Dear Fragstats and Grass GIS users,
To my pleasant surprise I have successfully run Fragstats on a Linux machine in conjunction with my Grass GIS database.
I tried the landscape index tools r.le within Grass, but ran into several problems (see earlier posts on the Grass mailing list). Than I started looking for an alternative. Fragstats is a powerful and well tested program, but it is only available for Windows.
However, when running the Fragstats setup program using CrossOver Office on my Linux machine, the installer finished without any errors! I have tried several options and methods and have not seen the program crash yet! I guess the success is a result of the combination of the little dependency of Fragstats on odd windows dll's and the progress made in the Wine project, the basis for CrossOver Office. I have not tested Fragstats on Wine.
Below you find the Grass code to prepare your data for Fragstats. I used the Albers Equal Area projection to prepare my rasters. Using sed (Linux utility) I removed the header from the exported ascii file. Fragstats only wants the points. I put the header content in a file called 'asc_header_aea.txt' so I could paste it back in later, as Fragstats returns exactly the same grid of points. Fragstats creates a new folder with an ascii grid (no header nor an extension!) for each index calculated, so I wrote a loop to go through the files, add the header and read the result into Grass. Then I queried the raster with a points vector and exported the results to a text file.
Hope this is helpful for other Grass/Linux users!
Cheers,
Sander.
########################################################################
## Export to ASCII and prepare file for Fragstats
dirOut=/grassdata/output
rastIn="nlc31"
rastOut=$dirOut/nlc31_aea
r.out.arc input=$rastIn output=$rastOut.asc dp=6
## remove header and replace -9999 with 9999
cd $dirOut
sed '1,6d' < nlc31_aea.asc > nlc31_aea_frgs.asc
########################################################################
## Import Fragstats results
## query with sa10min
## export to text file for analysis in R
map=nlc31
for index in MSIDI MSIEI SHDI SHEI SIDI SIEI ; do
## set resolution to 1 km; projection in meters!
g.region res=1000
## Add header to fragstats result and paste into ASCII file
frgsIn=/grassdata/output/${map:-nlc31}_aea_frgs.asc_MW1/${index:-MSIDI}
hdrAEA=/grassdata/output/asc_header_aea.txt
ascOut=/grassdata/output/${map:-nlc31}_aea_${index:-MSIDI}.asc
echo $frgsIn
cat $hdrAEA $frgsIn > $ascOut
## Import ASCII
ascIn=$ascOut
rastOut=${map:-nlc31}${index:-MSIDI}
r.in.arc input=$ascIn output=$rastOut
## Query raster with sa10min and export to file
vectTmp=tmp
g.remove vect=$vectTmp
g.copy vect=sa10min,$vectTmp
dirDBF="/grassdata/sa-aea/macwits/dbf/"
db.columns table=$vectTmp driver=dbf database=$dirDBF
## Add new column to attribute table
echo "ALTER TABLE $vectTmp ADD COLUMN value double " | db.execute
db.columns table=$vectTmp driver=dbf database=$dirDBF
## Query raster with vector
v.what.rast vect=$vectTmp rast=$rastOut col=value
dirFrags=/data1/gis/fragstats/macwits/output
textOut=$dirFrags/${map:-nlc31}_sa10min_${index:-MSIDI}.txt
echo " SELECT * FROM $vectTmp " | db.select fs="," > $textOut
done
########################################################################
--
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Dr. Sander P. Oom
Animal, Plant and Environmental Sciences,
University of the Witwatersrand
Private Bag 3, Wits 2050, South Africa
Tel (work) +27 (0)11 717 64 04
Tel (home) +27 (0)18 297 44 51
Fax +27 (0)18 299 24 64
Email sander@oomvanlieshout.net
Web www.oomvanlieshout.net/sander
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