Revision e1aa0df7
Added by selv in ga254@bulldogj about 11 years ago
| terrain/procedures/dem_variables/gmted2010_res_x10/sc1_wget_gmted2010-30_bj.sh | ||
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# download unzip and tif conversion of the Global Multi-resolution Terrain Elevation Data 2010 (GMTED2010) |
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# setting working directory |
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module load Tools/Python/2.7.3 |
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module load Libraries/GDAL/1.10.0 |
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module load Tools/PKTOOLS/2.4.2 |
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module load Libraries/OSGEO/1.10.0 |
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INDIR=/lustre0/scratch/ga254/dem_bj/GMTED2010 |
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cd $INDIR |
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# download all the zip file from http://topotools.cr.usgs.gov/gmted_viewer/gmted2010_global_grids.php |
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# using multiprocess approch |
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url=http://gmted.cr.usgs.gov/gmted/Grid_ZipFiles/ |
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echo $url"be30_grd.zip" $url"ds30_grd.zip" $url"mn30_grd.zip" | xargs -n 1 -P 7 wget -d /lustre0/scratch/ga254/dem_bj/GMTED2010 $1 |
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# unzip the file using multiprocess approch |
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ls $INDIR/zip/??30_grd.zip | xargs -n 1 -P 7 bash -c $' |
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INDIR=/lustre0/scratch/ga254/dem_bj/GMTED2010 |
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dir=`basename $1 .zip` |
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cd $INDIR/$dir |
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unzip $1 |
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# transform to tif and tiling them using multiprocess approch |
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# be30_grd.zip Breakline Emphasis , 30 arc-seconds |
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# ds30_grd.zip Systematic Subsample , 30 arc-seconds |
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# md30_grd.zip Median Statistic , 30 arc-seconds |
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# mi30_grd.zip Minimum Statistic , 30 arc-seconds |
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# mn30_grd.zip Mean Statistic , 30 arc-seconds |
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# mx30_grd.zip Maximum Statistic , 30 arc-seconds |
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# sd30_grd.zip Standard Dev. Statistic, 30 arc-seconds |
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echo be30_grd ds30_grd mn30_grd | xargs -n 1 -P 7 bash -c $' |
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dir=$1 |
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INDIR=/lustre0/scratch/ga254/dem_bj/GMTED2010/tiles/$dir |
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gdal_translate -co COMPRESS=LZW $INDIR/$dir $INDIR"_tif"/$dir.tif |
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' _ |
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# at the end fo this process the 50 tiles tiff has been created for each of the defined component |
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| terrain/procedures/dem_variables/gmted2010_res_x10/sc1_wget_gmted2010-7.5_bj.sh | ||
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| 1 |
# download unzip and tif conversion of the Global Multi-resolution Terrain Elevation Data 2010 (GMTED2010) |
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# setting working directory |
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INDIR=/lustre0/scratch/ga254/dem_bj/GMTED2010 |
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cd $INDIR |
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# download all the zip file from http://topotools.cr.usgs.gov/gmted_viewer/gmted2010_global_grids.php |
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# using multiprocess approch |
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url=http://gmted.cr.usgs.gov/gmted/Grid_ZipFiles/ |
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cd $INDIR/zip |
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echo $url"be75_grd.zip" $url"ds75_grd.zip" $url"md75_grd.zip" $url"mi75_grd.zip" $url"mx75_grd.zip" $url"sd75_grd.zip" | xargs -n 1 -P 7 wget $1 |
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# $url"mn75_grd.zip" |
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# unzip the file using multiprocess approch |
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ls $INDIR/zip/??75_grd.zip | xargs -n 1 -P 7 bash -c $' |
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INDIR=/lustre0/scratch/ga254/dem_bj/GMTED2010 |
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dir=`basename $1 .zip` |
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unzip -d $INDIR/tiles/$dir $1 |
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' _ |
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| terrain/procedures/dem_variables/gmted2010_res_x10/sc2_green_land_bj.sh | ||
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module load Tools/Python/2.7.3 |
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module load Libraries/GDAL/1.10.0 |
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module load Tools/PKTOOLS/2.4.2 |
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module load Libraries/OSGEO/1.10.0 |
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SHP=/lustre0/scratch/ga254/dem_bj/GMTED2010/tiles/shp |
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REFER=/lustre0/scratch/ga254/dem_bj/GMTED2010/tiles/reference_tif |
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rm -f $SHP/green_land30arc-sec.tif |
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gdal_rasterize -co COMPRESS=LZW -ot Byte -a id -l green_land -tr 0.008333333333333 0.008333333333333 -te $(/home2/ga254/bin/getCorners4Gwarp $REFER/geo30arcsec_reference.tif) $SHP/green_land.shp $SHP/green_land30arc-sec.tif |
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geo_string=$(/home2/ga254/bin/oft-bb $SHP/green_land30arc-sec.tif 1 | grep BB | awk '{ print $6,$7,$8-$6,$9-$7 }')
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# clip the tif |
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gdal_translate -srcwin $geo_string -co COMPRESS=LZW -ot Byte $SHP/green_land30arc-sec.tif $SHP/green_land30arc-sec_msk.tif |
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rm -f $SHP/green_land7.5arc-sec.tif |
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gdal_rasterize -co COMPRESS=LZW -ot Byte -a id -l green_land -tr 0.002083333333333 0.002083333333333 -te $(/home2/ga254/bin/getCorners4Gwarp $REFER/geo30arcsec_reference.tif) $SHP/green_land.shp $SHP/green_land7.5arc-sec.tif |
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geo_string=$(/home2/ga254/bin/oft-bb $SHP/green_land7.5arc-sec.tif 1 | grep BB | awk '{ print $6,$7,$8-$6,$9-$7 }')
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# clip the tif |
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gdal_translate -srcwin $geo_string -co COMPRESS=LZW -ot Byte $SHP/green_land7.5arc-sec.tif $SHP/green_land7.5arc-sec_msk.tif |
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# prepare the integration of greeland mn for mn md mx mn |
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TILES=/lustre0/scratch/ga254/dem_bj/GMTED2010/tiles |
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rm -f $TILES/mn75_grd_tif/green_land.tif |
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gdalwarp -r cubic -te $(~/bin/getCorners4Gwarp $TILES/shp/green_land7.5arc-sec_msk.tif ) -tr 0.002083333333333 0.002083333333333 $TILES/mn30_grd_tif/mn30_grd.tif $TILES/mn75_grd_tif/green_land.tif |
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pksetmask -i $TILES/mn75_grd_tif/green_land.tif -m $SHP/green_land7.5arc-sec_msk.tif -t 0 -f 0 -o $TILES/mn75_grd_tif/green_land_msk.tif |
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rm -f $TILES/ds75_grd_tif/green_land.tif |
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gdalwarp -r cubic -te $(~/bin/getCorners4Gwarp $TILES/shp/green_land7.5arc-sec_msk.tif ) -tr 0.002083333333333 0.002083333333333 $TILES/ds30_grd_tif/ds30_grd.tif $TILES/ds75_grd_tif/green_land.tif |
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pksetmask -i $TILES/ds75_grd_tif/green_land.tif -m $SHP/green_land7.5arc-sec_msk.tif -t 0 -f 0 -o $TILES/ds75_grd_tif/green_land_msk.tif |
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rm -f $TILES/be75_grd_tif/green_land.tif |
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gdalwarp -r cubic -te $(~/bin/getCorners4Gwarp $TILES/shp/green_land7.5arc-sec_msk.tif ) -tr 0.002083333333333 0.002083333333333 $TILES/be30_grd_tif/be30_grd.tif $TILES/be75_grd_tif/green_land.tif |
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pksetmask -i $TILES/be75_grd_tif/green_land.tif -m $SHP/green_land7.5arc-sec_msk.tif -t 0 -f 0 -o $TILES/be75_grd_tif/green_land_msk.tif |
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| terrain/procedures/dem_variables/gmted2010_res_x10/sc2a_dem_variables.sh | ||
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echo altitude variables with file $INDIR/$filename.tif |
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# median |
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pkfilter -m -32768 -dx 4 -dy 4 -f median -d 4 -i $INDIR/$filename.tif -o $OUTDIR/altitude/median/tiles/${filename}_${mm}.tif -co COMPRESS=LZW -ot Int16
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# stdev |
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pkfilter -m -32768 -dx 4 -dy 4 -f var -d 4 -i $INDIR/$filename.tif -o /tmp/ramdisk/tmp_${filename}_${mm}.tif -ot Int32 # max 1552385.000 sqrt(1245.947)
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gdal_calc.py -A /tmp/ramdisk/tmp_${filename}_${mm}.tif --calc="sqrt(A)" --type Int16 --overwrite --outfile $OUTDIR/altitude/stdev/tiles/${filename}_${mm}.tif
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rm -f /tmp/ramdisk/tmp_${filename}_${mm}.tif
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# min |
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pkfilter -m -32768 -dx 4 -dy 4 -f min -d 4 -i $INDIR/$filename.tif -o $OUTDIR/altitude/min/tiles/${filename}_${mm}.tif -co COMPRESS=LZW -ot Int16
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# max |
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pkfilter -m -32768 -dx 4 -dy 4 -f max -d 4 -i $INDIR/$filename.tif -o $OUTDIR/altitude/max/tiles/${filename}_${mm}.tif -co COMPRESS=LZW -ot Int16
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# mean |
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pkfilter -m -32768 -dx 4 -dy 4 -f mean -d 4 -i $INDIR/$filename.tif -o $OUTDIR/altitude/mean/tiles/${filename}_${mm}.tif -co COMPRESS=LZW -ot Int16
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# starting to use gdaldem to compute variables. Gdaldem use -9999 as no data. |
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echo slope with file $INDIR/$filename.tif |
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gdaldem slope -s 111120 -co COMPRESS=LZW $INDIR/$filename.tif $OUTDIR/slope/tiles/${filename}_${mm}.tif # -s to consider xy in degree and z in meters
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# slope median |
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pkfilter -m -9999 -dx 4 -dy 4 -f median -d 4 -i $OUTDIR/slope/tiles/${filename}_${mm}.tif -o $OUTDIR/slope/median/tiles/${filename}_${mm}.tif -co COMPRESS=LZW -ot Byte
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# slope stdev |
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pkfilter -m -9999 -dx 4 -dy 4 -f var -d 4 -i $OUTDIR/slope/tiles/${filename}_${mm}.tif -o /tmp/ramdisk/tmp_${filename}_${mm}.tif -ot Int32
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gdal_calc.py -A /tmp/ramdisk/tmp_${filename}_${mm}.tif --calc="sqrt(A)" --type Int16 --overwrite --outfile $OUTDIR/slope/stdev/tiles/${filename}_${mm}.tif
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rm -f /tmp/ramdisk/tmp_${filename}_${mm}.tif
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# slope min |
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pkfilter -m -9999 -dx 4 -dy 4 -f min -d 4 -i $OUTDIR/slope/tiles/${filename}_${mm}.tif -o $OUTDIR/slope/min/tiles/${filename}_${mm}.tif -co COMPRESS=LZW -ot Byte
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# slope max |
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pkfilter -m -9999 -dx 4 -dy 4 -f max -d 4 -i $OUTDIR/slope/tiles/${filename}_${mm}.tif -o $OUTDIR/slope/max/tiles/${filename}_${mm}.tif -co COMPRESS=LZW -ot Byte
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# slope mean |
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pkfilter -m -9999 -dx 4 -dy 4 -f mean -d 4 -i $OUTDIR/slope/tiles/${filename}_${mm}.tif -o $OUTDIR/slope/mean/tiles/${filename}_${mm}.tif -co COMPRESS=LZW -ot Byte
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# rm -f $OUTDIR/slope/tiles/$filename.tif |
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echo generate a Terrain Ruggedness Index TRI with file $file |
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gdaldem TRI -co COMPRESS=LZW $INDIR/$filename.tif $OUTDIR/tri/tiles/${filename}_${mm}.tif
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# tri median |
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pkfilter -m -9999 -dx 4 -dy 4 -f median -d 4 -i $OUTDIR/tri/tiles/${filename}_${mm}.tif -o $OUTDIR/tri/median/tiles/${filename}_${mm}.tif -co COMPRESS=LZW -ot Int16
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# tri stdev |
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pkfilter -m -9999 -dx 4 -dy 4 -f var -d 4 -i $OUTDIR/tri/tiles/${filename}_${mm}.tif -o /tmp/ramdisk/tmp_${filename}_${mm}.tif
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gdal_calc.py -A /tmp/ramdisk/tmp_${filename}_${mm}.tif --calc="sqrt(A)" --type Int16 --overwrite --outfile $OUTDIR/tri/stdev/tiles/${filename}_${mm}.tif
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rm -f /tmp/ramdisk/tmp_${filename}_${mm}.tif
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# tri min |
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pkfilter -m -9999 -dx 4 -dy 4 -f min -d 4 -i $OUTDIR/tri/tiles/${filename}_${mm}.tif -o $OUTDIR/tri/min/tiles/${filename}_${mm}.tif -co COMPRESS=LZW -ot Int16
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# tri max |
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pkfilter -m -9999 -dx 4 -dy 4 -f max -d 4 -i $OUTDIR/tri/tiles/${filename}_${mm}.tif -o $OUTDIR/tri/max/tiles/${filename}_${mm}.tif -co COMPRESS=LZW -ot Int16
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# tri mean |
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pkfilter -m -9999 -dx 4 -dy 4 -f mean -d 4 -i $OUTDIR/tri/tiles/${filename}_${mm}.tif -o $OUTDIR/tri/mean/tiles/${filename}_${mm}.tif -co COMPRESS=LZW -ot Int16
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# rm -f $OUTDIR/tri/tiles/$filename.tif |
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echo generate a Topographic Position Index TPI with file $INDIR/$filename.tif |
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gdaldem TPI -co COMPRESS=LZW $INDIR/$filename.tif $OUTDIR/tpi/tiles/${filename}_${mm}.tif # tpi has negative number
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oft-calc -ot Float32 $OUTDIR/tpi/tiles/${filename}_${mm}.tif $OUTDIR/tpi/tiles/${filename}_${mm}"_t10.tif" &> /dev/null <<EOF
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1 |
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#1 10 * |
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EOF |
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# tpi median |
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pkfilter -m -9999 -dx 4 -dy 4 -f median -d 4 -i $OUTDIR/tpi/tiles/${filename}_${mm}"_t10.tif" -o $OUTDIR/tpi/median/tiles/${filename}_${mm}.tif -co COMPRESS=LZW -ot Int16
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echo tpi stdev |
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pkfilter -m -9999 -dx 4 -dy 4 -f var -d 4 -i $OUTDIR/tpi/tiles/${filename}_${mm}"_t10.tif" -o /tmp/ramdisk/tmp_${filename}_${mm}.tif
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gdal_calc.py -A /tmp/ramdisk/tmp_${filename}_${mm}.tif --calc="sqrt(A)" --type Int32 --overwrite --outfile $OUTDIR/tpi/stdev/tiles/${filename}_${mm}.tif
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rm -f /tmp/ramdisk/tmp_${filename}_${mm}.tif
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# tpi min |
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pkfilter -m -9999 -dx 4 -dy 4 -f min -d 4 -i $OUTDIR/tpi/tiles/${filename}_${mm}"_t10.tif" -o $OUTDIR/tpi/min/tiles/${filename}_${mm}.tif -co COMPRESS=LZW -ot Int16
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# tpi max |
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pkfilter -m -9999 -dx 4 -dy 4 -f max -d 4 -i $OUTDIR/tpi/tiles/${filename}_${mm}"_t10.tif" -o $OUTDIR/tpi/max/tiles/${filename}_${mm}.tif -co COMPRESS=LZW -ot Int16
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# tpi mean |
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pkfilter -m -9999 -dx 4 -dy 4 -f mean -d 4 -i $OUTDIR/tpi/tiles/${filename}_${mm}"_t10.tif" -o $OUTDIR/tpi/mean/tiles/${filename}_${mm}.tif -co COMPRESS=LZW -ot Int16
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echo generate roughness with file $INDIR/$filename.tif |
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gdaldem roughness -co COMPRESS=LZW $INDIR/$filename.tif $OUTDIR/roughness/tiles/${filename}_${mm}.tif
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# roughness median |
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pkfilter -m -9999 -dx 4 -dy 4 -f median -d 4 -i $OUTDIR/roughness/tiles/${filename}_${mm}.tif -o $OUTDIR/roughness/median/tiles/${filename}_${mm}.tif -co COMPRESS=LZW -ot Int16
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echo roughness stdev |
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pkfilter -m -9999 -dx 4 -dy 4 -f var -d 4 -i $OUTDIR/roughness/tiles/${filename}_${mm}.tif -o /tmp/ramdisk/tmp_${filename}_${mm}.tif
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gdal_calc.py -A /tmp/ramdisk/tmp_${filename}_${mm}.tif --calc="sqrt(A)" --type Int32 --overwrite --outfile $OUTDIR/roughness/stdev/tiles/${filename}_${mm}.tif
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rm -f /tmp/ramdisk/tmp_${filename}_${mm}.tif
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# roughness min |
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pkfilter -m -9999 -dx 4 -dy 4 -f min -d 4 -i $OUTDIR/roughness/tiles/${filename}_${mm}.tif -o $OUTDIR/roughness/min/tiles/${filename}_${mm}.tif -co COMPRESS=LZW -ot Int16
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# roughness max |
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pkfilter -m -9999 -dx 4 -dy 4 -f max -d 4 -i $OUTDIR/roughness/tiles/${filename}_${mm}.tif -o $OUTDIR/roughness/max/tiles/${filename}_${mm}.tif -co COMPRESS=LZW -ot Int16
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# roughness mean |
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pkfilter -m -9999 -dx 4 -dy 4 -f mean -d 4 -i $OUTDIR/roughness/tiles/${filename}_${mm}.tif -o $OUTDIR/roughness/mean/tiles/${filename}_${mm}.tif -co COMPRESS=LZW -ot Int16
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# rm -f $OUTDIR/roughness/tiles/${filename}_${mm}.tif
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# echo altitude variables with file $INDIR/$filename.tif
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# # median
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# pkfilter -m -32768 -dx 4 -dy 4 -f median -d 4 -i $INDIR/$filename.tif -o $OUTDIR/altitude/median/tiles/${filename}_${mm}.tif -co COMPRESS=LZW -ot Int16
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# # stdev
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# pkfilter -m -32768 -dx 4 -dy 4 -f var -d 4 -i $INDIR/$filename.tif -o /tmp/ramdisk/tmp_${filename}_${mm}.tif -ot Int32 # max 1552385.000 sqrt(1245.947)
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# gdal_calc.py -A /tmp/ramdisk/tmp_${filename}_${mm}.tif --calc="sqrt(A)" --type Int16 --overwrite --outfile $OUTDIR/altitude/stdev/tiles/${filename}_${mm}.tif
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# rm -f /tmp/ramdisk/tmp_${filename}_${mm}.tif
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# # min
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# pkfilter -m -32768 -dx 4 -dy 4 -f min -d 4 -i $INDIR/$filename.tif -o $OUTDIR/altitude/min/tiles/${filename}_${mm}.tif -co COMPRESS=LZW -ot Int16
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# # max
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# pkfilter -m -32768 -dx 4 -dy 4 -f max -d 4 -i $INDIR/$filename.tif -o $OUTDIR/altitude/max/tiles/${filename}_${mm}.tif -co COMPRESS=LZW -ot Int16
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# # mean
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# pkfilter -m -32768 -dx 4 -dy 4 -f mean -d 4 -i $INDIR/$filename.tif -o $OUTDIR/altitude/mean/tiles/${filename}_${mm}.tif -co COMPRESS=LZW -ot Int16
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# # starting to use gdaldem to compute variables. Gdaldem use -9999 as no data.
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# echo slope with file $INDIR/$filename.tif
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# gdaldem slope -s 111120 -co COMPRESS=LZW $INDIR/$filename.tif $OUTDIR/slope/tiles/${filename}_${mm}.tif # -s to consider xy in degree and z in meters
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# # slope median
|
|
| 39 |
# pkfilter -m -9999 -dx 4 -dy 4 -f median -d 4 -i $OUTDIR/slope/tiles/${filename}_${mm}.tif -o $OUTDIR/slope/median/tiles/${filename}_${mm}.tif -co COMPRESS=LZW -ot Byte
|
|
| 40 |
# # slope stdev
|
|
| 41 |
# pkfilter -m -9999 -dx 4 -dy 4 -f var -d 4 -i $OUTDIR/slope/tiles/${filename}_${mm}.tif -o /tmp/ramdisk/tmp_${filename}_${mm}.tif -ot Int32
|
|
| 42 |
# gdal_calc.py -A /tmp/ramdisk/tmp_${filename}_${mm}.tif --calc="sqrt(A)" --type Int16 --overwrite --outfile $OUTDIR/slope/stdev/tiles/${filename}_${mm}.tif
|
|
| 43 |
# rm -f /tmp/ramdisk/tmp_${filename}_${mm}.tif
|
|
| 44 |
# # slope min
|
|
| 45 |
# pkfilter -m -9999 -dx 4 -dy 4 -f min -d 4 -i $OUTDIR/slope/tiles/${filename}_${mm}.tif -o $OUTDIR/slope/min/tiles/${filename}_${mm}.tif -co COMPRESS=LZW -ot Byte
|
|
| 46 |
# # slope max
|
|
| 47 |
# pkfilter -m -9999 -dx 4 -dy 4 -f max -d 4 -i $OUTDIR/slope/tiles/${filename}_${mm}.tif -o $OUTDIR/slope/max/tiles/${filename}_${mm}.tif -co COMPRESS=LZW -ot Byte
|
|
| 48 |
# # slope mean
|
|
| 49 |
# pkfilter -m -9999 -dx 4 -dy 4 -f mean -d 4 -i $OUTDIR/slope/tiles/${filename}_${mm}.tif -o $OUTDIR/slope/mean/tiles/${filename}_${mm}.tif -co COMPRESS=LZW -ot Byte
|
|
| 50 |
|
|
| 51 |
# # rm -f $OUTDIR/slope/tiles/$filename.tif
|
|
| 52 |
|
|
| 53 |
# echo generate a Terrain Ruggedness Index TRI with file $file
|
|
| 54 |
# gdaldem TRI -co COMPRESS=LZW $INDIR/$filename.tif $OUTDIR/tri/tiles/${filename}_${mm}.tif
|
|
| 55 |
# # tri median
|
|
| 56 |
# pkfilter -m -9999 -dx 4 -dy 4 -f median -d 4 -i $OUTDIR/tri/tiles/${filename}_${mm}.tif -o $OUTDIR/tri/median/tiles/${filename}_${mm}.tif -co COMPRESS=LZW -ot Int16
|
|
| 57 |
# # tri stdev
|
|
| 58 |
# pkfilter -m -9999 -dx 4 -dy 4 -f var -d 4 -i $OUTDIR/tri/tiles/${filename}_${mm}.tif -o /tmp/ramdisk/tmp_${filename}_${mm}.tif
|
|
| 59 |
# gdal_calc.py -A /tmp/ramdisk/tmp_${filename}_${mm}.tif --calc="sqrt(A)" --type Int16 --overwrite --outfile $OUTDIR/tri/stdev/tiles/${filename}_${mm}.tif
|
|
| 60 |
# rm -f /tmp/ramdisk/tmp_${filename}_${mm}.tif
|
|
| 61 |
# # tri min
|
|
| 62 |
# pkfilter -m -9999 -dx 4 -dy 4 -f min -d 4 -i $OUTDIR/tri/tiles/${filename}_${mm}.tif -o $OUTDIR/tri/min/tiles/${filename}_${mm}.tif -co COMPRESS=LZW -ot Int16
|
|
| 63 |
# # tri max
|
|
| 64 |
# pkfilter -m -9999 -dx 4 -dy 4 -f max -d 4 -i $OUTDIR/tri/tiles/${filename}_${mm}.tif -o $OUTDIR/tri/max/tiles/${filename}_${mm}.tif -co COMPRESS=LZW -ot Int16
|
|
| 65 |
# # tri mean
|
|
| 66 |
# pkfilter -m -9999 -dx 4 -dy 4 -f mean -d 4 -i $OUTDIR/tri/tiles/${filename}_${mm}.tif -o $OUTDIR/tri/mean/tiles/${filename}_${mm}.tif -co COMPRESS=LZW -ot Int16
|
|
| 67 |
|
|
| 68 |
# # rm -f $OUTDIR/tri/tiles/$filename.tif
|
|
| 69 |
|
|
| 70 |
# echo generate a Topographic Position Index TPI with file $INDIR/$filename.tif
|
|
| 71 |
|
|
| 72 |
# gdaldem TPI -co COMPRESS=LZW $INDIR/$filename.tif $OUTDIR/tpi/tiles/${filename}_${mm}.tif # tpi has negative number
|
|
| 73 |
|
|
| 74 |
# oft-calc -ot Float32 $OUTDIR/tpi/tiles/${filename}_${mm}.tif $OUTDIR/tpi/tiles/${filename}_${mm}"_t10.tif" &> /dev/null <<EOF
|
|
| 75 |
# 1
|
|
| 76 |
# #1 10 *
|
|
| 77 |
# EOF
|
|
| 78 |
|
|
| 79 |
# # tpi median
|
|
| 80 |
# pkfilter -m -9999 -dx 4 -dy 4 -f median -d 4 -i $OUTDIR/tpi/tiles/${filename}_${mm}"_t10.tif" -o $OUTDIR/tpi/median/tiles/${filename}_${mm}.tif -co COMPRESS=LZW -ot Int16
|
|
| 81 |
# echo tpi stdev
|
|
| 82 |
# pkfilter -m -9999 -dx 4 -dy 4 -f var -d 4 -i $OUTDIR/tpi/tiles/${filename}_${mm}"_t10.tif" -o /tmp/ramdisk/tmp_${filename}_${mm}.tif
|
|
| 83 |
# gdal_calc.py -A /tmp/ramdisk/tmp_${filename}_${mm}.tif --calc="sqrt(A)" --type Int32 --overwrite --outfile $OUTDIR/tpi/stdev/tiles/${filename}_${mm}.tif
|
|
| 84 |
# rm -f /tmp/ramdisk/tmp_${filename}_${mm}.tif
|
|
| 85 |
# # tpi min
|
|
| 86 |
# pkfilter -m -9999 -dx 4 -dy 4 -f min -d 4 -i $OUTDIR/tpi/tiles/${filename}_${mm}"_t10.tif" -o $OUTDIR/tpi/min/tiles/${filename}_${mm}.tif -co COMPRESS=LZW -ot Int16
|
|
| 87 |
# # tpi max
|
|
| 88 |
# pkfilter -m -9999 -dx 4 -dy 4 -f max -d 4 -i $OUTDIR/tpi/tiles/${filename}_${mm}"_t10.tif" -o $OUTDIR/tpi/max/tiles/${filename}_${mm}.tif -co COMPRESS=LZW -ot Int16
|
|
| 89 |
# # tpi mean
|
|
| 90 |
# pkfilter -m -9999 -dx 4 -dy 4 -f mean -d 4 -i $OUTDIR/tpi/tiles/${filename}_${mm}"_t10.tif" -o $OUTDIR/tpi/mean/tiles/${filename}_${mm}.tif -co COMPRESS=LZW -ot Int16
|
|
| 91 |
|
|
| 92 |
|
|
| 93 |
# echo generate roughness with file $INDIR/$filename.tif
|
|
| 94 |
|
|
| 95 |
# gdaldem roughness -co COMPRESS=LZW $INDIR/$filename.tif $OUTDIR/roughness/tiles/${filename}_${mm}.tif
|
|
| 96 |
|
|
| 97 |
# # roughness median
|
|
| 98 |
# pkfilter -m -9999 -dx 4 -dy 4 -f median -d 4 -i $OUTDIR/roughness/tiles/${filename}_${mm}.tif -o $OUTDIR/roughness/median/tiles/${filename}_${mm}.tif -co COMPRESS=LZW -ot Int16
|
|
| 99 |
# echo roughness stdev
|
|
| 100 |
# pkfilter -m -9999 -dx 4 -dy 4 -f var -d 4 -i $OUTDIR/roughness/tiles/${filename}_${mm}.tif -o /tmp/ramdisk/tmp_${filename}_${mm}.tif
|
|
| 101 |
# gdal_calc.py -A /tmp/ramdisk/tmp_${filename}_${mm}.tif --calc="sqrt(A)" --type Int32 --overwrite --outfile $OUTDIR/roughness/stdev/tiles/${filename}_${mm}.tif
|
|
| 102 |
# rm -f /tmp/ramdisk/tmp_${filename}_${mm}.tif
|
|
| 103 |
# # roughness min
|
|
| 104 |
# pkfilter -m -9999 -dx 4 -dy 4 -f min -d 4 -i $OUTDIR/roughness/tiles/${filename}_${mm}.tif -o $OUTDIR/roughness/min/tiles/${filename}_${mm}.tif -co COMPRESS=LZW -ot Int16
|
|
| 105 |
# # roughness max
|
|
| 106 |
# pkfilter -m -9999 -dx 4 -dy 4 -f max -d 4 -i $OUTDIR/roughness/tiles/${filename}_${mm}.tif -o $OUTDIR/roughness/max/tiles/${filename}_${mm}.tif -co COMPRESS=LZW -ot Int16
|
|
| 107 |
# # roughness mean
|
|
| 108 |
# pkfilter -m -9999 -dx 4 -dy 4 -f mean -d 4 -i $OUTDIR/roughness/tiles/${filename}_${mm}.tif -o $OUTDIR/roughness/mean/tiles/${filename}_${mm}.tif -co COMPRESS=LZW -ot Int16
|
|
| 109 |
|
|
| 110 |
# # rm -f $OUTDIR/roughness/tiles/${filename}_${mm}.tif
|
|
| 111 | 111 |
|
| 112 | 112 |
|
| 113 | 113 |
echo aspect with file $INDIR/$filename.tif |
| terrain/procedures/dem_variables/gmted2010_res_x10/sc3_class_treshold_density_merge.sh | ||
|---|---|---|
| 8 | 8 |
|
| 9 | 9 |
DIR=$1 |
| 10 | 10 |
mm=$2 |
| 11 |
INDIR=/mnt/data2/dem_variables/GMTED2010/altitude/class_${mm}/class${DIR}
|
|
| 12 |
INDIR_C=/mnt/data2/dem_variables/GMTED2010/altitude/class_${mm}/class
|
|
| 11 |
INDIR=/mnt/data2/dem_variables/GMTED2010/altitude/class_${mm}/class${DIR} # this has pixel value = 0.002083333333333
|
|
| 12 |
INDIR_C=/mnt/data2/dem_variables/GMTED2010/altitude/class_${mm}/class # this has pixel value = 0.002083333333333
|
|
| 13 | 13 |
OUTDIR=/mnt/data2/dem_variables/GMTED2010/altitude/percent_class_${mm}
|
| 14 | 14 |
|
| 15 | 15 |
rm -f $OUTDIR/file_processed_sc3.txt # the file has ben processed by the script sc1_dem_treshold_percent.sh |
| terrain/procedures/dem_variables/gmted2010_res_x10/sc3_tiling_gmted2010-7.5_bj.sh | ||
|---|---|---|
| 1 |
# download unzip and tif conversion of the Global Multi-resolution Terrain Elevation Data 2010 (GMTED2010) |
|
| 2 |
# setting working directory |
|
| 3 |
|
|
| 4 |
# transform to tif and tiling them using multiprocess approch |
|
| 5 |
# be75_grd.zip Breakline Emphasis , 7.5 arc-seconds |
|
| 6 |
# ds75_grd.zip Systematic Subsample , 7.5 arc-seconds |
|
| 7 |
# md75_grd.zip Median Statistic , 7.5 arc-seconds |
|
| 8 |
# mi75_grd.zip Minimum Statistic , 7.5 arc-seconds |
|
| 9 |
# mn75_grd.zip Mean Statistic , 7.5 arc-seconds |
|
| 10 |
# mx75_grd.zip Maximum Statistic , 7.5 arc-seconds |
|
| 11 |
# sd75_grd.zip Standard Dev. Statistic, 7.5 arc-seconds |
|
| 12 |
|
|
| 13 |
# rm /lustre0/scratch/ga254/stdout/* /lustre0/scratch/ga254/stderr/* |
|
| 14 |
# for DIR in md75_grd mi75_grd mn75_grd mx75_grd be75_grd ds75_grd sd75_grd ; do qsub -v DIR=$DIR /lustre0/scratch/ga254/scripts_bj_bk/environmental-layers/terrain/procedures/dem_variables/gmted2010_res_x10/sc3_tiling_gmted2010-7.5_bj.sh ; done |
|
| 15 |
|
|
| 16 |
# for DIR in md75_grd mi75_grd mn75_grd mx75_grd be75_grd ds75_grd sd75_grd ; do bash /lustre0/scratch/ga254/scripts_bj_bk/environmental-layers/terrain/procedures/dem_variables/gmted2010_res_x10/sc3_tiling_gmted2010-7.5_bj.sh $DIR ; done |
|
| 17 |
|
|
| 18 |
|
|
| 19 |
#PBS -S /bin/bash |
|
| 20 |
#PBS -q fas_normal |
|
| 21 |
#PBS -l mem=4gb |
|
| 22 |
#PBS -l walltime=4:00:00 |
|
| 23 |
#PBS -l nodes=1:ppn=4 |
|
| 24 |
#PBS -V |
|
| 25 |
#PBS -o /lustre0/scratch/ga254/stdout |
|
| 26 |
#PBS -e /lustre0/scratch/ga254/stderr |
|
| 27 |
|
|
| 28 |
|
|
| 29 |
# DIR=$1 |
|
| 30 |
|
|
| 31 |
INDIR=/lustre0/scratch/ga254/dem_bj/GMTED2010/tiles |
|
| 32 |
cd $INDIR |
|
| 33 |
|
|
| 34 |
# load moduels |
|
| 35 |
|
|
| 36 |
module load Tools/Python/2.7.3 |
|
| 37 |
module load Libraries/GDAL/1.10.0 |
|
| 38 |
module load Tools/PKTOOLS/2.4.2 |
|
| 39 |
module load Libraries/OSGEO/1.10.0 |
|
| 40 |
|
|
| 41 |
|
|
| 42 |
# -projwin ulx uly lrx lry |
|
| 43 |
gdal_translate -projwin -180 +90 0 0 -co COMPRESS=LZW -ot Int16 $INDIR/$DIR/$DIR $INDIR/$DIR"_tif"/$DIR"_NW.tif" |
|
| 44 |
gdal_translate -projwin 0 +90 180 0 -co COMPRESS=LZW -ot Int16 $INDIR/$DIR/$DIR $INDIR/$DIR"_tif"/$DIR"_NE.tif" |
|
| 45 |
gdal_translate -projwin -180 0 0 -90 -co COMPRESS=LZW -ot Int16 $INDIR/$DIR/$DIR $INDIR/$DIR"_tif"/$DIR"_SW.tif" |
|
| 46 |
gdal_translate -projwin 0 0 180 -90 -co COMPRESS=LZW -ot Int16 $INDIR/$DIR/$DIR $INDIR/$DIR"_tif"/$DIR"_SE.tif" |
|
| 47 |
|
|
| 48 |
|
|
| 49 |
gdal_edit.py -a_ullr -180 +90 0 0 $INDIR/$DIR"_tif"/$DIR"_NW.tif" |
|
| 50 |
gdal_edit.py -a_ullr 0 +90 180 0 $INDIR/$DIR"_tif"/$DIR"_NE.tif" |
|
| 51 |
gdal_edit.py -a_ullr -180 0 0 -90 $INDIR/$DIR"_tif"/$DIR"_SW.tif" |
|
| 52 |
gdal_edit.py -a_ullr 0 0 180 -90 $INDIR/$DIR"_tif"/$DIR"_SE.tif" |
|
| 53 |
|
|
| 54 |
gdalbuildvrt -overwrite $INDIR/$DIR"_tif"/$DIR.vrt $INDIR/$DIR"_tif"/$DIR"_"??.tif |
|
| 55 |
|
|
| 56 |
|
|
| 57 |
|
|
| 58 |
for nx in `seq 0 9` ; do for ny in `seq 0 4` ; do echo $nx $ny $DIR; done ; done | xargs -n 3 -P 4 bash -c $' |
|
| 59 |
nx=$1 |
|
| 60 |
ny=$2 |
|
| 61 |
DIR=$3 |
|
| 62 |
INDIR=/lustre0/scratch/ga254/dem_bj/GMTED2010/tiles/$DIR"_tif" |
|
| 63 |
|
|
| 64 |
xoff=$(echo 17280 \* $nx | bc) |
|
| 65 |
yoff=$(echo 2879 + 13440 \* $ny | bc) # 2879 the ofset of no data value in the northen part |
|
| 66 |
xsize=17296 # increase 16 pixel to avoid border effect, 4 in the aggregate version |
|
| 67 |
ysize=13456 # increase 16 pixel to avoid border effect |
|
| 68 |
gdal_translate -co ZLEVEL=9 -srcwin $xoff $yoff $xsize $ysize -co COMPRESS=LZW $INDIR/$DIR.vrt $INDIR/$nx"_"$ny.tif |
|
| 69 |
|
|
| 70 |
' _ |
|
| 71 |
|
|
| 72 |
|
|
| 73 |
rm $DIR"_tif"/${DIR}_??.tif
|
|
| 74 |
|
|
| 75 |
echo start to integrate greenland |
|
| 76 |
|
|
| 77 |
|
|
| 78 |
for tile in 2_0 3_0 4_0 2_1 3_1 4_1 ; do echo $tile $DIR ; done | xargs -n 2 -P 6 bash -c $' |
|
| 79 |
|
|
| 80 |
tile=$1 |
|
| 81 |
DIR=$2 |
|
| 82 |
INDIR=/lustre0/scratch/ga254/dem_bj/GMTED2010/tiles |
|
| 83 |
|
|
| 84 |
# get greenland mn and paste in mn md mx mn be |
|
| 85 |
if [ $DIR = mn75_grd ] || [ $DIR=md75_grd ] || [ $DIR=mx75_grd ] || [ $DIR=mn75_grd ] || $DIR = be75_grd ] ; then |
|
| 86 |
echo $DIR $tile |
|
| 87 |
pkmosaic -t 0 -min -30000 $(pkinfo -bb -i $INDIR/$DIR"_tif"/${tile}.tif) -co COMPRESS=LZW -co ZLEVEL=9 -m max -i $INDIR/$DIR"_tif"/${tile}.tif -i $INDIR/mn75_grd_tif/green_land_msk.tif -o $INDIR/$DIR"_tif"/${tile}g.tif
|
|
| 88 |
fi |
|
| 89 |
# get greenland ds and paste in ds |
|
| 90 |
if [ $DIR = ds75_grd ] ; then |
|
| 91 |
echo $DIR $tile |
|
| 92 |
pkmosaic -t 0 -min -30000 $(pkinfo -bb -i $INDIR/$DIR"_tif"/${tile}.tif) -co COMPRESS=LZW -co ZLEVEL=9 -m max -i $INDIR/$DIR"_tif"/${tile}.tif -i $INDIR/ds75_grd_tif/green_land_msk.tif -o $INDIR/$DIR"_tif"/${tile}g.tif
|
|
| 93 |
fi |
|
| 94 |
# standard deviation not computed for greenland becouse == to 0 |
|
| 95 |
|
|
| 96 |
mv $INDIR/$DIR"_tif"/${tile}.tif $INDIR/$DIR"_tif"/${tile}_no_green.tiff
|
|
| 97 |
|
|
| 98 |
mv $INDIR/$DIR"_tif"/${tile}g.tif $INDIR/$DIR"_tif"/${tile}.tif
|
|
| 99 |
|
|
| 100 |
' _ |
|
| 101 |
|
|
| 102 |
|
|
| 103 |
|
|
| 104 |
|
|
| 105 |
|
|
| 106 |
|
|
| 107 |
|
|
| terrain/procedures/dem_variables/gmted2010_res_x10/sc3a_dem_variables_merge.sh | ||
|---|---|---|
| 1 |
# calculate different variables for the dem |
|
| 2 |
# for dir1 in altitude ; do for dir2 in stdev ; do echo $dir1/$dir2 ; done ; done | xargs -n 1 -P 5 bash /mnt/data2/dem_variables/scripts/sc2_dem_merge.sh |
|
| 3 |
# for dir1 in altitude slope tri tpi roughness aspect ; do for dir2 in max mean median min stdev; do echo $dir1/$dir2 ds ; done ; done | xargs -n 2 -P 12 bash /mnt/data2/dem_variables/scripts/environmental-layers/terrain/procedures/dem_variables/gmted2010_res_x10/sc3a_dem_variables_merge.sh |
|
| 4 |
|
|
| 5 |
|
|
| 6 |
OUTDIR=/mnt/data2/dem_variables/GMTED2010 |
|
| 7 |
|
|
| 8 |
DIR=$1 |
|
| 9 |
dir1=$(echo ${DIR%/*}) # cancel the part after /
|
|
| 10 |
dir2=$(echo ${DIR#*/}) # cancel the part before /
|
|
| 11 |
mm=$2 |
|
| 12 |
|
|
| 13 |
if [ $dir1 = altitude ] ; then type=Int16 ; fi |
|
| 14 |
if [ $dir1 = aspect ] ; then type=Int16 ; fi |
|
| 15 |
if [ $dir1 = slope ] ; then type=Byte ; fi |
|
| 16 |
if [ $dir1 = tri ] ; then type=Int16 ; fi |
|
| 17 |
if [ $dir1 = tpi ] ; then type=Int16 ; fi |
|
| 18 |
if [ $dir1 = roughness ] ; then type=Int16 ; fi |
|
| 19 |
|
|
| 20 |
if [ $dir1 != aspect ]; then |
|
| 21 |
|
|
| 22 |
echo processing merging tiles in $dir1 |
|
| 23 |
|
|
| 24 |
rm -f $OUTDIR/$DIR/$dir1"_"$dir2.tif |
|
| 25 |
rm -f $OUTDIR/$DIR/$dir1"_"$dir2"_a".tif |
|
| 26 |
rm -f $OUTDIR/$DIR/$dir1"_"$dir2"_b".tif |
|
| 27 |
rm -f $OUTDIR/$DIR/$dir1"_"$dir2"_c".tif |
|
| 28 |
rm -f $OUTDIR/$DIR/$dir1"_"$dir2"_d".tif |
|
| 29 |
rm -f $OUTDIR/$DIR/$dir1"_"$dir2"_e".tif |
|
| 30 |
|
|
| 31 |
gdal_merge.py -o $OUTDIR/$DIR/$dir1"_"$dir2"_a".tif -ot $type -co COMPRESS=LZW $OUTDIR/$DIR/tiles/[0-1]_?_${mm}.tif
|
|
| 32 |
gdal_merge.py -o $OUTDIR/$DIR/$dir1"_"$dir2"_b".tif -ot $type -co COMPRESS=LZW $OUTDIR/$DIR/tiles/[2-3]_?_${mm}.tif
|
|
| 33 |
gdal_merge.py -o $OUTDIR/$DIR/$dir1"_"$dir2"_c".tif -ot $type -co COMPRESS=LZW $OUTDIR/$DIR/tiles/[4-5]_?_${mm}.tif
|
|
| 34 |
gdal_merge.py -o $OUTDIR/$DIR/$dir1"_"$dir2"_d".tif -ot $type -co COMPRESS=LZW $OUTDIR/$DIR/tiles/[6-7]_?_${mm}.tif
|
|
| 35 |
gdal_merge.py -o $OUTDIR/$DIR/$dir1"_"$dir2"_e".tif -ot $type -co COMPRESS=LZW $OUTDIR/$DIR/tiles/[8-9]_?_${mm}.tif
|
|
| 36 |
|
|
| 37 |
|
|
| 38 |
rm -f $OUTDIR/$DIR/$dir1"_"$dir2.tif |
|
| 39 |
|
|
| 40 |
gdal_merge.py -o $OUTDIR/$DIR/$dir1"_"$dir2.tif -ot $type -co COMPRESS=LZW $OUTDIR/$DIR/$dir1"_"$dir2"_a".tif $OUTDIR/$DIR/$dir1"_"$dir2"_b".tif $OUTDIR/$DIR/$dir1"_"$dir2"_c".tif $OUTDIR/$DIR/$dir1"_"$dir2"_d".tif $OUTDIR/$DIR/$dir1"_"$dir2"_e".tif |
|
| 41 |
|
|
| 42 |
rm -f $OUTDIR/$DIR/$dir1"_"$dir2"_a".tif |
|
| 43 |
rm -f $OUTDIR/$DIR/$dir1"_"$dir2"_b".tif |
|
| 44 |
rm -f $OUTDIR/$DIR/$dir1"_"$dir2"_c".tif |
|
| 45 |
rm -f $OUTDIR/$DIR/$dir1"_"$dir2"_d".tif |
|
| 46 |
rm -f $OUTDIR/$DIR/$dir1"_"$dir2"_e".tif |
|
| 47 |
|
|
| 48 |
gdal_translate -co COMPRESS=LZW -co ZLEVEL=9 $OUTDIR/$DIR/$dir1"_"$dir2.tif $OUTDIR/$DIR/${dir1}_${dir2}_${mm}.tif
|
|
| 49 |
rm -f $OUTDIR/$DIR/$dir1"_"$dir2.tif |
|
| 50 |
|
|
| 51 |
else # just applaied to the aspect variables |
|
| 52 |
|
|
| 53 |
echo processing merging tiles for the different aspect variables in $dir1 |
|
| 54 |
|
|
| 55 |
for aspect_var in "_sin_t10k" "_cos_t10k" "_Ew_t10k" "_Nw_t10k" ; do |
|
| 56 |
|
|
| 57 |
rm -f $OUTDIR/$DIR/$dir1"_"$dir2"_a"$aspect_var.tif |
|
| 58 |
rm -f $OUTDIR/$DIR/$dir1"_"$dir2"_b"$aspect_var.tif |
|
| 59 |
rm -f $OUTDIR/$DIR/$dir1"_"$dir2"_c"$aspect_var.tif |
|
| 60 |
rm -f $OUTDIR/$DIR/$dir1"_"$dir2"_d"$aspect_var.tif |
|
| 61 |
rm -f $OUTDIR/$DIR/$dir1"_"$dir2"_e"$aspect_var.tif |
|
| 62 |
|
|
| 63 |
gdal_merge.py -o $OUTDIR/$DIR/$dir1"_"$dir2"_a"$aspect_var.tif -ot $type -co COMPRESS=LZW $OUTDIR/$DIR/tiles/[0-1]_?_${mm}$aspect_var.tif
|
|
| 64 |
gdal_merge.py -o $OUTDIR/$DIR/$dir1"_"$dir2"_b"$aspect_var.tif -ot $type -co COMPRESS=LZW $OUTDIR/$DIR/tiles/[2-3]_?_${mm}$aspect_var.tif
|
|
| 65 |
gdal_merge.py -o $OUTDIR/$DIR/$dir1"_"$dir2"_c"$aspect_var.tif -ot $type -co COMPRESS=LZW $OUTDIR/$DIR/tiles/[4-5]_?_${mm}$aspect_var.tif
|
|
| 66 |
gdal_merge.py -o $OUTDIR/$DIR/$dir1"_"$dir2"_d"$aspect_var.tif -ot $type -co COMPRESS=LZW $OUTDIR/$DIR/tiles/[6-7]_?_${mm}$aspect_var.tif
|
|
| 67 |
gdal_merge.py -o $OUTDIR/$DIR/$dir1"_"$dir2"_e"$aspect_var.tif -ot $type -co COMPRESS=LZW $OUTDIR/$DIR/tiles/[8-9]_?_${mm}$aspect_var.tif
|
|
| 68 |
|
|
| 69 |
rm -f $OUTDIR/$DIR/$dir1"_"$dir2$aspect_var.tif |
|
| 70 |
|
|
| 71 |
gdal_merge.py -o $OUTDIR/$DIR/$dir1"_"$dir2$aspect_var.tif -ot $type -co COMPRESS=LZW $OUTDIR/$DIR/$dir1"_"$dir2"_a"$aspect_var.tif $OUTDIR/$DIR/$dir1"_"$dir2"_b"$aspect_var.tif $OUTDIR/$DIR/$dir1"_"$dir2"_c"$aspect_var.tif $OUTDIR/$DIR/$dir1"_"$dir2"_d"$aspect_var.tif $OUTDIR/$DIR/$dir1"_"$dir2"_e"$aspect_var.tif |
|
| 72 |
|
|
| 73 |
gdal_translate -co COMPRESS=LZW -co ZLEVEL=9 $OUTDIR/$DIR/$dir1"_"$dir2$aspect_var.tif $OUTDIR/$DIR/${dir1}_${dir2}_${mm}_${aspect_var}.tif
|
|
| 74 |
rm -f $OUTDIR/$DIR/$dir1"_"$dir2$aspect_var.tif |
|
| 75 |
|
|
| 76 |
rm -f $OUTDIR/$DIR/$dir1"_"$dir2"_a"$aspect_var.tif |
|
| 77 |
rm -f $OUTDIR/$DIR/$dir1"_"$dir2"_b"$aspect_var.tif |
|
| 78 |
rm -f $OUTDIR/$DIR/$dir1"_"$dir2"_c"$aspect_var.tif |
|
| 79 |
rm -f $OUTDIR/$DIR/$dir1"_"$dir2"_d"$aspect_var.tif |
|
| 80 |
rm -f $OUTDIR/$DIR/$dir1"_"$dir2"_e"$aspect_var.tif |
|
| 81 |
|
|
| 82 |
done |
|
| 83 |
|
|
| 84 |
fi |
|
| 85 |
|
|
| 86 |
|
|
| 87 |
|
|
| terrain/procedures/dem_variables/gmted2010_res_x10/sc4_pixel_correction_bj.sh | ||
|---|---|---|
| 1 |
# correct immage with anomalus pixel valus. |
|
| 2 |
# the file |
|
| 3 |
# giuseppea@turaco:/mnt/data2/dem_variables/GMTED2010/altitude/class_mi$ pkinfo -hist -i ../../tiles/mi75_grd_tif/5_1.tif | more |
|
| 4 |
# -931 1 anomalus |
|
| 5 |
# -898 1 anomalus |
|
| 6 |
# -498 1 |
|
| 7 |
# -461 1 |
|
| 8 |
|
|
| 9 |
# therefore the -931 -898 will be fill in withe the nearby pixel. |
|
| 10 |
|
|
| 11 |
cd /lustre0/scratch/ga254/dem_bj/GMTED2010/tiles/mi75_grd_tif |
|
| 12 |
cp 5_1.tif 5_1_orig.tiff |
|
| 13 |
pkgetmask -co COMPRESS=LZW -i 5_1.tif -min -890 -max 10000 -t 1 -f 0 -o 5_1_mask.tif |
|
| 14 |
pkfillnodata -i 5_1.tif -m 5_1_mask.tif -o 5_1_fill.tif |
|
| 15 |
mv 5_1_fill.tif 5_1.tif |
|
| 16 |
rm 5_1_mask.tif |
|
| 17 |
|
|
| 18 |
# corretta |
|
| 19 |
|
|
| 20 |
cd /lustre0/scratch/ga254/dem_bj/GMTED2010/tiles/ |
|
| 21 |
|
|
| 22 |
for dir in md75_grd_tif be75_grd_tif ds75_grd_tif mn75_grd_tif ;do |
|
| 23 |
cd $dir |
|
| 24 |
cp 5_1.tif 5_1_orig.tiff |
|
| 25 |
pkgetmask -co COMPRESS=LZW -i 5_1.tif -min -600 -max 10000 -t 1 -f 0 -o 5_1_mask.tif |
|
| 26 |
pkfillnodata -i 5_1.tif -m 5_1_mask.tif -o 5_1_fill.tif |
|
| 27 |
mv 5_1_fill.tif 5_1.tif |
|
| 28 |
rm 5_1_mask.tif |
|
| 29 |
done |
|
| 30 |
|
|
| 31 |
|
|
| 32 |
|
|
| 33 |
# the values becom -93 and -80 |
|
| 34 |
|
|
| 35 |
# -93 2830 |
|
| 36 |
# -93 2831 |
|
| 37 |
# |
|
| 38 |
# -80 19449 |
|
| 39 |
# -80 19450 |
|
| 40 |
|
|
| 41 |
## correction of a square box of 500 500 pixel. Set the value = to 179 as the near by pixel. |
|
| 42 |
cd /lustre0/scratch/ga254/dem_bj/GMTED2010/tiles/ |
|
| 43 |
|
|
| 44 |
for dir in mi75_grd_tif mn75_grd_tif md75_grd_tif ds75_grd_tif be75_grd_tif mx75_grd_tif ; do |
|
| 45 |
|
|
| 46 |
cd $dir |
|
| 47 |
gdal_translate -srcwin 10070 3830 500 500 2_1.tif 2_1_clip.tif |
|
| 48 |
|
|
| 49 |
pksetmask -co COMPRESS=LZW -t 0 -f 179 -i 2_1.tif -m 2_1_clip.tif -o 2_1_correct.tif |
|
| 50 |
mv 2_1.tif 2_1_orig.tiff |
|
| 51 |
mv 2_1_correct.tif 2_1.tif |
|
| 52 |
rm 2_1_clip.tif |
|
| 53 |
done |
|
| 54 |
|
|
| 55 |
|
|
| 56 |
# correction of a square in the caspian sea set value to -27 |
|
| 57 |
cd /lustre0/scratch/ga254/dem_bj/GMTED2010/tiles/ |
|
| 58 |
|
|
| 59 |
for dir in mx75_grd_tif md75_grd_tif be75_grd_tif ds75_grd_tif mn75_grd_tif mi75_grd_tif ;do |
|
| 60 |
cd $dir |
|
| 61 |
gdal_translate -srcwin 5719 5249 1050 1050 6_1.tif 6_1_clip1.tif |
|
| 62 |
gdal_translate -srcwin 6200 6200 1050 550 6_1.tif 6_1_clip2.tif |
|
| 63 |
gdal_translate -srcwin 6700 6700 1050 550 6_1.tif 6_1_clip3.tif |
|
| 64 |
gdal_translate -srcwin 7150 7000 550 700 6_1.tif 6_1_clip4.tif |
|
| 65 |
gdal_translate -srcwin 6700 7550 1050 1100 6_1.tif 6_1_clip5.tif |
|
| 66 |
gdal_translate -srcwin 7150 8000 1050 1150 6_1.tif 6_1_clip6.tif |
|
| 67 |
|
|
| 68 |
pksetmask -co COMPRESS=LZW -t 0 -f -27 -t 0 -f -27 -t 0 -f -27 -t 0 -f -27 -t 0 -f -27 -t 0 -f -27 -m 6_1_clip1.tif -m 6_1_clip2.tif -m 6_1_clip3.tif -m 6_1_clip4.tif -m 6_1_clip5.tif -m 6_1_clip6.tif -i 6_1.tif -o 6_1_correct.tif |
|
| 69 |
mv 6_1.tif 6_1_orig.tiff |
|
| 70 |
mv 6_1_correct.tif 6_1.tif |
|
| 71 |
rm 6_1_clip*.tif |
|
| 72 |
|
|
| 73 |
done |
|
| 74 |
|
|
| 75 |
|
|
| terrain/procedures/dem_variables/gmted2010_res_x10/sc5a_class_treshold_percent_bj.sh | ||
|---|---|---|
| 1 |
|
|
| 2 |
# calculate altitude area percent above a specific treshold |
|
| 3 |
# e.g 75% of class200 means that 75% of the pixels is >= 200 |
|
| 4 |
# for this case the treshold is set every 100 meter |
|
| 5 |
# geting the integer of the altitued / 100 |
|
| 6 |
# 230 become class 200 |
|
| 7 |
# 159 become class 100 |
|
| 8 |
|
|
| 9 |
# for file in /mnt/data2/dem_variables/GMTED2010/tiles/mi75_grd_tif/*.tif ; do echo $file mi ; done | xargs -n 2 -P 25 bash /mnt/data2/dem_variables/GMTED2010/scripts/sc2_class_treshold_percent.sh |
|
| 10 |
# for file in /mnt/data2/dem_variables/GMTED2010/tiles/mx75_grd_tif/*.tif ; do echo $file mx ; done | xargs -n 2 -P 25 bash /mnt/data2/dem_variables/GMTED2010/scripts/sc2_class_treshold_percent.sh |
|
| 11 |
|
|
| 12 |
# run the script in the @bulldogj |
|
| 13 |
|
|
| 14 |
# rm /lustre0/scratch/ga254/stderr/* ; rm /lustre0/scratch/ga254/stdout/* ; |
|
| 15 |
|
|
| 16 |
# for file in /home2/ga254/scratch/dem_bj/GMTED2010/tiles/mi75_grd_tif/*.tif ; do qsub -v file=$file,mm=mi /lustre0/scratch/ga254/scripts_bj/environmental-layers/terrain/procedures/dem_variables/gmted2010_res_x10/sc2_class_treshold_percent_bj.sh ; done |
|
| 17 |
|
|
| 18 |
# for file in /home2/ga254/scratch/dem_bj/GMTED2010/tiles/md75_grd_tif/*.tif ; do qsub -v file=$file,mm=md /lustre0/scratch/ga254/scripts_bj/environmental-layers/terrain/procedures/dem_variables/gmted2010_res_x10/sc2_class_treshold_percent_bj.sh ; done |
|
| 19 |
|
|
| 20 |
# for file in /home2/ga254/scratch/dem_bj/GMTED2010/tiles/mx75_grd_tif/*.tif ; do qsub -v file=$file,mm=mx /lustre0/scratch/ga254/scripts_bj/environmental-layers/terrain/procedures/dem_variables/gmted2010_res_x10/sc2_class_treshold_percent_bj.sh ; done |
|
| 21 |
|
|
| 22 |
# to check |
|
| 23 |
# ny=45 ; for n in `seq 1 9` ;do echo `gdallocationinfo -valonly altitude/class/5_1_class_tmp3.tif 2$n $ny` `gdallocationinfo -valonly tiles/mn75_grd_tif/5_1.tif 2$n $ny` ; done |
|
| 24 |
|
|
| 25 |
#PBS -S /bin/bash |
|
| 26 |
#PBS -q fas_normal |
|
| 27 |
#PBS -l mem=4gb |
|
| 28 |
#PBS -l walltime=10:00:00 |
|
| 29 |
#PBS -l nodes=10:ppn=4 |
|
| 30 |
#PBS -V |
|
| 31 |
#PBS -o /lustre0/scratch/ga254/stdout |
|
| 32 |
#PBS -e /lustre0/scratch/ga254/stderr |
|
| 33 |
|
|
| 34 |
# load moduels |
|
| 35 |
|
|
| 36 |
module load Tools/Python/2.7.3 |
|
| 37 |
module load Libraries/GDAL/1.10.0 |
|
| 38 |
module load Tools/PKTOOLS/2.4.2 |
|
| 39 |
module load Libraries/OSGEO/1.10.0 |
|
| 40 |
|
|
| 41 |
# file=$1 |
|
| 42 |
# mm=$2 |
|
| 43 |
|
|
| 44 |
file=${file}
|
|
| 45 |
mm=${mm}
|
|
| 46 |
|
|
| 47 |
filename=$(basename $file .tif) |
|
| 48 |
|
|
| 49 |
echo $file |
|
| 50 |
echo $mm |
|
| 51 |
|
|
| 52 |
INDIR=/home2/ga254/scratch/dem_bj/GMTED2010/tiles/$mm"75_grd_tif" |
|
| 53 |
OUTDIR=/home2/ga254/scratch/dem_bj/GMTED2010/altitude/class_$mm/class |
|
| 54 |
|
|
| 55 |
echo calcualte altitude every 100 meter using the the Int16 factors for $file |
|
| 56 |
|
|
| 57 |
time ( |
|
| 58 |
|
|
| 59 |
gdal_calc.py -A $INDIR/$filename.tif --calc="(A / 100)" --outfile=$OUTDIR/../tmp/$filename"_class_tmp1.tif" --type=Int16 --overwrite --co=COMPRESS=LZW |
|
| 60 |
gdal_calc.py -A $OUTDIR/../tmp/$filename"_class_tmp1.tif" --calc="(A * 100)" --outfile=$OUTDIR/../tmp/$filename"_class_tmp2.tif" --type=Int16 --overwrite --co=COMPRESS=LZW |
|
| 61 |
|
|
| 62 |
|
|
| 63 |
rm $OUTDIR/../tmp/$filename"_class_tmp1.tif" |
|
| 64 |
|
|
| 65 |
gdal_translate -co COMPRESS=LZW -co ZLEVEL=9 $OUTDIR/../tmp/$filename"_class_tmp2.tif" $OUTDIR/$filename"_class.tif" |
|
| 66 |
rm $OUTDIR/../tmp/$filename"_class_tmp2.tif" |
|
| 67 |
|
|
| 68 |
|
|
| 69 |
gdalinfo -mm $OUTDIR/$filename"_class.tif" | grep Computed | awk '{ gsub ("[=,]"," "); print int($(NF-1)), int($(NF))}' > $OUTDIR/../tmp/$filename"_min_max_"$mm.txt
|
|
| 70 |
|
|
| 71 |
echo min and max for $OUTDIR/../tmp/$filename"_min_max_"$mm.txt |
|
| 72 |
|
|
| 73 |
# start to calculate for each treshold percent pixel |
|
| 74 |
|
|
| 75 |
for class in $(seq `awk '{ print $1}' $OUTDIR/../tmp/${filename}_min_max_${mm}.txt` 100 `awk '{ print $2}' $OUTDIR/../tmp/${filename}_min_max_${mm}.txt` ) ; do
|
|
| 76 |
|
|
| 77 |
class_start=$class |
|
| 78 |
class_end=$(awk '{ print $2}' $OUTDIR/../tmp/${filename}_min_max_${mm}.txt)
|
|
| 79 |
class_string=$(for class_unique in $(seq $class_start 100 $class_end ) ; do echo -n "-class $class_unique " ; done) |
|
| 80 |
|
|
| 81 |
echo applaid the filter for the classes $class_string |
|
| 82 |
|
|
| 83 |
pkfilter -dx 4 -dy 4 $class_string -f density -d 4 -i $OUTDIR/$filename"_class.tif" -o $OUTDIR/../class$class/$filename"_C"$class"Perc.tif" -co COMPRESS=LZW -co ZLEVEL=9 -ot Byte |
|
| 84 |
|
|
| 85 |
done |
|
| 86 |
|
|
| 87 |
) |
|
| terrain/procedures/dem_variables/gmted2010_res_x10/sc5b_dem_variables_bj.sh | ||
|---|---|---|
| 1 |
# variables derived from the dem following commands in http://www.gdal.org/gdaldem.html # gdaldem_slope |
|
| 2 |
# to check ls *.tif | xargs -n 1 -P 30 bash -c $' gdalinfo -mm $1 |grep Max | awk \'{ gsub("[=,]", " ") ; print $3,$4 }\' ' _
|
|
| 3 |
|
|
| 4 |
# find /mnt/data2/dem_variables/GMTED2010/{aspect,roughness,slope,tpi,tri} -name *.tif | xargs -n 1 -P 10 rm ;
|
|
| 5 |
|
|
| 6 |
|
|
| 7 |
# rm /lustre0/scratch/ga254/stderr/* ; rm /lustre0/scratch/ga254/stdout/* |
|
| 8 |
|
|
| 9 |
# for file in `ls /lustre0/scratch/ga254/dem_bj/GMTED2010/tiles/md75_grd_tif/?_?.tif` ; do qsub -v file=$file /lustre0/scratch/ga254/scripts_bj_bk/environmental-layers/terrain/procedures/dem_variables/gmted2010_res_x10/sc5b_dem_variables_bj.sh ; done |
|
| 10 |
|
|
| 11 |
# for file in `ls /lustre0/scratch/ga254/dem_bj/GMTED2010/tiles/md75_grd_tif/?_?.tif` ; do bash /lustre0/scratch/ga254/scripts_bj_bk/environmental-layers/terrain/procedures/dem_variables/gmted2010_res_x10/sc5b_dem_variables_bj.sh $file ; done |
|
| 12 |
# file=$1 |
|
| 13 |
|
|
| 14 |
#PBS -S /bin/bash |
|
| 15 |
#PBS -q fas_normal |
|
| 16 |
#PBS -l mem=4gb |
|
| 17 |
#PBS -l walltime=5:00:00 |
|
| 18 |
#PBS -l nodes=1:ppn=4 |
|
| 19 |
#PBS -V |
|
| 20 |
#PBS -o /lustre0/scratch/ga254/stdout |
|
| 21 |
#PBS -e /lustre0/scratch/ga254/stderr |
|
| 22 |
|
|
| 23 |
|
|
| 24 |
# load moduels |
|
| 25 |
|
|
| 26 |
module load Tools/Python/2.7.3 |
|
| 27 |
module load Libraries/GDAL/1.10.0 |
|
| 28 |
module load Tools/PKTOOLS/2.4.2 |
|
| 29 |
module load Libraries/OSGEO/1.10.0 |
|
| 30 |
|
|
| 31 |
|
|
| 32 |
|
|
| 33 |
|
|
| 34 |
file=${file}
|
|
| 35 |
|
|
| 36 |
INDIR_MI=/lustre0/scratch/ga254/dem_bj/GMTED2010/tiles/mi75_grd_tif |
|
| 37 |
INDIR_MD=/lustre0/scratch/ga254/dem_bj/GMTED2010/tiles/md75_grd_tif |
|
| 38 |
INDIR_MX=/lustre0/scratch/ga254/dem_bj/GMTED2010/tiles/mx75_grd_tif |
|
| 39 |
INDIR_MN=/lustre0/scratch/ga254/dem_bj/GMTED2010/tiles/mn75_grd_tif |
|
| 40 |
TMP=/tmp |
|
| 41 |
|
|
| 42 |
export OUTDIR=/lustre0/scratch/ga254/dem_bj/GMTED2010 |
|
| 43 |
|
|
| 44 |
export filename=`basename $file .tif` |
|
| 45 |
|
|
| 46 |
time ( |
|
| 47 |
# 30 min for this |
|
| 48 |
echo max of the max with file $INDIR_MX/$filename.tif |
|
| 49 |
/home2/ga254/bin/bin/pkfilter -m -32768 -dx 4 -dy 4 -f max -d 4 -i $INDIR_MX/$filename.tif -o $OUTDIR/altitude/max_of_mx/tiles/${filename}.tif -co COMPRESS=LZW -ot Int16
|
|
| 50 |
|
|
| 51 |
|
|
| 52 |
echo max of the max with file $INDIR_MI/$filename.tif |
|
| 53 |
/home2/ga254/bin/bin/pkfilter -m -32768 -dx 4 -dy 4 -f min -d 4 -i $INDIR_MI/$filename.tif -o $OUTDIR/altitude/min_of_mi/tiles/${filename}.tif -co COMPRESS=LZW -ot Int16
|
|
| 54 |
|
|
| 55 |
echo mean of the mn with file $INDIR_MN/$filename.tif |
|
| 56 |
/home2/ga254/bin/bin/pkfilter -m -32768 -dx 4 -dy 4 -f mean -d 4 -i $INDIR_MN/$filename.tif -o $OUTDIR/altitude/mean_of_mn/tiles/${filename}.tif -co COMPRESS=LZW -ot Int16
|
|
| 57 |
|
|
| 58 |
echo meadian of the md with file $INDIR_MD/$filename.tif |
|
| 59 |
/home2/ga254/bin/bin/pkfilter -m -32768 -dx 4 -dy 4 -f median -d 4 -i $INDIR_MD/$filename.tif -o $OUTDIR/altitude/median_of_md/tiles/${filename}.tif -co COMPRESS=LZW -ot Int16
|
|
| 60 |
|
|
| 61 |
echo stdev of mn with file $INDIR_MN/$filename.tif |
|
| 62 |
|
|
| 63 |
/home2/ga254/bin/bin/pkfilter -m -32768 -dx 4 -dy 4 -f var -d 4 -i $INDIR_MN/$filename.tif -co COMPRESS=LZW -o $TMP/tmp_${filename}.tif -ot Int32 # max 1552385.000 sqrt(1245.947)
|
|
| 64 |
gdal_calc.py --co=COMPRESS=LZW -A $TMP/tmp_${filename}.tif --calc="sqrt(A)" --type Int16 --overwrite --outfile $OUTDIR/altitude/stdev_of_mn/tiles/${filename}.tif
|
|
| 65 |
rm -f $TMP/tmp_${filename}.tif
|
|
| 66 |
|
|
| 67 |
echo stdev of md with file $INDIR_MD/$filename.tif |
|
| 68 |
|
|
| 69 |
/home2/ga254/bin/bin/pkfilter -m -32768 -dx 4 -dy 4 -f var -d 4 -i $INDIR_MD/$filename.tif -co COMPRESS=LZW -o $TMP/tmp_${filename}.tif -ot Int32 # max 1552385.000 sqrt(1245.947)
|
|
| 70 |
gdal_calc.py --co=COMPRESS=LZW -A $TMP/tmp_${filename}.tif --calc="sqrt(A)" --type Int16 --overwrite --outfile $OUTDIR/altitude/stdev_of_md/tiles/${filename}.tif
|
|
| 71 |
rm -f $TMP/tmp_${filename}.tif
|
|
| 72 |
|
|
| 73 |
|
|
| 74 |
|
|
| 75 |
# form here only md will be used |
|
| 76 |
|
|
| 77 |
INDIR=$INDIR_MD |
|
| 78 |
mm=md |
|
| 79 |
|
|
| 80 |
# starting to use gdaldem to compute variables. Gdaldem use -9999 as no data. |
|
| 81 |
|
|
| 82 |
echo slope with file $INDIR/$filename.tif |
|
| 83 |
gdaldem slope -s 111120 -co COMPRESS=LZW $INDIR/$filename.tif $OUTDIR/slope/tiles/${filename}_${mm}.tif # -s to consider xy in degree and z in meters
|
|
| 84 |
# slope median |
|
| 85 |
/home2/ga254/bin/bin/pkfilter -m -9999 -dx 4 -dy 4 -f median -d 4 -i $OUTDIR/slope/tiles/${filename}_${mm}.tif -o $OUTDIR/slope/median/tiles/${filename}_${mm}.tif -co COMPRESS=LZW -ot Byte
|
|
| 86 |
# slope stdev |
|
| 87 |
/home2/ga254/bin/bin/pkfilter -m -9999 -dx 4 -dy 4 -f var -d 4 -i $OUTDIR/slope/tiles/${filename}_${mm}.tif -co COMPRESS=LZW -o $TMP/tmp_${filename}_${mm}.tif -ot Int32
|
|
| 88 |
gdal_calc.py --co=COMPRESS=LZW -A $TMP/tmp_${filename}_${mm}.tif --calc="sqrt(A)" --type Int16 --overwrite --outfile $OUTDIR/slope/stdev/tiles/${filename}_${mm}.tif
|
|
| 89 |
rm -f $TMP/tmp_${filename}_${mm}.tif
|
|
| 90 |
# slope min |
|
| 91 |
/home2/ga254/bin/bin/pkfilter -m -9999 -dx 4 -dy 4 -f min -d 4 -i $OUTDIR/slope/tiles/${filename}_${mm}.tif -o $OUTDIR/slope/min/tiles/${filename}_${mm}.tif -co COMPRESS=LZW -ot Byte
|
|
| 92 |
# slope max |
|
| 93 |
/home2/ga254/bin/bin/pkfilter -m -9999 -dx 4 -dy 4 -f max -d 4 -i $OUTDIR/slope/tiles/${filename}_${mm}.tif -o $OUTDIR/slope/max/tiles/${filename}_${mm}.tif -co COMPRESS=LZW -ot Byte
|
|
| 94 |
# slope mean |
|
| 95 |
/home2/ga254/bin/bin/pkfilter -m -9999 -dx 4 -dy 4 -f mean -d 4 -i $OUTDIR/slope/tiles/${filename}_${mm}.tif -o $OUTDIR/slope/mean/tiles/${filename}_${mm}.tif -co COMPRESS=LZW -ot Byte
|
|
| 96 |
|
|
| 97 |
# rm -f $OUTDIR/slope/tiles/$filename.tif |
|
| 98 |
|
|
| 99 |
echo generate a Terrain Ruggedness Index TRI with file $file |
|
| 100 |
gdaldem TRI -co COMPRESS=LZW $INDIR/$filename.tif $OUTDIR/tri/tiles/${filename}_${mm}.tif
|
|
| 101 |
# tri median |
|
| 102 |
/home2/ga254/bin/bin/pkfilter -m -9999 -dx 4 -dy 4 -f median -d 4 -i $OUTDIR/tri/tiles/${filename}_${mm}.tif -o $OUTDIR/tri/median/tiles/${filename}_${mm}.tif -co COMPRESS=LZW -ot Int16
|
|
| 103 |
# tri stdev |
|
| 104 |
/home2/ga254/bin/bin/pkfilter -m -9999 -dx 4 -dy 4 -f var -d 4 -i $OUTDIR/tri/tiles/${filename}_${mm}.tif -co COMPRESS=LZW -o $TMP/tmp_${filename}_${mm}.tif
|
|
| 105 |
gdal_calc.py --co=COMPRESS=LZW -A $TMP/tmp_${filename}_${mm}.tif --calc="sqrt(A)" --type Int16 --overwrite --outfile $OUTDIR/tri/stdev/tiles/${filename}_${mm}.tif
|
|
| 106 |
rm -f $TMP/tmp_${filename}_${mm}.tif
|
|
| 107 |
# tri min |
|
| 108 |
/home2/ga254/bin/bin/pkfilter -m -9999 -dx 4 -dy 4 -f min -d 4 -i $OUTDIR/tri/tiles/${filename}_${mm}.tif -o $OUTDIR/tri/min/tiles/${filename}_${mm}.tif -co COMPRESS=LZW -ot Int16
|
|
| 109 |
# tri max |
|
| 110 |
/home2/ga254/bin/bin/pkfilter -m -9999 -dx 4 -dy 4 -f max -d 4 -i $OUTDIR/tri/tiles/${filename}_${mm}.tif -o $OUTDIR/tri/max/tiles/${filename}_${mm}.tif -co COMPRESS=LZW -ot Int16
|
|
| 111 |
# tri mean |
|
| 112 |
/home2/ga254/bin/bin/pkfilter -m -9999 -dx 4 -dy 4 -f mean -d 4 -i $OUTDIR/tri/tiles/${filename}_${mm}.tif -o $OUTDIR/tri/mean/tiles/${filename}_${mm}.tif -co COMPRESS=LZW -ot Int16
|
|
| 113 |
|
|
| 114 |
# rm -f $OUTDIR/tri/tiles/$filename.tif |
|
| 115 |
|
|
| 116 |
echo generate a Topographic Position Index TPI with file $INDIR/$filename.tif |
|
| 117 |
|
|
| 118 |
gdaldem TPI -co COMPRESS=LZW $INDIR/$filename.tif $OUTDIR/tpi/tiles/${filename}_${mm}.tif # tpi has negative number
|
|
| 119 |
|
|
| 120 |
/home2/ga254/bin/oft-calc -ot Float32 $OUTDIR/tri/tiles/${filename}_${mm}.tif $OUTDIR/tpi/tiles/${filename}_${mm}"_t10.tif" &> /dev/null <<EOF
|
|
| 121 |
1 |
|
| 122 |
#1 10 * |
|
| 123 |
EOF |
|
| 124 |
|
|
| 125 |
# tpi median |
|
| 126 |
/home2/ga254/bin/bin/pkfilter -m -9999 -dx 4 -dy 4 -f median -d 4 -i $OUTDIR/tpi/tiles/${filename}_${mm}"_t10.tif" -o $OUTDIR/tpi/median/tiles/${filename}_${mm}.tif -co COMPRESS=LZW -ot Int16
|
|
| 127 |
echo tpi stdev |
|
| 128 |
/home2/ga254/bin/bin/pkfilter -m -9999 -dx 4 -dy 4 -f var -d 4 -i $OUTDIR/tpi/tiles/${filename}_${mm}"_t10.tif" -co COMPRESS=LZW -o $TMP/tmp_${filename}_${mm}.tif
|
|
| 129 |
gdal_calc.py --co=COMPRESS=LZW -A $TMP/tmp_${filename}_${mm}.tif --calc="sqrt(A)" --type Int32 --overwrite --outfile $OUTDIR/tpi/stdev/tiles/${filename}_${mm}.tif
|
|
| 130 |
rm -f $TMP/tmp_${filename}_${mm}.tif
|
|
| 131 |
# tpi min |
|
| 132 |
/home2/ga254/bin/bin/pkfilter -m -9999 -dx 4 -dy 4 -f min -d 4 -i $OUTDIR/tpi/tiles/${filename}_${mm}"_t10.tif" -o $OUTDIR/tpi/min/tiles/${filename}_${mm}.tif -co COMPRESS=LZW -ot Int16
|
|
| 133 |
# tpi max |
|
| 134 |
/home2/ga254/bin/bin/pkfilter -m -9999 -dx 4 -dy 4 -f max -d 4 -i $OUTDIR/tpi/tiles/${filename}_${mm}"_t10.tif" -o $OUTDIR/tpi/max/tiles/${filename}_${mm}.tif -co COMPRESS=LZW -ot Int16
|
|
| 135 |
# tpi mean |
|
| 136 |
/home2/ga254/bin/bin/pkfilter -m -9999 -dx 4 -dy 4 -f mean -d 4 -i $OUTDIR/tpi/tiles/${filename}_${mm}"_t10.tif" -o $OUTDIR/tpi/mean/tiles/${filename}_${mm}.tif -co COMPRESS=LZW -ot Int16
|
|
| 137 |
|
|
| 138 |
|
|
| 139 |
echo generate roughness with file $INDIR/$filename.tif |
|
| 140 |
|
|
| 141 |
gdaldem roughness -co COMPRESS=LZW $INDIR/$filename.tif $OUTDIR/roughness/tiles/${filename}_${mm}.tif
|
|
| 142 |
|
|
| 143 |
# roughness median |
|
| 144 |
/home2/ga254/bin/bin/pkfilter -m -9999 -dx 4 -dy 4 -f median -d 4 -i $OUTDIR/roughness/tiles/${filename}_${mm}.tif -o $OUTDIR/roughness/median/tiles/${filename}_${mm}.tif -co COMPRESS=LZW -ot Int16
|
|
| 145 |
echo roughness stdev |
|
| 146 |
/home2/ga254/bin/bin/pkfilter -m -9999 -dx 4 -dy 4 -f var -d 4 -i $OUTDIR/roughness/tiles/${filename}_${mm}.tif -co COMPRESS=LZW -o $TMP/tmp_${filename}_${mm}.tif
|
|
| 147 |
gdal_calc.py --co=COMPRESS=LZW -A $TMP/tmp_${filename}_${mm}.tif --calc="sqrt(A)" --type Int32 --overwrite --outfile $OUTDIR/roughness/stdev/tiles/${filename}_${mm}.tif
|
|
| 148 |
rm -f $TMP/tmp_${filename}_${mm}.tif
|
|
| 149 |
# roughness min |
|
| 150 |
/home2/ga254/bin/bin/pkfilter -m -9999 -dx 4 -dy 4 -f min -d 4 -i $OUTDIR/roughness/tiles/${filename}_${mm}.tif -o $OUTDIR/roughness/min/tiles/${filename}_${mm}.tif -co COMPRESS=LZW -ot Int16
|
|
| 151 |
# roughness max |
|
| 152 |
/home2/ga254/bin/bin/pkfilter -m -9999 -dx 4 -dy 4 -f max -d 4 -i $OUTDIR/roughness/tiles/${filename}_${mm}.tif -o $OUTDIR/roughness/max/tiles/${filename}_${mm}.tif -co COMPRESS=LZW -ot Int16
|
|
| 153 |
# roughness mean |
|
| 154 |
/home2/ga254/bin/bin/pkfilter -m -9999 -dx 4 -dy 4 -f mean -d 4 -i $OUTDIR/roughness/tiles/${filename}_${mm}.tif -o $OUTDIR/roughness/mean/tiles/${filename}_${mm}.tif -co COMPRESS=LZW -ot Int16
|
|
| 155 |
|
|
| 156 |
# rm -f $OUTDIR/roughness/tiles/${filename}_${mm}.tif
|
|
| 157 |
|
|
| 158 |
|
|
| 159 |
echo aspect with file $INDIR/$filename.tif |
|
| 160 |
|
|
| 161 |
gdaldem aspect -zero_for_flat -co COMPRESS=LZW $INDIR/$filename.tif $OUTDIR/aspect/tiles/${filename}_${mm}.tif
|
|
| 162 |
|
|
| 163 |
# r1 aspect , r2 slope |
|
| 164 |
|
|
| 165 |
gdal_calc.py --co=COMPRESS=LZW --NoDataValue -9999 -A $OUTDIR/aspect/tiles/${filename}_${mm}.tif --calc="(sin(A))" --outfile $OUTDIR/aspect/tiles/${filename}_${mm}"_sin.tif" --overwrite --type Float32
|
|
| 166 |
gdal_calc.py --co=COMPRESS=LZW --NoDataValue -9999 -A $OUTDIR/aspect/tiles/${filename}_${mm}.tif --calc="(cos(A))" --outfile $OUTDIR/aspect/tiles/${filename}_${mm}"_cos.tif" --overwrite --type Float32
|
|
| 167 |
|
|
| 168 |
gdal_calc.py --co=COMPRESS=LZW --NoDataValue -9999 -A $OUTDIR/slope/tiles/${filename}_${mm}.tif -B $OUTDIR/aspect/tiles/${filename}_${mm}"_sin.tif" --calc="((sin(A))*B)" --outfile $OUTDIR/aspect/tiles/${filename}_${mm}"_Ew.tif" --overwrite --type Float32
|
|
| 169 |
gdal_calc.py --co=COMPRESS=LZW --NoDataValue -9999 -A $OUTDIR/slope/tiles/${filename}_${mm}.tif -B $OUTDIR/aspect/tiles/${filename}_${mm}"_cos.tif" --calc="((sin(A))*B)" --outfile $OUTDIR/aspect/tiles/${filename}_${mm}"_Nw.tif" --overwrite --type Float32
|
|
| 170 |
|
|
| 171 |
echo aspect sin cos Ew Nw median |
|
| 172 |
# sin |
|
| 173 |
/home2/ga254/bin/bin/pkfilter -m -9999 -dx 4 -dy 4 -f median -d 4 -i $OUTDIR/aspect/tiles/${filename}_${mm}"_sin.tif" -o $OUTDIR/aspect/median/tiles/${filename}_${mm}"_sin_f.tif" -co COMPRESS=LZW -ot Float32
|
|
| 174 |
/home2/ga254/bin/oft-calc -ot Int16 $OUTDIR/aspect/median/tiles/${filename}_${mm}"_sin_f.tif" $TMP/${filename}_${mm}"_sin_t10k_tmp.tif" &> /dev/null <<EOF
|
|
| 175 |
1 |
|
| 176 |
#1 10000 * |
|
| 177 |
EOF |
|
| 178 |
gdal_translate -co COMPRESS=LZW -ot Int16 $TMP/${filename}_${mm}"_sin_t10k_tmp.tif" $OUTDIR/aspect/median/tiles/${filename}_${mm}"_sin_t10k.tif"
|
|
| 179 |
rm $TMP/${filename}_${mm}"_sin_t10k_tmp.tif"
|
|
| 180 |
# cos |
|
| 181 |
/home2/ga254/bin/bin/pkfilter -m -9999 -dx 4 -dy 4 -f median -d 4 -i $OUTDIR/aspect/tiles/${filename}_${mm}"_cos.tif" -o $OUTDIR/aspect/median/tiles/${filename}_${mm}"_cos_f.tif" -co COMPRESS=LZW -ot Float32
|
|
| 182 |
/home2/ga254/bin/oft-calc -ot Int16 $OUTDIR/aspect/median/tiles/${filename}_${mm}"_cos_f.tif" $TMP/${filename}_${mm}"_cos_t10k_tmp.tif" &> /dev/null <<EOF
|
|
| 183 |
1 |
|
| 184 |
#1 10000 * |
|
| 185 |
EOF |
|
| 186 |
gdal_translate -co COMPRESS=LZW -ot Int16 $TMP/${filename}_${mm}"_cos_t10k_tmp.tif" $OUTDIR/aspect/median/tiles/${filename}_${mm}"_cos_t10k.tif"
|
|
| 187 |
rm $TMP/${filename}_${mm}"_cos_t10k_tmp.tif"
|
|
| 188 |
# Ew |
|
| 189 |
/home2/ga254/bin/bin/pkfilter -m -9999 -dx 4 -dy 4 -f median -d 4 -i $OUTDIR/aspect/tiles/${filename}_${mm}"_Ew.tif" -o $OUTDIR/aspect/median/tiles/${filename}_${mm}"_Ew_f.tif" -co COMPRESS=LZW -ot Float32
|
|
| 190 |
/home2/ga254/bin/oft-calc -ot Int16 $OUTDIR/aspect/median/tiles/${filename}_${mm}"_Ew_f.tif" $TMP/${filename}_${mm}"_Ew_t10k_tmp.tif" &> /dev/null <<EOF
|
|
| 191 |
1 |
|
| 192 |
#1 10000 * |
|
| 193 |
EOF |
|
| 194 |
gdal_translate -co COMPRESS=LZW -ot Int16 $TMP/${filename}_${mm}"_Ew_t10k_tmp.tif" $OUTDIR/aspect/median/tiles/${filename}_${mm}"_Ew_t10k.tif"
|
|
| 195 |
rm $TMP/${filename}_${mm}"_Ew_t10k_tmp.tif"
|
|
| 196 |
# Nw |
|
| 197 |
/home2/ga254/bin/bin/pkfilter -m -9999 -dx 4 -dy 4 -f median -d 4 -i $OUTDIR/aspect/tiles/${filename}_${mm}"_Nw.tif" -o $OUTDIR/aspect/median/tiles/${filename}_${mm}"_Nw_f.tif" -co COMPRESS=LZW -ot Float32
|
|
| 198 |
/home2/ga254/bin/oft-calc -ot Int16 $OUTDIR/aspect/median/tiles/${filename}_${mm}"_Nw_f.tif" $TMP/${filename}_${mm}"_Nw_t10k_tmp.tif" &> /dev/null <<EOF
|
|
| 199 |
1 |
|
| 200 |
#1 10000 * |
|
| 201 |
EOF |
|
| 202 |
gdal_translate -co COMPRESS=LZW -ot Int16 $TMP/${filename}_${mm}"_Nw_t10k_tmp.tif" $OUTDIR/aspect/median/tiles/${filename}_${mm}"_Nw_t10k.tif"
|
|
| 203 |
rm $TMP/${filename}_${mm}"_Nw_t10k_tmp.tif"
|
|
| 204 |
|
|
| 205 |
|
|
| 206 |
echo aspect sin cos Ew Nw mean |
|
| 207 |
# sin |
|
| 208 |
/home2/ga254/bin/bin/pkfilter -m -9999 -dx 4 -dy 4 -f mean -d 4 -i $OUTDIR/aspect/tiles/${filename}_${mm}"_sin.tif" -o $OUTDIR/aspect/mean/tiles/${filename}_${mm}"_sin_f.tif" -co COMPRESS=LZW -ot Float32
|
|
| 209 |
/home2/ga254/bin/oft-calc -ot Int16 $OUTDIR/aspect/mean/tiles/${filename}_${mm}"_sin_f.tif" $TMP/${filename}_${mm}"_sin_t10k_tmp.tif" &> /dev/null <<EOF
|
|
| 210 |
1 |
|
| 211 |
#1 10000 * |
|
| 212 |
EOF |
|
| 213 |
gdal_translate -co COMPRESS=LZW -ot Int16 $TMP/${filename}_${mm}"_sin_t10k_tmp.tif" $OUTDIR/aspect/mean/tiles/${filename}_${mm}"_sin_t10k.tif"
|
|
| 214 |
rm $TMP/${filename}_${mm}"_sin_t10k_tmp.tif"
|
|
| 215 |
# cos |
|
| 216 |
/home2/ga254/bin/bin/pkfilter -m -9999 -dx 4 -dy 4 -f mean -d 4 -i $OUTDIR/aspect/tiles/${filename}_${mm}"_cos.tif" -o $OUTDIR/aspect/mean/tiles/${filename}_${mm}"_cos_f.tif" -co COMPRESS=LZW -ot Float32
|
|
| 217 |
/home2/ga254/bin/oft-calc -ot Int16 $OUTDIR/aspect/mean/tiles/${filename}_${mm}"_cos_f.tif" $TMP/${filename}_${mm}"_cos_t10k_tmp.tif" &> /dev/null <<EOF
|
|
| 218 |
1 |
|
| 219 |
#1 10000 * |
|
| 220 |
EOF |
|
| 221 |
gdal_translate -co COMPRESS=LZW -ot Int16 $TMP/${filename}_${mm}"_cos_t10k_tmp.tif" $OUTDIR/aspect/mean/tiles/${filename}_${mm}"_cos_t10k.tif"
|
|
| 222 |
rm $TMP/${filename}_${mm}"_cos_t10k_tmp.tif"
|
|
| 223 |
# Ew |
|
| 224 |
/home2/ga254/bin/bin/pkfilter -m -9999 -dx 4 -dy 4 -f mean -d 4 -i $OUTDIR/aspect/tiles/${filename}_${mm}"_Ew.tif" -o $OUTDIR/aspect/mean/tiles/${filename}_${mm}"_Ew_f.tif" -co COMPRESS=LZW -ot Float32
|
|
| 225 |
/home2/ga254/bin/oft-calc -ot Int16 $OUTDIR/aspect/mean/tiles/${filename}_${mm}"_Ew_f.tif" $TMP/${filename}_${mm}"_Ew_t10k_tmp.tif" &> /dev/null <<EOF
|
|
| 226 |
1 |
|
| 227 |
#1 10000 * |
|
| 228 |
EOF |
|
| 229 |
gdal_translate -co COMPRESS=LZW -ot Int16 $TMP/${filename}_${mm}"_Ew_t10k_tmp.tif" $OUTDIR/aspect/mean/tiles/${filename}_${mm}"_Ew_t10k.tif"
|
|
| 230 |
rm $TMP/${filename}_${mm}"_Ew_t10k_tmp.tif"
|
|
| 231 |
# Nw |
|
| 232 |
/home2/ga254/bin/bin/pkfilter -m -9999 -dx 4 -dy 4 -f mean -d 4 -i $OUTDIR/aspect/tiles/${filename}_${mm}"_Nw.tif" -o $OUTDIR/aspect/mean/tiles/${filename}_${mm}"_Nw_f.tif" -co COMPRESS=LZW -ot Float32
|
|
| 233 |
/home2/ga254/bin/oft-calc -ot Int16 $OUTDIR/aspect/mean/tiles/${filename}_${mm}"_Nw_f.tif" $TMP/${filename}_${mm}"_Nw_t10k_tmp.tif" &> /dev/null <<EOF
|
|
| 234 |
1 |
|
| 235 |
#1 10000 * |
|
| 236 |
EOF |
|
| 237 |
gdal_translate -co COMPRESS=LZW -ot Int16 $TMP/${filename}_${mm}"_Nw_t10k_tmp.tif" &> /dev/null <<EOF
|
|
| 238 |
1 |
|
| 239 |
#1 10000 * |
|
| 240 |
EOF |
|
| 241 |
gdal_translate -co COMPRESS=LZW -ot Int16 $TMP/${filename}_${mm}"_Nw_t10k_tmp.tif" $OUTDIR/aspect/mean/tiles/${filename}_${mm}"_Nw_t10k.tif"
|
|
| 242 |
rm $TMP/${filename}_${mm}"_Nw_t10k_tmp.tif"
|
|
| 243 |
|
|
| 244 |
echo aspect sin cos Ew Nw max |
|
| 245 |
# sin |
|
| 246 |
/home2/ga254/bin/bin/pkfilter -m -9999 -dx 4 -dy 4 -f max -d 4 -i $OUTDIR/aspect/tiles/${filename}_${mm}"_sin.tif" -o $OUTDIR/aspect/max/tiles/${filename}_${mm}"_sin_f.tif" -co COMPRESS=LZW -ot Float32
|
|
| 247 |
/home2/ga254/bin/oft-calc -ot Int16 $OUTDIR/aspect/max/tiles/${filename}_${mm}"_sin_f.tif" $TMP/${filename}_${mm}"_sin_t10k_tmp.tif" &> /dev/null <<EOF
|
|
| 248 |
1 |
|
| 249 |
#1 10000 * |
|
| 250 |
EOF |
|
| 251 |
gdal_translate -co COMPRESS=LZW -ot Int16 $TMP/${filename}_${mm}"_sin_t10k_tmp.tif" $OUTDIR/aspect/max/tiles/${filename}_${mm}"_sin_t10k.tif"
|
|
| 252 |
rm $TMP/${filename}_${mm}"_sin_t10k_tmp.tif"
|
|
| 253 |
# cos |
|
| 254 |
/home2/ga254/bin/bin/pkfilter -m -9999 -dx 4 -dy 4 -f max -d 4 -i $OUTDIR/aspect/tiles/${filename}_${mm}"_cos.tif" -o $OUTDIR/aspect/max/tiles/${filename}_${mm}"_cos_f.tif" -co COMPRESS=LZW -ot Float32
|
|
| 255 |
/home2/ga254/bin/oft-calc -ot Int16 $OUTDIR/aspect/max/tiles/${filename}_${mm}"_cos_f.tif" $TMP/${filename}_${mm}"_cos_t10k_tmp.tif" &> /dev/null <<EOF
|
|
| 256 |
1 |
|
| 257 |
#1 10000 * |
|
| 258 |
EOF |
|
| 259 |
gdal_translate -co COMPRESS=LZW -ot Int16 $TMP/${filename}_${mm}"_cos_t10k_tmp.tif" $OUTDIR/aspect/max/tiles/${filename}_${mm}"_cos_t10k.tif"
|
|
| 260 |
rm $TMP/${filename}_${mm}"_cos_t10k_tmp.tif"
|
|
| 261 |
# Ew |
|
| 262 |
/home2/ga254/bin/bin/pkfilter -m -9999 -dx 4 -dy 4 -f max -d 4 -i $OUTDIR/aspect/tiles/${filename}_${mm}"_Ew.tif" -o $OUTDIR/aspect/max/tiles/${filename}_${mm}"_Ew_f.tif" -co COMPRESS=LZW -ot Float32
|
|
| 263 |
/home2/ga254/bin/oft-calc -ot Int16 $OUTDIR/aspect/max/tiles/${filename}_${mm}"_Ew_f.tif" $TMP/${filename}_${mm}"_Ew_t10k_tmp.tif" &> /dev/null <<EOF
|
|
| 264 |
1 |
|
| 265 |
#1 10000 * |
|
| 266 |
EOF |
|
| 267 |
gdal_translate -co COMPRESS=LZW -ot Int16 $TMP/${filename}_${mm}"_Ew_t10k_tmp.tif" $OUTDIR/aspect/max/tiles/${filename}_${mm}"_Ew_t10k.tif"
|
|
| 268 |
rm $TMP/${filename}_${mm}"_Ew_t10k_tmp.tif"
|
|
| 269 |
# Nw |
|
| 270 |
/home2/ga254/bin/bin/pkfilter -m -9999 -dx 4 -dy 4 -f max -d 4 -i $OUTDIR/aspect/tiles/${filename}_${mm}"_Nw.tif" -o $OUTDIR/aspect/max/tiles/${filename}_${mm}"_Nw_f.tif" -co COMPRESS=LZW -ot Float32
|
|
| 271 |
/home2/ga254/bin/oft-calc -ot Int16 $OUTDIR/aspect/max/tiles/${filename}_${mm}"_Nw_f.tif" $TMP/${filename}_${mm}"_Nw_t10k_tmp.tif" &> /dev/null <<EOF
|
|
| 272 |
1 |
|
| 273 |
#1 10000 * |
|
| 274 |
EOF |
|
| 275 |
gdal_translate -co COMPRESS=LZW -ot Int16 $TMP/${filename}_${mm}"_Nw_t10k_tmp.tif" $OUTDIR/aspect/max/tiles/${filename}_${mm}"_Nw_t10k.tif"
|
|
| 276 |
rm $TMP/${filename}_${mm}"_Nw_t10k_tmp.tif"
|
|
| 277 |
|
|
| 278 |
echo aspect sin cos Ew Nw min |
|
| 279 |
# sin |
|
| 280 |
/home2/ga254/bin/bin/pkfilter -m -9999 -dx 4 -dy 4 -f min -d 4 -i $OUTDIR/aspect/tiles/${filename}_${mm}"_sin.tif" -o $OUTDIR/aspect/min/tiles/${filename}_${mm}"_sin_f.tif" -co COMPRESS=LZW -ot Float32
|
|
| 281 |
/home2/ga254/bin/oft-calc -ot Int16 $OUTDIR/aspect/min/tiles/${filename}_${mm}"_sin_f.tif" $TMP/${filename}_${mm}"_sin_t10k_tmp.tif" &> /dev/null <<EOF
|
|
| 282 |
1 |
|
| 283 |
#1 10000 * |
|
| 284 |
EOF |
|
| 285 |
gdal_translate -co COMPRESS=LZW -ot Int16 $TMP/${filename}_${mm}"_sin_t10k_tmp.tif" $OUTDIR/aspect/min/tiles/${filename}_${mm}"_sin_t10k.tif"
|
|
| 286 |
rm $TMP/${filename}_${mm}"_sin_t10k_tmp.tif"
|
|
| 287 |
# cos |
|
| 288 |
/home2/ga254/bin/bin/pkfilter -m -9999 -dx 4 -dy 4 -f min -d 4 -i $OUTDIR/aspect/tiles/${filename}_${mm}"_cos.tif" -o $OUTDIR/aspect/min/tiles/${filename}_${mm}"_cos_f.tif" -co COMPRESS=LZW -ot Float32
|
|
| 289 |
/home2/ga254/bin/oft-calc -ot Int16 $OUTDIR/aspect/min/tiles/${filename}_${mm}"_cos_f.tif" $TMP/${filename}_${mm}"_cos_t10k_tmp.tif" &> /dev/null <<EOF
|
|
| 290 |
1 |
|
| 291 |
#1 10000 * |
|
| 292 |
EOF |
|
| 293 |
gdal_translate -co COMPRESS=LZW -ot Int16 $TMP/${filename}_${mm}"_cos_t10k_tmp.tif" $OUTDIR/aspect/min/tiles/${filename}_${mm}"_cos_t10k.tif"
|
|
| 294 |
rm $TMP/${filename}_${mm}"_cos_t10k_tmp.tif"
|
|
| 295 |
# Ew |
|
| 296 |
/home2/ga254/bin/bin/pkfilter -m -9999 -dx 4 -dy 4 -f min -d 4 -i $OUTDIR/aspect/tiles/${filename}_${mm}"_Ew.tif" -o $OUTDIR/aspect/min/tiles/${filename}_${mm}"_Ew_f.tif" -co COMPRESS=LZW -ot Float32
|
|
| 297 |
/home2/ga254/bin/oft-calc -ot Int16 $OUTDIR/aspect/min/tiles/${filename}_${mm}"_Ew_f.tif" $TMP/${filename}_${mm}"_Ew_t10k_tmp.tif" &> /dev/null <<EOF
|
|
| 298 |
1 |
|
| 299 |
#1 10000 * |
|
| 300 |
EOF |
|
| 301 |
gdal_translate -co COMPRESS=LZW -ot Int16 $TMP/${filename}_${mm}"_Ew_t10k_tmp.tif" $OUTDIR/aspect/min/tiles/${filename}_${mm}"_Ew_t10k.tif"
|
|
| 302 |
rm $TMP/${filename}_${mm}"_Ew_t10k_tmp.tif"
|
|
| 303 |
# Nw |
|
| 304 |
/home2/ga254/bin/bin/pkfilter -m -9999 -dx 4 -dy 4 -f min -d 4 -i $OUTDIR/aspect/tiles/${filename}_${mm}"_Nw.tif" -o $OUTDIR/aspect/min/tiles/${filename}_${mm}"_Nw_f.tif" -co COMPRESS=LZW -ot Float32
|
|
| 305 |
/home2/ga254/bin/oft-calc -ot Int16 $OUTDIR/aspect/min/tiles/${filename}_${mm}"_Nw_f.tif" $TMP/${filename}_${mm}"_Nw_t10k_tmp.tif" &> /dev/null <<EOF
|
|
| 306 |
1 |
|
| 307 |
#1 10000 * |
|
| 308 |
EOF |
|
| 309 |
gdal_translate -co COMPRESS=LZW -ot Int16 $TMP/${filename}_${mm}"_Nw_t10k_tmp.tif" $OUTDIR/aspect/min/tiles/${filename}_${mm}"_Nw_t10k.tif"
|
|
| 310 |
rm $TMP/${filename}_${mm}"_Nw_t10k_tmp.tif"
|
|
| 311 |
|
|
| 312 |
echo aspect sin cos Ew Nw stdev |
|
| 313 |
# stdev |
|
| 314 |
/home2/ga254/bin/bin/pkfilter -m -9999 -dx 4 -dy 4 -f var -d 4 -i $OUTDIR/aspect/tiles/${filename}_${mm}"_sin.tif" -o $OUTDIR/aspect/stdev/tiles/${filename}_${mm}"_sin_f.tif" -co COMPRESS=LZW -ot Float32
|
|
| 315 |
gdal_calc.py --co=COMPRESS=LZW -A $OUTDIR/aspect/stdev/tiles/${filename}_${mm}"_sin_f.tif" --calc="(sqrt(A))*10000" --type Int16 --overwrite --outfile $TMP/${filename}_${mm}"_sin_t10k_tmp.tif"
|
|
| 316 |
gdal_translate -co COMPRESS=LZW -ot Int16 $TMP/${filename}_${mm}"_sin_t10k_tmp.tif" $OUTDIR/aspect/stdev/tiles/${filename}_${mm}"_sin_t10k.tif"
|
|
| 317 |
rm $TMP/${filename}_${mm}"_sin_t10k_tmp.tif"
|
|
| 318 |
# cos |
|
| 319 |
/home2/ga254/bin/bin/pkfilter -m -9999 -dx 4 -dy 4 -f var -d 4 -i $OUTDIR/aspect/tiles/${filename}_${mm}"_cos.tif" -o $OUTDIR/aspect/stdev/tiles/${filename}_${mm}"_cos_f.tif" -co COMPRESS=LZW -ot Float32
|
|
| 320 |
gdal_calc.py --co=COMPRESS=LZW -A $OUTDIR/aspect/stdev/tiles/${filename}_${mm}"_cos_f.tif" --calc="(sqrt(A))*10000" --type Int16 --overwrite --outfile $TMP/${filename}_${mm}"_cos_t10k_tmp.tif"
|
|
| 321 |
gdal_translate -co COMPRESS=LZW -ot Int16 $TMP/${filename}_${mm}"_cos_t10k_tmp.tif" $OUTDIR/aspect/stdev/tiles/${filename}_${mm}"_cos_t10k.tif"
|
|
| 322 |
rm $TMP/${filename}_${mm}"_cos_t10k_tmp.tif"
|
|
| 323 |
# Ew |
|
| 324 |
/home2/ga254/bin/bin/pkfilter -m -9999 -dx 4 -dy 4 -f var -d 4 -i $OUTDIR/aspect/tiles/${filename}_${mm}"_Ew.tif" -o $OUTDIR/aspect/stdev/tiles/${filename}_${mm}"_Ew_f.tif" -co COMPRESS=LZW -ot Float32
|
|
| 325 |
gdal_calc.py --co=COMPRESS=LZW -A $OUTDIR/aspect/stdev/tiles/${filename}_${mm}"_Ew_f.tif" --calc="(sqrt(A))*10000" --type Int16 --overwrite --outfile $TMP/${filename}_${mm}"_Ew_t10k_tmp.tif"
|
|
| 326 |
gdal_translate -co COMPRESS=LZW -ot Int16 $TMP/${filename}_${mm}"_Ew_t10k_tmp.tif" $OUTDIR/aspect/stdev/tiles/${filename}_${mm}"_Ew_t10k.tif"
|
|
| 327 |
rm $TMP/${filename}_${mm}"_Ew_t10k_tmp.tif"
|
|
| 328 |
# Nw |
|
| 329 |
/home2/ga254/bin/bin/pkfilter -m -9999 -dx 4 -dy 4 -f var -d 4 -i $OUTDIR/aspect/tiles/${filename}_${mm}"_Nw.tif" -o $OUTDIR/aspect/stdev/tiles/${filename}_${mm}"_Nw_f.tif" -co COMPRESS=LZW -ot Float32
|
|
| 330 |
gdal_calc.py --co=COMPRESS=LZW -A $OUTDIR/aspect/stdev/tiles/${filename}_${mm}"_Nw_f.tif" --calc="(sqrt(A))*10000" --type Int16 --overwrite --outfile $TMP/${filename}_${mm}"_Nw_t10k_tmp.tif"
|
|
| 331 |
gdal_translate -co COMPRESS=LZW -ot Int16 $TMP/${filename}_${mm}"_Nw_t10k_tmp.tif" $OUTDIR/aspect/stdev/tiles/${filename}_${mm}"_Nw_t10k.tif"
|
|
| 332 |
rm $TMP/${filename}_${mm}"_Nw_t10k_tmp.tif"
|
|
| 333 |
|
|
| 334 |
# Look for lines such as "Max Util Resources Per Task" in the output file from your job. |
|
| 335 |
|
|
| 336 |
|
|
| 337 |
) |
|
| 338 |
|
|
| 339 |
checkjob -v $PBS_JOBID |
|
| terrain/procedures/dem_variables/gmted2010_res_x10/sc6a_class_treshold_density_merge_bj.sh | ||
|---|---|---|
| 1 |
|
|
| 2 |
# perform a merging action for the /mnt/data2/dem_variables/GMTED2010/altitude/class_mi and /mnt/data2/dem_variables/GMTED2010/altitude/class_mx |
|
| 3 |
# create in avery clever way missing tiles. The missing tiles were appear if all the pixel where above or below a treshold, therfore all 100% or 0% |
|
| 4 |
|
|
| 5 |
# for dir in `seq -500 100 8600` ; do echo $dir mi ; done | xargs -n 2 -P 20 bash /mnt/data2/dem_variables/scripts/environmental-layers/terrain/procedures/dem_variables/gmted2010_res_x10/sc3_class_treshold_density_merge.sh |
|
| 6 |
|
|
| 7 |
# for dir in `seq -500 100 8700` ; do echo $dir mx ; done | xargs -n 2 -P 20 bash /mnt/data2/dem_variables/scripts/environmental-layers/terrain/procedures/dem_variables/gmted2010_res_x10/sc3_class_treshold_density_merge.sh |
|
| 8 |
|
|
| 9 |
|
|
| 10 |
|
|
| 11 |
# run the script in the @bulldogj |
|
| 12 |
|
|
| 13 |
# rm /lustre0/scratch/ga254/stderr/* ; rm /lustre0/scratch/ga254/stdout/* ; |
|
| 14 |
|
|
| 15 |
# create tif with value 0 or 100 used to refeel the area |
|
| 16 |
|
|
| 17 |
# xargs controllare il risultato di qeusta linea sotto. |
|
| 18 |
|
|
| 19 |
# ls /home2/ga254/scratch/dem_bj/GMTED2010/tiles/md75_grd_tif/*.tif | xargs -n 1 -P 100 bash -c $' file=$1 ; filename=`basename $file .tif` ; pkgetmask -min 10000 -max 10001 -t 0 -ot Byte -i $file -co COMPRESS=LZW -co ZLEVEL=9 -o /home2/ga254/scratch/dem_bj/GMTED2010/altitude/value0/$filename.tif ; gdalwarp -tr 0.008333333333333 0.008333333333333 -co COMPRESS=LZW -co ZLEVEL=9 /home2/ga254/scratch/dem_bj/GMTED2010/altitude/value0/tmp_$filename.tif /home2/ga254/scratch/dem_bj/GMTED2010/altitude/value0/$filename.tif; pkgetmask -min 10000 -max 10001 -t 0 -f 100 -ot Byte -i $file -co COMPRESS=LZW -co ZLEVEL=9 -o /home2/ga254/scratch/dem_bj/GMTED2010/altitude/value100/tmp_$filename.tif ; gdalwarp -tr 0.008333333333333 0.008333333333333 -co COMPRESS=LZW -co ZLEVEL=9 /home2/ga254/scratch/dem_bj/GMTED2010/altitude/value100/tmp_$filename.tif /home2/ga254/scratch/dem_bj/GMTED2010/altitude/value100/$filename.tif ; rm /home2/ga254/scratch/dem_bj/GMTED2010/altitude/value100/tmp_$filename.tif ' _ |
|
| 20 |
|
|
| 21 |
|
|
| 22 |
# to que after the completition of sc2 |
|
| 23 |
|
|
| 24 |
# n=`qstat | grep percent_bj | wc -l` ; for time in `seq 1 100` ; do if [ $n -eq 0 ] ; then echo run the script ; ; exit ; else sleep 60 ; echo sleeping ; fi ; done |
|
| 25 |
|
|
| 26 |
# for dir in `seq -400 100 8600` ; do qsub -v dir=$dir,mm=mi /lustre0/scratch/ga254/scripts_bj/environmental-layers/terrain/procedures/dem_variables/gmted2010_res_x10/sc3_class_treshold_density_merge_bj.sh ; done # 400 8600 range confirrmed (-500 tutti i valore == 100) |
|
| 27 |
# for dir in `seq -500 100 8700` ; do qsub -v dir=$dir,mm=md /lustre0/scratch/ga254/scripts_bj/environmental-layers/terrain/procedures/dem_variables/gmted2010_res_x10/sc3_class_treshold_density_merge_bj.sh ; done # -500 8700 range confirrmed |
|
| 28 |
# for dir in `seq -500 100 8700` ; do qsub -v dir=$dir,mm=mx /lustre0/scratch/ga254/scripts_bj/environmental-layers/terrain/procedures/dem_variables/gmted2010_res_x10/sc3_class_treshold_density_merge_bj.sh ; done # -500 8700 range confirrmed |
|
| 29 |
|
|
| 30 |
|
|
| 31 |
#PBS -S /bin/bash |
|
| 32 |
#PBS -q fas_normal |
|
| 33 |
#PBS -l mem=4gb |
|
| 34 |
#PBS -l walltime=2:00:00 # portato a 2 ore perche a 1 ora veniva bloccato. |
|
| 35 |
#PBS -l nodes=1:ppn=4 |
|
| 36 |
#PBS -V |
|
| 37 |
#PBS -o /lustre0/scratch/ga254/stdout |
|
| 38 |
#PBS -e /lustre0/scratch/ga254/stderr |
|
| 39 |
|
|
| 40 |
|
|
| 41 |
# load moduels |
|
| 42 |
|
|
| 43 |
module load Tools/Python/2.7.3 |
|
| 44 |
module load Libraries/GDAL/1.10.0 |
|
| 45 |
module load Tools/PKTOOLS/2.4.2 |
|
| 46 |
module load Libraries/OSGEO/1.10.0 |
|
| 47 |
|
|
| 48 |
# DIR=$1 |
|
| 49 |
# mm=$2 |
|
| 50 |
|
|
| 51 |
DIR=${dir}
|
|
| 52 |
mm=${mm}
|
|
| 53 |
INDIR=/home2/ga254/scratch/dem_bj/GMTED2010/altitude/class_${mm}/class${DIR} # this has pixel value = 0.002083333333333
|
|
| 54 |
INDIR_C=/home2/ga254/scratch/dem_bj/GMTED2010/altitude/class_${mm}/class # this has pixel value = 0.002083333333333
|
|
| 55 |
INDIR_Cm100=/home2/ga254/scratch/dem_bj/GMTED2010/altitude/class_${mm}/class-100 # this has pixel value = 0.008333333333333 this is the only class with all (50) tiles
|
|
| 56 |
OUTDIR=/home2/ga254/scratch/dem_bj/GMTED2010/altitude/percent_class_${mm}
|
|
| 57 |
TMP=/home2/ga254/scratch/dem_bj/GMTED2010/tmp |
|
| 58 |
|
|
| 59 |
|
|
| 60 |
rm -f $OUTDIR/file_processed_sc3.txt # the file has ben processed by the script sc1_dem_treshold_percent.sh |
|
| 61 |
|
|
| 62 |
for file in `ls $INDIR_C/*.tif` ; do |
|
| 63 |
tile=`basename $file _class.tif` |
|
| 64 |
|
|
| 65 |
if [ -f $INDIR/$tile"_C"$DIR"Perc.tif" ] ; then |
|
| 66 |
echo the file $INDIR/$tile"_C"$DIR"Perc.tif" exist and will be merged as it is |
|
| 67 |
echo $tile"_C"$DIR"Perc.tif" >> $OUTDIR/file_processed_sc3.txt # usefull to list file processed by script sc1, in case of delation use this. |
|
| 68 |
else |
|
| 69 |
|
|
| 70 |
gdalinfo -mm $INDIR_C/$tile"_class.tif" | grep Computed | awk '{ gsub ("[=,]"," "); print int($(NF-1)), int($(NF))}' > $TMP/${tile}_class${DIR}_min_max_${mm}.txt
|
|
| 71 |
|
|
| 72 |
min=`awk '{ print $1}' $TMP/${tile}_class${DIR}_min_max_${mm}.txt `
|
|
| 73 |
max=`awk '{ print $2}' $TMP/${tile}_class${DIR}_min_max_${mm}.txt `
|
|
| 74 |
rm -f $TMP/${tile}_class${DIR}_min_max_${mm}.txt
|
|
| 75 |
|
|
| 76 |
echo $min and $max compare to $DIR |
|
| 77 |
|
|
| 78 |
if [ $max -lt $DIR ] ; then |
|
| 79 |
echo copy the $INDIR/$tile"_C"$DIR"Perc.tif" with 0 value |
|
| 80 |
echo $INDIR/$tile"_C"$DIR"Perc.tif" with 0 value >> $INDIR/refill_file_list.txt |
|
| 81 |
# pkgetmask -min 10000 -max 10001 -t 0 -ot Byte -i $INDIR_Cm100/$tile"_C-100Perc.tif" -co COMPRESS=LZW -o $INDIR/$tile"_C"$DIR"Perc.tif" |
|
| 82 |
# change the previus line with this to avoid constant calculation |
|
| 83 |
cp /home2/ga254/scratch/dem_bj/GMTED2010/altitude/value0/$tile".tif" $INDIR/$tile"_C"$DIR"Perc.tif" |
|
| 84 |
|
|
| 85 |
fi |
|
| 86 |
|
|
| 87 |
if [ $min -gt $DIR ] ; then |
|
| 88 |
echo copy the $INDIR/$tile"_C"$DIR"Perc.tif" with 100 value |
|
| 89 |
echo $INDIR/$tile"_C"$DIR"Perc.tif" with 100 value >> $INDIR/refill_file_list.txt |
|
| 90 |
# pkgetmask -min 10000 -max 10001 -t 0 -f 100 -ot Byte -co COMPRESS=LZW -i $INDIR_Cm100/$tile"_C-100Perc.tif" -o $INDIR/$tile"_C"$DIR"Perc.tif" |
|
| 91 |
cp /home2/ga254/scratch/dem_bj/GMTED2010/altitude/value100/$tile".tif" $INDIR/$tile"_C"$DIR"Perc.tif" |
|
| 92 |
|
|
| 93 |
fi |
|
| 94 |
|
|
| 95 |
fi |
|
| 96 |
|
|
| 97 |
done |
|
| 98 |
|
|
| 99 |
echo STARTING THE MERGING ACTION |
|
| 100 |
rm -f $OUTDIR/perc_$DIR.tif |
|
| 101 |
gdal_merge.py -co COMPRESS=LZW -ot Byte -o $OUTDIR/perc_$DIR.tif $INDIR/*.tif |
|
| 102 |
|
|
| 103 |
if [ -f $OUTDIR/color-bw.txt ] ; then |
|
| 104 |
echo the $OUTDIR/color-bw.txt exist ; |
|
| 105 |
else |
|
| 106 |
pkcreatect -g -min 0 -max 100 | sort -k 1,1 -rg | awk '{ print NR-1 , $2 ,$3 ,$4 ,$5 }' > $OUTDIR/color-bw.txt
|
|
| 107 |
fi |
|
| 108 |
|
|
| 109 |
pkcreatect -ct $OUTDIR/color-bw.txt -co COMPRESS=LZW -co INTERLEAVE=BAND -d "Percent of elevation values >= ${DIR}m" -i $OUTDIR/perc_$DIR.tif -o $OUTDIR/threshold_${DIR}_GMTED2010_${mm}.tif
|
|
| 110 |
|
|
| 111 |
rm $OUTDIR/perc_$DIR.tif |
|
| terrain/procedures/dem_variables/gmted2010_res_x10/sc6b_dem_variables_merge_bj.sh | ||
|---|---|---|
| 1 |
# calculate different variables for the dem |
|
| 2 |
|
|
| 3 |
# rm /lustre0/scratch/ga254/stderr/* ; rm /lustre0/scratch/ga254/stdout/* |
|
| 4 |
|
|
| 5 |
# for dir1 in slope tri tpi roughness aspect ; do for dir2 in max mean median min stdev; do qsub -v DIR=$dir1/$dir2,mm=md /lustre0/scratch/ga254/scripts_bj_bk/environmental-layers/terrain/procedures/dem_variables/gmted2010_res_x10/sc6b_dem_variables_merge_bj.sh ; done ; done |
|
| 6 |
|
|
| 7 |
# for dir1 in tri ; do for dir2 in max ; do bash /lustre0/scratch/ga254/scripts_bj_bk/environmental-layers/terrain/procedures/dem_variables/gmted2010_res_x10/sc6b_dem_variables_merge_bj.sh $dir1/$dir2 md ; done ; done |
|
| 8 |
|
|
| 9 |
# for dir1 in altitude ; do for dir2 in max_of_mx mean_of_mn median_of_md min_of_mi stdev_of_md stdev_of_mn; do qsub -v DIR=$dir1/$dir2,mm=md /lustre0/scratch/ga254/scripts_bj_bk/environmental-layers/terrain/procedures/dem_variables/gmted2010_res_x10/sc6b_dem_variables_merge_bj.sh ; done ; done |
|
| 10 |
|
|
| 11 |
# for dir1 in altitude ; do for dir2 in max_of_mx mean_of_mn median_of_md min_of_mi stdev_of_md stdev_of_mn; do bash /lustre0/scratch/ga254/scripts_bj_bk/environmental-layers/terrain/procedures/dem_variables/gmted2010_res_x10/sc6b_dem_variables_merge_bj.sh $dir1/$dir2 md ; done ; done |
|
| 12 |
|
|
| 13 |
#PBS -S /bin/bash |
|
| 14 |
#PBS -q fas_normal |
|
| 15 |
#PBS -l mem=10gb |
|
| 16 |
#PBS -l walltime=4:00:00 |
|
| 17 |
#PBS -l nodes=1:ppn=4 |
|
| 18 |
#PBS -V |
|
| 19 |
#PBS -o /lustre0/scratch/ga254/stdout |
|
| 20 |
#PBS -e /lustre0/scratch/ga254/stderr |
|
| 21 |
|
|
| 22 |
# load moduels |
|
| 23 |
|
|
| 24 |
module load Tools/Python/2.7.3 |
|
| 25 |
module load Libraries/GDAL/1.10.0 |
|
| 26 |
module load Tools/PKTOOLS/2.4.2 |
|
| 27 |
module load Libraries/OSGEO/1.10.0 |
|
| 28 |
|
|
| 29 |
time ( |
|
| 30 |
export OUTDIR=/lustre0/scratch/ga254/dem_bj/GMTED2010 |
|
| 31 |
|
|
| 32 |
# export DIR=$1 |
|
| 33 |
# export mm=$2 |
|
| 34 |
|
|
| 35 |
export DIR=$DIR |
|
| 36 |
export mm=md |
|
| 37 |
|
|
| 38 |
export dir1=$(echo ${DIR%/*}) # cancel the part after /
|
|
| 39 |
export dir2=$(echo ${DIR#*/}) # cancel the part before /
|
|
| 40 |
|
|
| 41 |
|
|
| 42 |
if [ $dir1 = altitude ] ; then type=Int16 ; fi |
|
| 43 |
if [ $dir1 = aspect ] ; then type=Int16 ; fi |
|
| 44 |
if [ $dir1 = slope ] ; then type=Byte ; fi |
|
| 45 |
if [ $dir1 = tri ] ; then type=Int16 ; fi |
|
| 46 |
if [ $dir1 = tpi ] ; then type=Int16 ; fi |
|
| 47 |
if [ $dir1 = roughness ] ; then type=Int16 ; fi |
|
| 48 |
|
|
| 49 |
if [ $dir1 != aspect ]; then |
|
| 50 |
|
|
| 51 |
echo processing merging tiles in $dir1 $dir2 |
|
| 52 |
|
|
| 53 |
rm -f $OUTDIR/$DIR/$dir1"_"$dir2.tif |
|
| 54 |
rm -f $OUTDIR/$DIR/$dir1"_"$dir2"_a".tif |
|
| 55 |
rm -f $OUTDIR/$DIR/$dir1"_"$dir2"_b".tif |
|
| 56 |
rm -f $OUTDIR/$DIR/$dir1"_"$dir2"_c".tif |
|
| 57 |
rm -f $OUTDIR/$DIR/$dir1"_"$dir2"_d".tif |
|
| 58 |
rm -f $OUTDIR/$DIR/$dir1"_"$dir2"_e".tif |
|
| 59 |
|
|
| 60 |
|
|
| 61 |
if [ $dir1 = altitude ] ; then |
|
| 62 |
|
|
| 63 |
echo clipping tiles in $dir1 $dir2 $OUTDIR/$DIR/tiles/[0-1]_?.tif |
|
| 64 |
|
|
| 65 |
echo left tiles center |
|
| 66 |
ls $OUTDIR/$DIR/tiles/0_[1-3].tif | xargs -n 1 -P 3 bash -c $' |
|
| 67 |
file=$1 ; filename=`basename $file` ; xoff=0 ; yoff=2 ; xsize=4322 ; ysize=3360 |
|
| 68 |
gdal_translate -co ZLEVEL=9 -srcwin $xoff $yoff $xsize $ysize -co COMPRESS=LZW $file $OUTDIR/$DIR/tiles/clip$filename |
|
| 69 |
' _ |
|
| 70 |
|
|
| 71 |
echo right tiles center |
|
| 72 |
ls $OUTDIR/$DIR/tiles/9_[1-3].tif | xargs -n 1 -P 3 bash -c $' |
|
| 73 |
file=$1 ; filename=`basename $file` ; xoff=2 ; yoff=2 ; xsize=4322 ; ysize=3360 ; |
|
| 74 |
gdal_translate -co ZLEVEL=9 -srcwin $xoff $yoff $xsize $ysize -co COMPRESS=LZW $file $OUTDIR/$DIR/tiles/clip$filename |
|
| 75 |
' _ |
|
| 76 |
|
|
| 77 |
echo top tiles center |
|
| 78 |
ls $OUTDIR/$DIR/tiles/[1-8]_0.tif | xargs -n 1 -P 8 bash -c $' |
|
| 79 |
file=$1 ; filename=`basename $file` ; xoff=2 ; yoff=0 ; xsize=4320 ; ysize=3362 |
|
| 80 |
gdal_translate -co ZLEVEL=9 -srcwin $xoff $yoff $xsize $ysize -co COMPRESS=LZW $file $OUTDIR/$DIR/tiles/clip$filename |
|
| 81 |
' _ |
|
| 82 |
|
|
| 83 |
echo botton tiles center |
|
| 84 |
ls $OUTDIR/$DIR/tiles/[1-8]_4.tif | xargs -n 1 -P 8 bash -c $' |
|
| 85 |
file=$1 ; filename=`basename $file` ; xoff=2 ; yoff=2 ; xsize=4320 ; ysize=3362 |
|
| 86 |
gdal_translate -co ZLEVEL=9 -srcwin $xoff $yoff $xsize $ysize -co COMPRESS=LZW $file $OUTDIR/$DIR/tiles/clip$filename |
|
| 87 |
' _ |
|
| 88 |
|
|
| 89 |
echo top left |
|
| 90 |
file=$OUTDIR/$DIR/tiles/0_0.tif ; filename=`basename $file` ; xoff=0 ; yoff=0 ; xsize=4322 ; ysize=3362 |
|
| 91 |
gdal_translate -co ZLEVEL=9 -srcwin $xoff $yoff $xsize $ysize -co COMPRESS=LZW $file $OUTDIR/$DIR/tiles/clip$filename |
|
| 92 |
|
|
| 93 |
echo top right |
|
| 94 |
file=$OUTDIR/$DIR/tiles/9_0.tif ; filename=`basename $file` ; xoff=2 ; yoff=0 ; xsize=4322 ; ysize=3362 |
|
| 95 |
gdal_translate -co ZLEVEL=9 -srcwin $xoff $yoff $xsize $ysize -co COMPRESS=LZW $file $OUTDIR/$DIR/tiles/clip$filename |
|
| 96 |
|
|
| 97 |
echo botton left |
|
| 98 |
file=$OUTDIR/$DIR/tiles/0_4.tif ; filename=`basename $file` ; xoff=0 ; yoff=2 ; xsize=4322 ; ysize=3362 |
|
| 99 |
gdal_translate -co ZLEVEL=9 -srcwin $xoff $yoff $xsize $ysize -co COMPRESS=LZW $file $OUTDIR/$DIR/tiles/clip$filename |
|
| 100 |
|
|
| 101 |
echo botton right |
|
| 102 |
file=$OUTDIR/$DIR/tiles/9_4.tif ; filename=`basename $file` ; xoff=2 ; yoff=2 ; xsize=4322 ; ysize=3362 |
|
| 103 |
gdal_translate -co ZLEVEL=9 -srcwin $xoff $yoff $xsize $ysize -co COMPRESS=LZW $file $OUTDIR/$DIR/tiles/clip$filename |
|
| 104 |
|
|
| 105 |
echo central immage |
|
| 106 |
ls $OUTDIR/$DIR/tiles/[1-8]_[1-3].tif | xargs -n 1 -P 8 bash -c $' |
|
| 107 |
file=$1 ; filename=`basename $file` ; xoff=2 ; yoff=2 ; xsize=4320 ; ysize=3360 |
|
| 108 |
gdal_translate -co ZLEVEL=9 -srcwin $xoff $yoff $xsize $ysize -co COMPRESS=LZW $file $OUTDIR/$DIR/tiles/clip$filename |
|
| 109 |
|
|
| 110 |
' _ |
|
| 111 |
|
|
| 112 |
|
|
| 113 |
/home2/ga254/bin/gdal_merge_bylines.py -o $OUTDIR/$DIR/$dir1"_"$dir2"_a".tif -ot $type -co COMPRESS=LZW $OUTDIR/$DIR/tiles/clip[0-1]_?.tif |
|
| 114 |
/home2/ga254/bin/gdal_merge_bylines.py -o $OUTDIR/$DIR/$dir1"_"$dir2"_b".tif -ot $type -co COMPRESS=LZW $OUTDIR/$DIR/tiles/clip[2-3]_?.tif |
|
| 115 |
/home2/ga254/bin/gdal_merge_bylines.py -o $OUTDIR/$DIR/$dir1"_"$dir2"_c".tif -ot $type -co COMPRESS=LZW $OUTDIR/$DIR/tiles/clip[4-5]_?.tif |
|
| 116 |
/home2/ga254/bin/gdal_merge_bylines.py -o $OUTDIR/$DIR/$dir1"_"$dir2"_d".tif -ot $type -co COMPRESS=LZW $OUTDIR/$DIR/tiles/clip[6-7]_?.tif |
|
| 117 |
/home2/ga254/bin/gdal_merge_bylines.py -o $OUTDIR/$DIR/$dir1"_"$dir2"_e".tif -ot $type -co COMPRESS=LZW $OUTDIR/$DIR/tiles/clip[8-9]_?.tif |
|
| 118 |
|
|
| 119 |
else |
|
| 120 |
|
|
| 121 |
echo left tiles center |
|
| 122 |
ls $OUTDIR/$DIR/tiles/0_[1-3]_${mm}.tif | xargs -n 1 -P 3 bash -c $'
|
|
| 123 |
file=$1 ; filename=`basename $file` ; xoff=0 ; yoff=2 ; xsize=4322 ; ysize=3360 |
|
| 124 |
gdal_translate -co ZLEVEL=9 -srcwin $xoff $yoff $xsize $ysize -co COMPRESS=LZW $file $OUTDIR/$DIR/tiles/clip$filename |
|
| 125 |
' _ |
|
| 126 |
|
|
| 127 |
echo right tiles center |
|
| 128 |
ls $OUTDIR/$DIR/tiles/9_[1-3]_${mm}.tif | xargs -n 1 -P 3 bash -c $'
|
|
| 129 |
file=$1 ;filename=`basename $file` ; xoff=2 ; yoff=2 ; xsize=4322 ; ysize=3360 ; |
|
| 130 |
gdal_translate -co ZLEVEL=9 -srcwin $xoff $yoff $xsize $ysize -co COMPRESS=LZW $file $OUTDIR/$DIR/tiles/clip$filename |
|
| 131 |
' _ |
|
| 132 |
|
|
| 133 |
echo top tiles center |
|
| 134 |
ls $OUTDIR/$DIR/tiles/[1-8]_0_${mm}.tif | xargs -n 1 -P 8 bash -c $'
|
|
| 135 |
file=$1 ;filename=`basename $file` ; xoff=2 ; yoff=0 ; xsize=4320 ; ysize=3362 |
|
| 136 |
gdal_translate -co ZLEVEL=9 -srcwin $xoff $yoff $xsize $ysize -co COMPRESS=LZW $file $OUTDIR/$DIR/tiles/clip$filename |
|
| 137 |
' _ |
|
| 138 |
|
|
| 139 |
echo botton tiles center |
|
| 140 |
ls $OUTDIR/$DIR/tiles/[1-8]_4_${mm}.tif | xargs -n 1 -P 8 bash -c $'
|
|
| 141 |
file=$1 ;filename=`basename $file` ; xoff=2 ; yoff=2 ; xsize=4320 ; ysize=3362 |
|
| 142 |
gdal_translate -co ZLEVEL=9 -srcwin $xoff $yoff $xsize $ysize -co COMPRESS=LZW $file $OUTDIR/$DIR/tiles/clip$filename |
|
| 143 |
' _ |
|
| 144 |
|
|
| 145 |
echo top left |
|
| 146 |
file=$OUTDIR/$DIR/tiles/0_0_${mm}.tif ; filename=`basename $file` ; xoff=0 ; yoff=0 ; xsize=4322 ; ysize=3362
|
|
| 147 |
gdal_translate -co ZLEVEL=9 -srcwin $xoff $yoff $xsize $ysize -co COMPRESS=LZW $file $OUTDIR/$DIR/tiles/clip$filename |
|
| 148 |
|
|
| 149 |
echo top right |
|
| 150 |
file=$OUTDIR/$DIR/tiles/9_0_${mm}.tif ;filename=`basename $file` ; xoff=2 ; yoff=0 ; xsize=4322 ; ysize=3362
|
|
| 151 |
gdal_translate -co ZLEVEL=9 -srcwin $xoff $yoff $xsize $ysize -co COMPRESS=LZW $file $OUTDIR/$DIR/tiles/clip$filename |
|
| 152 |
|
|
| 153 |
echo botton left |
|
| 154 |
file=$OUTDIR/$DIR/tiles/0_4_${mm}.tif ;filename=`basename $file` ; xoff=0 ; yoff=2 ; xsize=4322 ; ysize=3362
|
|
| 155 |
gdal_translate -co ZLEVEL=9 -srcwin $xoff $yoff $xsize $ysize -co COMPRESS=LZW $file $OUTDIR/$DIR/tiles/clip$filename |
|
| 156 |
|
|
| 157 |
echo botton right |
|
| 158 |
file=$OUTDIR/$DIR/tiles/9_4_${mm}.tif ;filename=`basename $file` ; xoff=2 ; yoff=2 ; xsize=4322 ; ysize=3362
|
|
| 159 |
gdal_translate -co ZLEVEL=9 -srcwin $xoff $yoff $xsize $ysize -co COMPRESS=LZW $file $OUTDIR/$DIR/tiles/clip$filename |
|
| 160 |
|
|
| 161 |
echo central immage |
|
| 162 |
ls $OUTDIR/$DIR/tiles/[1-8]_[1-3]_${mm}.tif | xargs -n 1 -P 8 bash -c $'
|
|
| 163 |
file=$1 ; filename=`basename $file` ; xoff=2 ; yoff=2 ; xsize=4320 ; ysize=3360 |
|
| 164 |
gdal_translate -co ZLEVEL=9 -srcwin $xoff $yoff $xsize $ysize -co COMPRESS=LZW $file $OUTDIR/$DIR/tiles/clip$filename |
|
| 165 |
|
|
| 166 |
' _ |
|
| 167 |
|
|
| 168 |
|
|
| 169 |
/home2/ga254/bin/gdal_merge_bylines.py -o $OUTDIR/$DIR/$dir1"_"$dir2"_a".tif -ot $type -co COMPRESS=LZW $OUTDIR/$DIR/tiles/clip[0-1]_?_${mm}.tif
|
|
| 170 |
/home2/ga254/bin/gdal_merge_bylines.py -o $OUTDIR/$DIR/$dir1"_"$dir2"_b".tif -ot $type -co COMPRESS=LZW $OUTDIR/$DIR/tiles/clip[2-3]_?_${mm}.tif
|
|
| 171 |
/home2/ga254/bin/gdal_merge_bylines.py -o $OUTDIR/$DIR/$dir1"_"$dir2"_c".tif -ot $type -co COMPRESS=LZW $OUTDIR/$DIR/tiles/clip[4-5]_?_${mm}.tif
|
|
| 172 |
/home2/ga254/bin/gdal_merge_bylines.py -o $OUTDIR/$DIR/$dir1"_"$dir2"_d".tif -ot $type -co COMPRESS=LZW $OUTDIR/$DIR/tiles/clip[6-7]_?_${mm}.tif
|
|
| 173 |
/home2/ga254/bin/gdal_merge_bylines.py -o $OUTDIR/$DIR/$dir1"_"$dir2"_e".tif -ot $type -co COMPRESS=LZW $OUTDIR/$DIR/tiles/clip[8-9]_?_${mm}.tif
|
|
| 174 |
|
|
| 175 |
fi |
|
| 176 |
|
|
| 177 |
rm -f $OUTDIR/$DIR/$dir1"_"$dir2.tif |
|
| 178 |
|
|
| 179 |
/home2/ga254/bin/gdal_merge_bylines.py -o $OUTDIR/$DIR/$dir1"_"$dir2.tif -ot $type -co COMPRESS=LZW $OUTDIR/$DIR/$dir1"_"$dir2"_a".tif $OUTDIR/$DIR/$dir1"_"$dir2"_b".tif $OUTDIR/$DIR/$dir1"_"$dir2"_c".tif $OUTDIR/$DIR/$dir1"_"$dir2"_d".tif $OUTDIR/$DIR/$dir1"_"$dir2"_e".tif |
|
| 180 |
|
|
| 181 |
rm -f $OUTDIR/$DIR/$dir1"_"$dir2"_a".tif |
|
| 182 |
rm -f $OUTDIR/$DIR/$dir1"_"$dir2"_b".tif |
|
| 183 |
rm -f $OUTDIR/$DIR/$dir1"_"$dir2"_c".tif |
|
| 184 |
rm -f $OUTDIR/$DIR/$dir1"_"$dir2"_d".tif |
|
| 185 |
rm -f $OUTDIR/$DIR/$dir1"_"$dir2"_e".tif |
|
| 186 |
|
|
| 187 |
gdal_translate -co COMPRESS=LZW -co ZLEVEL=9 $OUTDIR/$DIR/$dir1"_"$dir2.tif $OUTDIR/$DIR/${dir1}_${dir2}_${mm}.tif
|
|
| 188 |
rm -f $OUTDIR/$DIR/$dir1"_"$dir2.tif |
|
| 189 |
|
|
| 190 |
else # just applaied to the aspect variables |
|
| 191 |
|
|
| 192 |
echo processing merging tiles for the different aspect variables in $dir1 |
|
| 193 |
|
|
| 194 |
for aspect_var in "_sin_t10k" "_cos_t10k" "_Ew_t10k" "_Nw_t10k" ; do |
|
| 195 |
|
|
| 196 |
# left tiles center |
|
| 197 |
ls $OUTDIR/$DIR/tiles/0_[1-3]_${mm}$aspect_var.tif | xargs -n 1 -P 3 bash -c $'
|
|
| 198 |
file=$1 ; filename=`basename $file` ; xoff=0 ; yoff=2 ; xsize=4322 ; ysize=3360 |
|
| 199 |
gdal_translate -co ZLEVEL=9 -srcwin $xoff $yoff $xsize $ysize -co COMPRESS=LZW $file $OUTDIR/$DIR/tiles/clip$filename |
|
| 200 |
' _ |
|
| 201 |
|
|
| 202 |
# right tiles center |
|
| 203 |
ls $OUTDIR/$DIR/tiles/9_[1-3]_${mm}$aspect_var.tif | xargs -n 1 -P 3 bash -c $'
|
|
| 204 |
file=$1 ;filename=`basename $file` ; xoff=2 ; yoff=2 ; xsize=4322 ; ysize=3360 ; |
|
| 205 |
gdal_translate -co ZLEVEL=9 -srcwin $xoff $yoff $xsize $ysize -co COMPRESS=LZW $file $OUTDIR/$DIR/tiles/clip$filename |
|
| 206 |
' _ |
|
| 207 |
|
|
| 208 |
# top tiles center |
|
| 209 |
ls $OUTDIR/$DIR/tiles/[1-8]_0_${mm}$aspect_var.tif | xargs -n 1 -P 8 bash -c $'
|
|
| 210 |
file=$1 ;filename=`basename $file` ; xoff=2 ; yoff=0 ; xsize=4320 ; ysize=3362 |
|
| 211 |
gdal_translate -co ZLEVEL=9 -srcwin $xoff $yoff $xsize $ysize -co COMPRESS=LZW $file $OUTDIR/$DIR/tiles/clip$filename |
|
| 212 |
' _ |
|
| 213 |
|
|
| 214 |
# botton tiles center |
|
| 215 |
ls $OUTDIR/$DIR/tiles/[1-8]_4_${mm}$aspect_var.tif | xargs -n 1 -P 8 bash -c $'
|
|
| 216 |
file=$1 ;filename=`basename $file` ; xoff=2 ; yoff=2 ; xsize=4320 ; ysize=3362 |
|
| 217 |
gdal_translate -co ZLEVEL=9 -srcwin $xoff $yoff $xsize $ysize -co COMPRESS=LZW $file $OUTDIR/$DIR/tiles/clip$filename |
|
| 218 |
' _ |
|
| 219 |
|
|
| 220 |
# top left |
|
| 221 |
file=$OUTDIR/$DIR/tiles/0_0_${mm}$aspect_var.tif ;filename=`basename $file` ; xoff=0 ; yoff=0 ; xsize=4322 ; ysize=3362
|
|
| 222 |
gdal_translate -co ZLEVEL=9 -srcwin $xoff $yoff $xsize $ysize -co COMPRESS=LZW $file $OUTDIR/$DIR/tiles/clip$filename |
|
| 223 |
|
|
| 224 |
# top right |
|
| 225 |
file=$OUTDIR/$DIR/tiles/9_0_${mm}$aspect_var.tif ;filename=`basename $file` ; xoff=2 ; yoff=0 ; xsize=4322 ; ysize=3362
|
|
| 226 |
gdal_translate -co ZLEVEL=9 -srcwin $xoff $yoff $xsize $ysize -co COMPRESS=LZW $file $OUTDIR/$DIR/tiles/clip$filename |
|
| 227 |
|
|
| 228 |
# botton left |
|
| 229 |
file=$OUTDIR/$DIR/tiles/0_4_${mm}$aspect_var.tif ;filename=`basename $file` ; xoff=0 ; yoff=2 ; xsize=4322 ; ysize=3362
|
|
| 230 |
gdal_translate -co ZLEVEL=9 -srcwin $xoff $yoff $xsize $ysize -co COMPRESS=LZW $file $OUTDIR/$DIR/tiles/clip$filename |
|
| 231 |
|
|
| 232 |
# botton right |
|
| 233 |
file=$OUTDIR/$DIR/tiles/9_4_${mm}$aspect_var.tif ;filename=`basename $file` ; xoff=2 ; yoff=2 ; xsize=4322 ; ysize=3362
|
|
| 234 |
gdal_translate -co ZLEVEL=9 -srcwin $xoff $yoff $xsize $ysize -co COMPRESS=LZW $file $OUTDIR/$DIR/tiles/clip$filename |
|
| 235 |
|
|
| 236 |
# central immage |
|
| 237 |
ls $OUTDIR/$DIR/tiles/[1-8]_[1-3]_${mm}$aspect_var.tif | xargs -n 1 -P 8 bash -c $'
|
|
| 238 |
file=$1 ; filename=`basename $file` ; xoff=2 ; yoff=2 ; xsize=4320 ; ysize=3360 |
|
| 239 |
gdal_translate -co ZLEVEL=9 -srcwin $xoff $yoff $xsize $ysize -co COMPRESS=LZW $file $OUTDIR/$DIR/tiles/clip$filename |
|
| 240 |
|
|
| 241 |
' _ |
|
| 242 |
|
|
| 243 |
|
|
| 244 |
rm -f $OUTDIR/$DIR/$dir1"_"$dir2"_a"$aspect_var.tif |
|
| 245 |
rm -f $OUTDIR/$DIR/$dir1"_"$dir2"_b"$aspect_var.tif |
|
| 246 |
rm -f $OUTDIR/$DIR/$dir1"_"$dir2"_c"$aspect_var.tif |
|
| 247 |
rm -f $OUTDIR/$DIR/$dir1"_"$dir2"_d"$aspect_var.tif |
|
| 248 |
rm -f $OUTDIR/$DIR/$dir1"_"$dir2"_e"$aspect_var.tif |
|
| 249 |
|
|
| 250 |
/home2/ga254/bin/gdal_merge_bylines.py -o $OUTDIR/$DIR/$dir1"_"$dir2"_a"$aspect_var.tif -ot $type -co COMPRESS=LZW $OUTDIR/$DIR/tiles/clip[0-1]_?_${mm}$aspect_var.tif
|
|
| 251 |
/home2/ga254/bin/gdal_merge_bylines.py -o $OUTDIR/$DIR/$dir1"_"$dir2"_b"$aspect_var.tif -ot $type -co COMPRESS=LZW $OUTDIR/$DIR/tiles/clip[2-3]_?_${mm}$aspect_var.tif
|
|
| 252 |
/home2/ga254/bin/gdal_merge_bylines.py -o $OUTDIR/$DIR/$dir1"_"$dir2"_c"$aspect_var.tif -ot $type -co COMPRESS=LZW $OUTDIR/$DIR/tiles/clip[4-5]_?_${mm}$aspect_var.tif
|
|
| 253 |
/home2/ga254/bin/gdal_merge_bylines.py -o $OUTDIR/$DIR/$dir1"_"$dir2"_d"$aspect_var.tif -ot $type -co COMPRESS=LZW $OUTDIR/$DIR/tiles/clip[6-7]_?_${mm}$aspect_var.tif
|
|
| 254 |
/home2/ga254/bin/gdal_merge_bylines.py -o $OUTDIR/$DIR/$dir1"_"$dir2"_e"$aspect_var.tif -ot $type -co COMPRESS=LZW $OUTDIR/$DIR/tiles/clip[8-9]_?_${mm}$aspect_var.tif
|
|
| 255 |
|
|
| 256 |
rm -f $OUTDIR/$DIR/$dir1"_"$dir2$aspect_var.tif |
|
| 257 |
|
|
| 258 |
/home2/ga254/bin/gdal_merge_bylines.py -o $OUTDIR/$DIR/$dir1"_"$dir2$aspect_var.tif -ot $type -co COMPRESS=LZW $OUTDIR/$DIR/$dir1"_"$dir2"_a"$aspect_var.tif $OUTDIR/$DIR/$dir1"_"$dir2"_b"$aspect_var.tif $OUTDIR/$DIR/$dir1"_"$dir2"_c"$aspect_var.tif $OUTDIR/$DIR/$dir1"_"$dir2"_d"$aspect_var.tif $OUTDIR/$DIR/$dir1"_"$dir2"_e"$aspect_var.tif |
|
| 259 |
|
|
| 260 |
gdal_translate -co COMPRESS=LZW -co ZLEVEL=9 $OUTDIR/$DIR/$dir1"_"$dir2$aspect_var.tif $OUTDIR/$DIR/${dir1}_${dir2}_${mm}_${aspect_var}.tif
|
|
| 261 |
rm -f $OUTDIR/$DIR/$dir1"_"$dir2$aspect_var.tif |
|
| 262 |
|
|
| 263 |
rm -f $OUTDIR/$DIR/$dir1"_"$dir2"_a"$aspect_var.tif |
|
| 264 |
rm -f $OUTDIR/$DIR/$dir1"_"$dir2"_b"$aspect_var.tif |
|
| 265 |
rm -f $OUTDIR/$DIR/$dir1"_"$dir2"_c"$aspect_var.tif |
|
| 266 |
rm -f $OUTDIR/$DIR/$dir1"_"$dir2"_d"$aspect_var.tif |
|
| 267 |
rm -f $OUTDIR/$DIR/$dir1"_"$dir2"_e"$aspect_var.tif |
|
| 268 |
|
|
| 269 |
done |
|
| 270 |
|
|
| 271 |
fi |
|
| 272 |
|
|
| 273 |
) |
|
| 274 |
|
|
| 275 |
checkjob -v $PBS_JOBID |
|
| 276 |
|
|
| 277 |
|
|
| 278 |
|
|
Also available in: Unified diff
setting for buldogJcluster; insert greenland ; impruved tiling