Marine Science

this page is a work in progress

Tools for marine scientists

Bathymetry processing

Please expand

• Basic DEM creation: v.in.ascii + v.surf.rst
• r.in.xyz for processing multibeam sonar swaths
• r.surf.nnbathy add-on script for creating bathymetic DEMs from input x,y,z data

Bathymetric data

• See the Global datasets wiki page for more datasets (ETOPO, GEBCO, etc.)

• Smith and Sandwell 1-minute global elevation v10.1, May 13, 2008

http://topex.ucsd.edu/marine_topo/mar_topo.html (712mb)

global_topo_1min/README_V10.1.txt file:

Version 9.1 has a very different FORMAT than V8.2
The main differences are that the grid spacing in 
longitude is now 1 minute rather than 2 minutes.
In addition, the latitude range is increased to 
+/- 80.738.  Like the old versions, the elevation(+)
and depth(-) are stored as 2-byte integers to the nearest meter.
An odd depth of say -2001m signifies that this pixel was constrained
by a real depth sounding while an even depth of say -2000m is
a predicted depth.

Here are the parameters for the old and new versions:
param    V8.2     V9.2
___________________________
nlon     10800    21600
nlat     12672    17280
rlt0   -72.006  -80.738
rltf    72.006   80.738
___________________________

The binary format of the integers is bigendian so the bytes need to be 
swapped if you are running on an Intel processor.
Here is a typical command for swapping bytes:
dd if=topo_9.1.img of=topo_9.1.img.swab bs=21600 conv=swab.

• GMT's img2grd + grd2xyz shows FP elevation values to the nearest cm not meter. Are these from contributed datasets? How does that fit with the odd/even real/interpolated soundings?

Import using GMT

• see also the GRASS and GMT wiki page.

Process with GMT's img2grd to convert from spherical Mercator projection to geographic coordinates, then import into GRASS

http://osdir.com/ml/gis.gmt.user/2005-04/msg00087.html

 img2grd topo_10.1.img -T1 -S1 -V -R0/360/-80.738/80.738 -m1 -D -Gtopo_all.grd
 # (out of memory, needs 1.4gb)
 # try just for NZ   (W/E/S/N bounds)
 REGION=160/180/-50/-30
 img2grd topo_10.1.img -T1 -S1 -V -R"$REGION" -m1 -D -Gtopo_NZ.grd
 grd2xyz topo_NZ.grd -S > topo_NZ.xyz

 # get adjusted region bounds and resolution from img2grd output
 # ** check that rows and columns match **
 g.region n=-29.9945810754 s=-50.0056468984 w=160E e=180 \
    ewres=0:01 nsres=0.0126094 -p

 r.in.xyz in=topo_NZ.xyz out=topo_NZ_1min fs=tab
 r.colors output=topo_NZ_1min color=etopo2

To save a step or some disk space, in the above you could set the region first then pipe grd2xyz directly into r.in.xyz instead of creating the .xyz file.

 # create a r.in.xyz "n" map to test input point coverage
 r.in.xyz in=topo_NZ.xyz out=topo_NZ_1min_n fs=tab method=n
 # check rast map stats, min=max=1 and there should be no null cells
 r.univar topo_NZ_1min_n
 # cleanup
 g.remove topo_NZ_1min_n

or, import GMT .grd file directly (old GMT grd format introduces FP +0.005 elev shift error??). New GMT netCDF format .grd files can be imported with the r.in.gdal module.

 # convert COARDS-compliant netCDF grdfile to old GMT native .grd
 grdreformat topo_NZ.grd topo_NZ_old.grd=bf
 # import
 r.in.bin -hf in=topo_NZ_old.grd out=topo_NZ_old

Import directly

To load it into GRASS lat/lon location (spherical):

Location setup:

http://thread.gmane.org/gmane.comp.gis.gmt.user/918

http://article.gmane.org/gmane.comp.gis.proj-4.devel/192/

Is it even possible to load directly into GRASS?

Set up Mercator/Sphere location:

• g.setproj commands for manual projection settings

Projection type> D "other"
proj> merc
No datum
ellipsoid> sphere
radius> default (doesn't matter)
Scale Factor> 1.0
Latitude of True Scale> 0
Central Meridian> 0

Which creates:

G63> g.proj -j
+proj=merc
+k_0=1.0000000000
+lat_ts=0.0000000000
+lon_0=0.0000000000
+a=6370997
+b=6370997
+no_defs
+to_meter=1.0

G63> g.proj -w
PROJCS["Mercator",
   GEOGCS["unnamed",
       DATUM["unknown",
           SPHEROID["unnamed",6370997,"inf"]],
       PRIMEM["Greenwich",0],
       UNIT["degree",0.0174532925199433]],
   PROJECTION["Mercator_2SP"],
   PARAMETER["standard_parallel_1",0],
   PARAMETER["latitude_of_origin",0],
   PARAMETER["central_meridian",0],
   PARAMETER["false_easting",0],
   PARAMETER["false_northing",0],
   UNIT["meter",1]]

• Some web searches show people using the MRWORLD projection??
  • "MRWORLD" also seen in ftp://topex.ucsd.edu/pub/global_topo_1min/topo_9.1b.img.ers
  • gdal's ermapper support files has params: (/usr/share/gdal/ecw_cs.dat)

MRWORLD:PROJCS["unnamed",PROJECTION["Mercator_1SP"],
 PARAMETER["latitude_of_origin",0],
 PARAMETER["central_meridian",0],
 PARAMETER["scale_factor",1],
 PARAMETER["false_easting",20000000],
 PARAMETER["false_northing",0]]

Note Mercator_1SP vs. Mercator_2SP in the above. (does 2 std parallels merc with only one defined == 1 std par merc?)

• Load using r.in.bin

 # the following does not work correctly, just a trial
 # offset n,s,e,w by 1/2 a grid cell?
 r.in.bin input=topo_9.1b.img output=topo_9.1b \
      title="1' worldwide relief (1.852 km-sq)" \
      -b -s bytes=2 rows=17280 cols=21600 \
      n=80.738 s=-80.738 w=0 e=360

  r.colors output=topo_9.1b color=etopo2

Official coloring

Download the "official" GMT color rules from:

wget ftp://topex.ucsd.edu/pub/global_topo_1min/gmt_examples/map/topo.cpt

Convert HSV GMT cpt color rules to RGB GRASS color rules with the r.cpt2grass add-on script.

r.cpt2grass in=topo.cpt out=palette_topo.gcolors

(HSV -> RGB conversion in that script is now partially functional)

Multibeam sonar processing

• See the LIDAR and Multi-beam Swath bathymetry data wiki help page
• r.in.xyz can import multibeam sonar swaths from a raw x,y,z stream and bin them on the fly using statistical filters.

MB-System

• MB-System is Free software for the processing and display of swath and sidescan sonar data. It can handle both multibeam bathymetry and sidescan sonar image data.

• Details and examples can be found on the GRASS-wiki MB-System page.

Mirone

• http://w3.ualg.pt/~jluis/mirone/index.htm

• From the Google Code project description:

"Mirone is a Windows MATLAB-based framework tool that allows the display and manipulation of a large number of grid/images formats through its interface with the GDAL library. Its main purpose is to provide users with an easy-to-use graphical interface to manipulate GMT grids. In addition it offers a wide range of tools dedicated to topics in the earth sciences, including tools for multibeam mission planning, elastic deformation studies, tsunami propagation modeling, earth magnetic field computations and magnetic Parker inversions, Euler rotations and poles computations, plate tectonic reconstructions, and seismicity and focal mechanism plotting. The high quality mapping and cartographic capabilities for which GMT is renowned is guaranteed through Mirone’s ability to automatically generate GMT cshell scripts and dos batch files."

You can interface with it via GDAL/GMT/netCDF formats, or directly transfer Matlab arrays with the r.out.mat and r.in.mat modules.

Sidescan sonar processing

• MB-System, as above.

• i.warp script for georectifying and mosaicking scanned paper rolls into a GeoTIFF with GDAL's gdalwarp program

• v.swathwidth script for planning swath bathymetry surveys

Wave exposure

• Using GRASS to prepare and process data for the SWAN Wave Model
  • preparing input DEM
  • r.in.mat and r.out.mat

Circulation models

• Preparing input grids
  • r.in.mat and r.out.mat
  • triangular grids: see Pavel's work (of nnbathy fame) and Laura's work (of r.terraflow fame)

Tutorials

Remote Sensing

• Importing MODIS Aqua SST and chlorophyll-a data, SeaWiFS chlorophyll-a, and Pathfinder AVHRR SST satellite images.

Mapping and Cartography

• Using GMT with GRASS
• Using vector electronic navigation charts with GRASS
• Using rasterized navigation charts with GRASS