Marine Science

2012-03-15T10:45:16Z

⚠️Seumas: /* Mirone */ updated link

== Tools for marine scientists ==

=== Bathymetry processing ===

'''''Please expand'''''
* Basic DEM creation: {{cmd|v.in.ascii}} + {{cmd|v.surf.rst}}
* {{cmd|r.in.xyz}} for processing multibeam sonar swaths
* {{AddonCmd|r.surf.nnbathy}} add-on script for creating bathymetic DEMs from input x,y,z data
* {{AddonCmd|v.in.mbsys_fnv}} add-on script for importing nav data from MB-System

==== 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 {{cmd|r.in.xyz}} instead of creating the <tt>.xyz</tt> 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 {{cmd|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:
* {{cmd|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 [http://trac.osgeo.org/grass/browser/grass-addons/raster/r.colors.tools 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|LIDAR and Multi-beam Swath bathymetry data]] wiki help page
* {{cmd|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 ====

* The [[MB-System]] wiki page contains details and examples.

* MB-System ([http://www.ldeo.columbia.edu/res/pi/MB-System/ website]) 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.

==== Mirone ====

* http://w3.ualg.pt/~jluis/mirone/

* 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 {{cmd|r.out.mat}} and {{cmd|r.in.mat}} modules.

=== Sidescan sonar processing ===

* [[MB-System]], as above.

* [[GRASS_AddOns#i.warp|i.warp]] script for georectifying and mosaicking scanned paper rolls into a GeoTIFF with [http://www.gdal.org/ GDAL]'s gdalwarp program

* [http://david.p.finlayson.googlepages.com/swathwidth 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
** {{cmd|r.in.mat}} and {{cmd|r.out.mat}} for import and export from Matlab or [http://www.gnu.org/software/octave/ Octave].

=== Circulation models ===

* Preparing input grids
** {{cmd|r.in.mat}} and {{cmd|r.out.mat}}
** triangular grids: see Pavel's work (of {{AddonCmd|r.surf.nnbathy}} fame) and Laura's work (of {{cmd|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 ==

* [[GRASS_and_GMT|Using GMT with GRASS]]
* [[S-57_data|Using vector electronic navigation charts with GRASS]]
* [[BSB_data|Using rasterized navigation charts with GRASS]]

[[Category:Applications]]
[[Category:Documentation]]

GRASS 6 Tutorial

2011-08-23T15:31:59Z

⚠️Seumas: link to previous tutorial on the same domain

The Free Software/Open Source GIS GRASS 6 is fully operational and stable version for production use. This tutorial tries to
give you a hand to familiarize yourself with the improved functionality, especially in the vector engine and attribute management.
For further reading, see the references below.

'''Disclaimer:''' In case the examples described here do not work properly, you are kindly invited to send us further examples and/or code bugfixes/enhancements. Enjoy the WIKI!

This tutorial is intended for GRASS users who want to migrate from a previous release to the new GRASS Version. If you are a beginner, please also consider additional [http://grass.itc.it/gdp/tutorials.php books or tutorials].

'''''NOTE: This tutorial here still awaits the merge of the [http://grass.osgeo.org/grass57/tutorial/ previous GRASS 5.7 tutorial].'''''

==Introduction==

New GRASS development has made major improvements to the vector
architecture. The most significant change includes a new 2- and
3-dimensional vector library that manages vector attributes in
standard database management systems (DBMS). This system provides the
power of true relational databases for vector attribute management
while preserving the flexibility of traditional GRASS topological
tools. GRASS now also incorporates true 3-dimensional voxels in the
[http://grass.itc.it/gdp/nviz/index.html NVIZ] visualization environment as well as [http://grass.itc.it/grass60/index.php numerous enhancements] to
virtually every tool in the GRASS library.

==Getting started in general==

* [[GRASS_Help| Introductory Material]] for GRASS
* [http://www.linux.org/lessons/ Introductory Material] for Linux

==Getting started - how to migrate to the new GRASS version==

* [[Grass Six Tutorial Getting Started]]
* [[GRASS_Help#Migration_from_other_GIS_Software|Migration tips]] from other GIS softwares

==Raster data management==

* The raster management works as it did in previous GRASS versions.
: Tutorials and books written for GRASS 4 and 5 should for the most part still work.
* [http://grass.ibiblio.org/grass63/manuals/html63_user/rasterintro.html Raster data processing introduction] from the main help manual.

==Vector data management==

* [http://grass.ibiblio.org/grass63/manuals/html63_user/vectorintro.html Vector data processing introduction] from the main help manual.

===[[Grass Six Tutorial Default Settings]]===
- Default settings for vector geometry;
for vector attributes; for db.* modules

===[[Grass Six Tutorial Geometry Management]]===
http://grass.osgeo.org/grass57/tutorial/geom_storage.html
- General notes on Geometry
management; Managing the default settings;
GRASS vector architecture; Geometry stored in native format;
Geometry stored in SHAPE file;
Import/export of vector data Geometry;
Generating vector geometry from various sources

===[[Grass Six Tutorial Attribute Management]]===
http://grass.osgeo.org/grass57/tutorial/attrib_storage.html
- General notes on Attribute
management; Managing the default settings; Examples;
Database Schema

==Usage examples==

''There await porting from the GRASS 5.7 tutorial''

===Basic usage examples===
http://grass.osgeo.org/grass57/tutorial/ex_basic.html

===Complex usage examples===
http://grass.osgeo.org/grass57/tutorial/ex_complex.html

===Vector network analysis examples===

* New Spearfish examples: [http://grass.osgeo.org/grass63/manuals/html63_user/v.net.html v.net], [http://grass.osgeo.org/grass63/manuals/html63_user/v.net.iso.html v.net.iso], [http://grass.osgeo.org/grass63/manuals/html63_user/v.net.path.html v.net.path] etc.
* Old tutorial: http://grass.osgeo.org/grass57/tutorial/network.html

===Vector overlay/clipping examples===
http://grass.osgeo.org/grass57/tutorial/vectoroverlay.html

===Examples from US National Atlas===
http://grass.osgeo.org/grass57/tutorial/usa_demo.html

===FAQ (Frequently Asked Questions)===
* [[Faq|GRASS Wiki FAQ]]

* [[Grass Six Tutorial Faq]]

==Troubleshooting==
http://grass.osgeo.org/grass57/tutorial/troubleshooting.html

* Grass Six Tutorial Troubleshooting

==Links of interest==

* GRASS-GMT Examples: http://169.237.35.250/~dylan/grass_user_group/

==Further reading==

===GRASS and R kriging interpolation===

====Mini How to interpolate using kriging with GRASS and R====

[[How to interpolate point value using kriging method with R and GRASS 6]]

==== References ====
* GRASS [http://grass.osgeo.org/gdp/tutorials.php books and tutorials]
* GRASS 6 Tutorial: http://www.gdf-hannover.de/literature
* Translation Portal for GRASS 6 Tutorial http://www.gdf-hannover.de/translation

[[Category:Documentation]]

GRASS-Wiki - User contributions [en]

Marine Science

GRASS 6 Tutorial