Create a contour file (cont.lev), with for instance the following 5
contour levels (note that contour 0 will be annotated):
-8000 C
-3000 C
-2000 C
0 A
3000 C

• Use -Ccont.lev to plot those contours:

grdcontour etopo5.grd -R0/360/-70/70 -JM7i \
-Ccont.lev -P -B30 > etopo5_cont.ps

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Contouring gridded data sets

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Color image of gridded data sets
• Before you can display your gridded data set as a color image, you
need to creat a color map = a table that links your data range (e.g.,
elevation) with colors

• There are two ways to create a color map:

– makecpt -Ctopo -T-12000/8000/2000 -Z > etopo5.cpt
-12000 201 119 217 -10000 201 119 217
-10000 138 162 230 -8000 138 162 230
-8000 138 243 207 -6000 138 243 207
-6000 189 243 133 -4000 189 243 133
-4000 240 176 134 -2000 240 176 134
-2000 116 163 179 0 116 163 179
0 220 214 142 2000 220 214 142
2000 246 232 202 4000 246 232 202
4000 255 249 245 6000 255 249 245
6000 255 252 250 8000 255 252 250
B 236 140 255
F 255 255 255
N 128 128 128

– grd2cpt etopo5.grd -Cglobe -Z > etopo5.cpt

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Color image of gridded data sets

Once you have a color map (etopo5.cpt), plot the image with
grdimage:
grdimage etopo5.grd -R0/360/-70/70 -JM7i \
-Cetopo5.cpt -P -B30 > etopo5_map.ps

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Add illumination
• Illumination (= shading) can be added to the color image

• But a grd file that contains the illumination data must be created first

• Illumination will be a function of the spatial gradient of the elevation in

the direction of illumination ⇒ use grdgradient

• Then illumination needs to be normalized between -1 and +1 ⇒ use

grdhisteq and grdmath
• The recipe is:
grdgradient etopo5.grd -A300 -Getopo5.grad -Nt
grdhisteq etopo5.grad -Getopo5.hist -N
grdinfo etopo5.hist
grdmath etopo5.hist 4.41977 / = etopo5.norm

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Add illumination
Add illumination with -I:
grdimage etopo5.grd -Ietopo5.norm -R0/360/-70/70 \
-JM7i -Cetopo5.cpt -P -B30 > etopo5_map.ps

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Try different color maps

Download rob2.cpt from the class web site and produce:

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Try different color maps

Download myglobe.cpt from the class web site and produce:

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Global Digital Elevation Models
• ETOPO5: global bathymetry and topography, grid spacing = 5 minutes
(about 10 km)

• GTOPO30: global topography only

– Horizontal grid spacing = 30 arc seconds (approximately 1 km).

– http://edcdaac.usgs.gov/gtopo30/gtopo30.html

• SRTM: global topography only

– Horizontal grid spacing = 1 arc second (30 m) for continental U.S.,
3 arc seconds (90 m) for rest of the world

– http://www2.jpl.nasa.gov/srtm/

– http://edc.usgs.gov/products/elevation.html

– http://edcsgs9.cr.usgs.gov/pub/data/srtm/
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Global Digital Elevation Models

• Log on to
http://edcdaac.usgs.gov/gtopo30/gtopo30.html

• Download north-east Africa: E020N40.tar.gz

• Uncompress with gunzip E020N40.tar.gz

• Untar with tar xvf E020N40.tar

• Keep E020N40.DEM but delete E020N40.tar and the all other

archive files (to save space)

• Reminder: to monitor your disk quota: quota -v username

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Converting a DEM into GMT grd format
• Most DEMs do not come in GMT format: they need to be converted
into netCDF format before they can be used and displayed with GMT

• grdraster performs this conversion from any binary format to

netCDF

• grdraster reads a file called grdraster.info that describes

the format of the file to be converted

• By default, GMT looks for grdraster.info in directory

$GMTHOME/share/dbase
• If you do not have write permissions in $GMTHOME/share/dbase
(which is most likely), then you need to set an environement variable to
the directory that contain your grdraster.info file:
setenv GMT_GRIDDIR my_directory
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Converting a DEM into GMT grd format

• grdraster.info file contains one line per file to be converted, for
instance:
17 "GTOPO30 NE AFRICA" "m" -R20/60/-10/40 -I0.5m P i 1 0 -9999 E020N40.DEM B
18 "SRTM LEVEL 3" "m" -R38/39/7/8 -I3c G i 1 0 -9999 N07E038.hgt B

• Format of grdraster.info is (for file 17):

– 17 = file number
– GTOPO30 NE AFRICA = comment
– m = unit (meters)
– -R20/60/-10/40 = boundaries of binary data file
– -I0.5m = horizontal sampling in binary file
– P/G = pixel versus grid registration
– 1 = scale to apply to binary file in conversion
– 0 = offset to apply to binary file in conversion
– -9999 = values to use if data is NaN
– E020N40.DEM = binary file name
– B/L = big/little endian computer

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Converting a DEM into GMT grd format

• Convert E020N40.DEM into GMT format using:

grdraster 17 -R20/60/-10/40 -Gne_africa.grd

• To produce a smaller file, center on the Afar depression:

grdcut ne_africa.grd -Gne_africa_sub.grd -R40/44/10/13

• Or directly from the grdraster command:

grdraster 17 -R40/44/10/13 -Gne_africa_sub.grd

• Then plot:
grdimage ne_africa_sub.grd -Ine_africa_sub.norm -R40/44/10/13
-JM7i -Cmyglobe.cpt -P -B1 > ne_africa_sub.ps

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It starts to show pixels...

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More on displaying gridded files
Let’s resample the grd files every 0.1 minutes:
grdsample ne_africa_sub.grd -Gne_africa_sub_resampled.grd -I0.1m
grdsample ne_africa_sub.norm -Gne_africa_sub_resampled.norm -I0.1m
grdimage ne_africa_sub_resampled.grd -Ine_africa_sub_resampled.norm \
-R40/44/10/13 -JM7i -Cmyglobe.cpt -P -B1 > ne_africa_sub.ps

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Merging bathymetry and topography from different

files
• Plot bathymetry first:
grdimage -R35/60/0/20 -JM7i etopo5.grd -Cmyglobe.cpt -P -K -Y1.5 >! all.ps

• Cut the topography grid over land:

pscoast -R -JM -Dh -Gc -K -O >> all.ps
grdimage -R -JM ne_africa.grd -Cmyglobe.cpt -K -O >> all.ps
pscoast -Q -O -K >> all.ps

• Plot coastlines:
pscoast -R -JM -B5 -Di -W2/0 -A100 -O -K >> all.ps

• Note that your could grdcut etopo5.grd and resample the resulting
file at a higher resolution with grdsample
• Add a color scale:
psscale -D3.5/-0.5/7/0.15h -Ba1000:Elevation:/:m: -Cmyglobe.cpt -O >> all.ps

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Grid files in 3D
• First, let’s cut the large etopo grid into a smaller subset:
grdcut etopo5.grd -R-76/-55/9/23 -Gnecar.grd
grdcut etopo5.norm -R-76/-55/9/23 -Gnecar.norm

• Then, let’s use grdview to plot:

grdview necar.grd -JM8.5i -Cmyglobe.cpt -Qs -JZ1i
-E70/20 -Wc -B1a2 -Inecar.norm > necar.ps
– -Qm/s/i: plot mesh, surface, or image

– -JZ: vertical scale

– -E: view point azimuth/elevation

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A 3D view of the NE Caribbean plate boundary

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