Adds sodermanland cities, and a batch script to sbatch them

.gitignore

+*~
+*#*#
+slurm*

src/batch.sh

+#!/bin/bash
+#
+#SBATCH -t 05:30:00
+#SBATCH -N 1
+#SBATCH --ntasks=16
+#SBATCH --mail-type=ALL
+#SBATCH --mail-user=ludvik.brodl@smhi.se
+
+
+
+z=''
+las_root_folder=''
+las_names=''
+output_folder=''
+
+while getopts 'hi:d:o:z:' flag; do
+  case "${flag}" in
+    h) echo "$package - batch script to run many LAS files in parallell "
+       echo " "
+       echo "$package [options] application [arguments]"
+       echo " "
+       echo "options:"
+       echo "-h,                       show brief help"
+       echo "-d,                       las root folder"
+       echo "-i,                       las file names in a file"
+       echo "                          i.e:"
+       echo "                          10C017_65425_5450_25.rar"
+       echo "                          10C017_65425_5475_25.rar"
+       echo "-o                        output folder"
+       echo "-z                        integer, specifiying the maximum height of LAS data," 
+       echo "                          modifies data above this height."
+       exit 0
+       ;;
+    d) las_root_folder="${OPTARG}" ;;
+    i) las_names="${OPTARG}" ;;
+    o) output_folder="${OPTARG}" ;;
+    z) z="${OPTARG}" ;;
+    *) error "Unexpected option ${flag}" ;;
+  esac
+done
+
+if [ -z "$z" ] || [ -z "$las_root_folder" ] || [ -z "$las_names" ] || [ -z "$output_folder" ]; then
+  echo "One or more variables not set. Use -h for help."
+  exit 1
+fi
+
+echo $las_root_folder
+echo $las_names
+echo $output_folder
+echo $z
+
+module load geos/3.4.2-i1501
+module load gcc/6.2.0
+. /home/sm_davse/virtualenvs/gdalenv/bin/activate
+export PATH=/home/sm_davse/LAS/LAStools/bin:/home/sm_ludbr/LAS/dvlp:$PATH
+
+while read line
+do
+   echo $line
+   /home/sm_ludbr/LAS/dvlp/grid_tile.sh $las_root_folder$line $output_folder $z </dev/null &
+done < $las_names
+
+wait
+echo "Done"

src/batch.sh.beforekent

+#!/bin/bash
+#
+#SBATCH -t 05:30:00
+#SBATCH -N 1
+#SBATCH --ntasks=16
+#SBATCH --mail-type=ALL
+#SBATCH --mail-user=ludvik.brodl@smhi.se
+
+set -x
+
+z=''
+las_root_folder=''
+las_names=''
+output_folder=''
+
+while getopts 'hi:d:o:z:' flag; do
+  case "${flag}" in
+    h) echo "$package - batch script to run many LAS files in parallell "
+       echo " "
+       echo "$package [options] application [arguments]"
+       echo " "
+       echo "options:"
+       echo "-h,                       show brief help"
+       echo "-d,                       las root folder"
+       echo "-i,                       las file names in a file"
+       echo "                          i.e:"
+       echo "                          10C017_65425_5450_25.rar"
+       echo "                          10C017_65425_5475_25.rar"
+       echo "-o                        output folder"
+       echo "-z                        integer, specifiying the maximum height of LAS data," 
+       echo "                          modifies data above this height."
+       exit 0
+       ;;
+    d) las_root_folder="${OPTARG}" ;;
+    i) las_names="${OPTARG}" ;;
+    o) output_folder="${OPTARG}" ;;
+    z) z="${OPTARG}" ;;
+    *) error "Unexpected option ${flag}" ;;
+  esac
+done
+
+if [ -z "$z" ] || [ -z "$las_root_folder" ] || [ -z "$las_names" ] || [ -z "$output_folder" ]; then
+  echo "One or more variables not set. Use -h for help."
+  exit 1
+fi
+
+echo $las_root_folder
+echo $las_names
+echo $output_folder
+echo $z
+
+module load geos/3.4.2-i1501
+module load gcc/6.2.0
+. /home/sm_davse/virtualenvs/gdalenv/bin/activate
+export PATH=/home/sm_davse/LAS/LAStools/bin:/home/sm_ludbr/LAS/dvlp:$PATH
+
+cat $las_names | while read line
+do
+   echo $line
+   bash /home/sm_ludbr/LAS/dvlp/grid_tile.sh $las_root_folder$line $output_folder $z &
+done
+
+wait
+echo "Done"

src/batch.sh.copy

+#!/bin/bash
+#
+#SBATCH -t 05:30:00
+#SBATCH -N 1
+#SBATCH --ntasks=16
+#SBATCH --mail-type=ALL
+#SBATCH --mail-user=ludvik.brodl@smhi.se
+
+# set -x
+
+z=''
+las_root_folder=''
+las_names=''
+output_folder=''
+
+while getopts 'hi:d:o:z:' flag; do
+  case "${flag}" in
+    h) echo "$package - batch script to run many LAS files in parallell "
+       echo " "
+       echo "$package [options] application [arguments]"
+       echo " "
+       echo "options:"
+       echo "-h,                       show brief help"
+       echo "-d,                       las root folder"
+       echo "-i,                       las file names in a file"
+       echo "                          i.e:"
+       echo "                          10C017_65425_5450_25.rar"
+       echo "                          10C017_65425_5475_25.rar"
+       echo "-o                        output folder"
+       echo "-z                        integer, specifiying the maximum height of LAS data," 
+       echo "                          modifies data above this height."
+       exit 0
+       ;;
+    d) las_root_folder="${OPTARG}" ;;
+    i) las_names="${OPTARG}" ;;
+    o) output_folder="${OPTARG}" ;;
+    z) z="${OPTARG}" ;;
+    *) error "Unexpected option ${flag}" ;;
+  esac
+done
+
+if [ -z "$z" ] || [ -z "$las_root_folder" ] || [ -z "$las_names" ] || [ -z "$output_folder" ]; then
+  echo "One or more variables not set. Use -h for help."
+  exit 1
+fi
+
+echo $las_root_folder
+echo $las_names
+echo $output_folder
+echo $z
+
+module load geos/3.4.2-i1501
+module load gcc/6.2.0
+. /home/sm_davse/virtualenvs/gdalenv/bin/activate
+export PATH=/home/sm_davse/LAS/LAStools/bin:/home/sm_ludbr/LAS/dvlp:$PATH
+
+cat $las_names | while read line
+do
+   echo SPAWNING $line
+   bash /home/sm_ludbr/LAS/dvlp/grid_tile.sh $las_root_folder$line $output_folder $z &
+done
+
+echo WAITING
+wait
+echo WAIT DONE
+

src/batch_calc_grid.sh

+#!/bin/bash
+#
+#SBATCH -t 02:30:00
+#SBATCH -N 1
+#SBATCH --mail-type=ALL
+#SBATCH --mail-user=ludvik.brodl@smhi.se
+
+module load geos/3.4.2-i1501
+module load gcc/6.2.0
+. /home/sm_davse/virtualenvs/gdalenv/bin/activate
+export PATH=/home/sm_davse/LAS/LAStools/bin:/home/sm_ludbr/LAS/dvlp:$PATH
+
+grid_tile.sh $1 $2 $3
\ No newline at end of file

src/batch_main.sh

+#!/bin/bash
+
+
+z=''
+las_root_folder=''
+las_names=''
+output_folder=''
+
+while getopts 'hi:d:o:z:' flag; do
+  case "${flag}" in
+    h) echo "$package - batch script to run many LAS files in parallell "
+       echo " "
+       echo "$package [options] application [arguments]"
+       echo " "
+       echo "options:"
+       echo "-h,                       show brief help"
+       echo "-d,                       las root folder"
+       echo "-i,                       las file names in a file"
+       echo "                          i.e:"
+       echo "                          10C017_65425_5450_25.rar"
+       echo "                          10C017_65425_5475_25.rar"
+       echo "-o                        output folder"
+       echo "-z                        integer, specifiying the maximum height of LAS data," 
+       echo "                          modifies data above this height."
+       exit 0
+       ;;
+    d) las_root_folder="${OPTARG}" ;;
+    i) las_names="${OPTARG}" ;;
+    o) output_folder="${OPTARG}" ;;
+    z) z="${OPTARG}" ;;
+    *) error "Unexpected option ${flag}" ;;
+  esac
+done
+
+if [ -z "$z" ] || [ -z "$las_root_folder" ] || [ -z "$las_names" ] || [ -z "$output_folder" ]; then
+  echo "One or more variables not set. Use -h for help."
+  exit 1
+fi
+
+
+cat $las_names | while read line
+do
+   sbatch batch_calc_grid.sh $las_root_folder$line $output_folder $z '-J' $line
+done
\ No newline at end of file

src/flen.txt

+10C019_65450_5875_25.rar
+10C019_65450_5900_25.rar
+10C019_65450_5925_25.rar
+10C019_65475_5875_25.rar
+10C019_65475_5900_25.rar
+10C019_65475_5925_25.rar
+10C026_65500_5875_25.rar
+10C026_65500_5900_25.rar
+10C026_65500_5925_25.rar

src/gnesta.txt

+10C021_65425_6275_25.rar
+10C021_65425_6300_25.rar
+10C021_65425_6325_25.rar
+10C021_65425_6350_25.rar
+10C021_65450_6275_25.rar
+10C021_65450_6300_25.rar
+10C021_65450_6325_25.rar
+10C021_65450_6350_25.rar
+10C021_65475_6275_25.rar
+10C021_65475_6300_25.rar
+10C021_65475_6325_25.rar
+10C021_65475_6350_25.rar

src/katrineholm.txt

+10C018_65350_5650_25.rar
+10C018_65350_5675_25.rar
+10C018_65350_5700_25.rar
+10C018_65375_5650_25.rar
+10C018_65375_5675_25.rar
+10C018_65375_5700_25.rar
+10C018_65400_5650_25.rar
+10C018_65400_5675_25.rar
+10C018_65400_5700_25.rar

src/loop_kommun.sh

+#!/bin/bash
+
+#set -o nounset
+set -o errexit
+set -x
+
+#$1 the root of the LAS .rar files.
+#$2 a .txt file containing the filenames for the .rar files to be run
+#$3 z threshold of LAS data.
+#$4 is the output folder for the LAS files
+#$5 planing to use this for the acceptable degrees to include in the output.
+
+module load geos/3.4.2-i1501
+module load gcc/6.2.0
+. /home/sm_davse/virtualenvs/gdalenv/bin/activate
+export PATH=/home/sm_davse/LAS/LAStools/bin:/home/sm_ludbr/LAS/dvlp:$PATH
+
+cat $2 | while read line
+do
+   echo $line
+   /home/sm_ludbr/LAS/dvlp/grid_tile.sh $1$line $4 $3 &
+done
+
+#grid_tile.sh /home/sm_davse/LAS/las/5629_170003/10C017/10C017_65400_5450_25.rar /home/sm_ludbr/temp/ 200

src/nykoping.txt

+10C020_65100_6125_25.rar
+10C020_65100_6150_25.rar
+10C020_65100_6175_25.rar
+10C020_65100_6200_25.rar
+10C020_65125_6125_25.rar
+10C020_65125_6150_25.rar
+10C020_65125_6175_25.rar
+10C020_65125_6200_25.rar
+10C020_65150_6125_25.rar
+10C020_65150_6150_25.rar
+10C020_65150_6175_25.rar
+10C020_65150_6200_25.rar
+10C020_65175_6125_25.rar
+10C020_65175_6150_25.rar
+10C020_65175_6175_25.rar
+10C020_65175_6200_25.rar

src/oxelosund.txt

+10C020_65000_6150_25.rar
+10C020_65000_6175_25.rar
+10C020_65000_6200_25.rar
+10C020_65000_6225_25.rar
+10C020_65025_6150_25.rar
+10C020_65025_6175_25.rar
+10C020_65025_6200_25.rar
+10C020_65025_6225_25.rar
+10C020_65050_6150_25.rar
+10C020_65050_6175_25.rar
+10C020_65050_6200_25.rar
+10C020_65050_6225_25.rar
+10C020_65075_6150_25.rar
+10C020_65075_6175_25.rar
+10C020_65075_6200_25.rar
+10C020_65075_6225_25.rar

src/run_all_cities.sh

+#!/bin/bash
+
+sbatch batch.sh -o /home/sm_ludbr/temp/ -i flen.txt -d /nobackup/smhid13/sm_ludbr/las_data/ -z 200
+sbatch batch.sh -o /home/sm_ludbr/temp/ -i gnesta.txt -d /nobackup/smhid13/sm_ludbr/las_data/ -z 200
+sbatch batch.sh -o /home/sm_ludbr/temp/ -i katrineholm.txt -d /nobackup/smhid13/sm_ludbr/las_data/ -z 200
+sbatch batch.sh -o /home/sm_ludbr/temp/ -i nykoping.txt -d /nobackup/smhid13/sm_ludbr/las_data/ -z 200
+
+sbatch batch.sh -o /home/sm_ludbr/temp/ -i oxelosund.txt -d /nobackup/smhid13/sm_ludbr/las_data/ -z 200
+sbatch batch.sh -o /home/sm_ludbr/temp/ -i strangnas.txt -d /nobackup/smhid13/sm_ludbr/las_data/ -z 200
+sbatch batch.sh -o /home/sm_ludbr/temp/ -i trosa.txt -d /nobackup/smhid13/sm_ludbr/las_data/ -z 200
+sbatch batch.sh -o /home/sm_ludbr/temp/ -i vingaker.txt -d /nobackup/smhid13/sm_ludbr/las_data/ -z 200
\ No newline at end of file

src/strangnas.txt

+10C027_65800_6100_25.rar
+10C027_65800_6125_25.rar
+10C027_65800_6150_25.rar
+10C027_65800_6175_25.rar
+10C027_65825_6100_25.rar
+10C027_65825_6125_25.rar
+10C027_65825_6150_25.rar
+10C027_65825_6175_25.rar
+10C027_65850_6100_25.rar
+10C027_65850_6125_25.rar
+10C027_65850_6150_25.rar
+10C027_65850_6175_25.rar

src/trosa.txt

+10C021_65250_6425_25.rar
+10C021_65250_6450_25.rar
+10C021_65250_6475_25.rar
+10C021_65250_6500_25.rar
+10C021_65275_6425_25.rar
+10C021_65275_6450_25.rar
+10C021_65275_6475_25.rar
+10C021_65275_6500_25.rar
+10C021_65300_6425_25.rar
+10C021_65300_6450_25.rar
+10C021_65300_6475_25.rar
+10C021_65300_6500_25.rar
+10C021_65325_6425_25.rar
+10C021_65325_6450_25.rar
+10C021_65325_6475_25.rar
+10C021_65325_6500_25.rar

src/vingaker.txt

+10C017_65425_5450_25.rar
+10C017_65425_5475_25.rar
+10C017_65450_5450_25.rar
+10C017_65450_5475_25.rar
+10C017_65475_5450_25.rar
+10C017_65475_5475_25.rar
+10C018_65425_5500_25.rar
+10C018_65425_5525_25.rar
+10C018_65450_5500_25.rar
+10C018_65450_5525_25.rar
+10C018_65475_5500_25.rar
+10C018_65475_5525_25.rar