Skip to content

Commit fdcfafd

Browse files
davidfrantzdavidfrantz
committed
Merge branch 'getopt-procmask' into develop
2 parents 3afa67c + 7a42bc6 commit fdcfafd

File tree

1 file changed

+158
-63
lines changed

1 file changed

+158
-63
lines changed

‎bash/force-procmask.sh‎

Lines changed: 158 additions & 63 deletions
Original file line numberDiff line numberDiff line change
@@ -22,112 +22,207 @@
2222
#
2323
##########################################################################
2424

25+
# functions/definitions ------------------------------------------------------------------
26+
export PROG=`basename $0`;
27+
export BIN="$( cd "$( dirname "${BASH_SOURCE[0]}" )" >/dev/null 2>&1 && pwd )"
28+
29+
MANDATORY_ARGS=2
30+
31+
export CALC_EXE="gdal_calc.py"
32+
export PARALLEL_EXE="parallel"
33+
34+
echoerr(){ echo "$PROG: $@" 1>&2; } # warnings and/or errormessages go to STDERR
35+
export -f echoerr
36+
37+
export DEBUG=false # display debug messages?
38+
debug(){ if [ "$DEBUG" == "true" ]; then echo "DEBUG: $@"; fi } # debug message
39+
export -f debug
40+
41+
cmd_not_found(){ # check required external commands
42+
for cmd in "$@"; do
43+
stat=`which $cmd`
44+
if [ $? != 0 ] ; then echoerr "\"$cmd\": external command not found, terminating..."; exit 1; fi
45+
done
46+
}
47+
export -f cmd_not_found
48+
49+
50+
help(){
51+
cat <<HELP
52+
53+
Usage: $PROG [-sldobj] input-basename calc-expr
54+
55+
optional:
56+
-s = pixel resolution of cubed data, defaults to 10
57+
-l = input-layer: band number in case of multi-band input rasters,
58+
defaults to 1
59+
-d = input directory: the datacube directory
60+
defaults to current directory
61+
'datacube-definition.prj' needs to exist in there
62+
-o = output directory: the directory where you want to store the cubes
63+
defaults to current directory
64+
-b = basename of output file (without extension)
65+
defaults to the basename of the input-file,
66+
appended by '_procmask'
67+
-j = number of jobs, defaults to 'as many as possible'
68+
69+
Positional arguments:
70+
- input-basename: basename of input data
71+
- calc-expr: Calculation in gdalnumeric syntax, e.g. 'A>2500'"
72+
The input variable is 'A'
73+
For details about GDAL expressions, see
74+
https://gdal.org/programs/gdal_calc.html
75+
76+
-----
77+
see https://force-eo.readthedocs.io/en/latest/components/auxilliary/procmask.html
78+
79+
HELP
80+
exit 1
81+
}
82+
export -f help
83+
84+
# important, check required commands !!! dies on missing
85+
cmd_not_found "$CALC_EXE $PARALLEL_EXE"
2586

2687
function mask(){
2788

2889
FILE=$1
2990
TILE=$(dirname $FILE)
3091

31-
mkdir -p $OUT/$TILE
32-
33-
gdal_calc.py -A $FILE --A_band=$IBAND --outfile=$OUT/$TILE/$OBASE --calc=$CALC --NoDataValue=255 --type=Byte --format='GTiff' --creation-option='COMPRESS=LZW' --creation-option='PREDICTOR=2' --creation-option='NUM_THREADS=ALL_CPUS' --creation-option='BIGTIFF=YES' --creation-option="BLOCKXSIZE=$XBLOCK" --creation-option="BLOCKYSIZE=$YBLOCK"
92+
mkdir -p $DOUT/$TILE
93+
94+
gdal_calc.py \
95+
-A $FILE \
96+
--A_band=$LAYER \
97+
--outfile=$DOUT/$TILE/$FOUT \
98+
--calc=$CALC \
99+
--NoDataValue=255 \
100+
--type=Byte \
101+
--format='GTiff' \
102+
--creation-option='COMPRESS=LZW' \
103+
--creation-option='PREDICTOR=2' \
104+
--creation-option='NUM_THREADS=ALL_CPUS' \
105+
--creation-option='BIGTIFF=YES' \
106+
--creation-option="BLOCKXSIZE=$XBLOCK" \
107+
--creation-option="BLOCKYSIZE=$YBLOCK"
34108

35109
}
36-
37110
export -f mask
38111

39112

40-
EXPECTED_ARGS=7
41-
42-
if [ $# -ne $EXPECTED_ARGS ]
43-
then
44-
echo "Usage: `basename $0` input-cube output-cube"
45-
echo " input-base output-base"
46-
echo " input-band calc-expr resolution"
47-
echo ""
48-
echo " input-cube: directory of input cubes"
49-
echo " output-cube: directory of output cubes"
50-
echo " input-base: basename of cubed input raster"
51-
echo " output-base: basename of cubed processing masks"
52-
echo " input-base: band of cubed input raster, "
53-
echo " from which to generate the processing mask"
54-
echo " calc-expr: Calculation in gdalnumeric syntax, e.g. 'A>2500'"
55-
echo " The input variable is 'A'"
56-
echo " For details about GDAL expressions, see "
57-
echo " https://gdal.org/programs/gdal_calc.html"
58-
echo " resolution: the resolution of the cubed data"
59-
echo ""
60-
exit
113+
# now get the options --------------------------------------------------------------------
114+
ARGS=`getopt -o hvis:l:d:o:b:j: --long help,version,info,resolution:,layer:,input:,output:,basename:,jobs: -n "$0" -- "$@"`
115+
if [ $? != 0 ] ; then help; fi
116+
eval set -- "$ARGS"
117+
118+
RES=10
119+
LAYER=1
120+
DINP=$PWD
121+
DOUT=$PWD
122+
OBASE="DEFAULT"
123+
NJOB=0
124+
125+
while :; do
126+
case "$1" in
127+
-h|--help) help ;;
128+
-v|--version) echo "version-print to be implemented"; exit 0;;
129+
-i|--info) echo "Processing masks from raster images"; exit 0;;
130+
-s|--resolution) RES="$2"; shift ;;
131+
-l|--layer) LAYER="$2"; shift;;
132+
-d|--input) DINP=$(readlink -f" $2"); shift ;;
133+
-o|--output) DOUT=$(readlink -f "$2"); shift ;;
134+
-b|--basename) OBASE="$2"; shift ;;
135+
-j|--jobs) NJOB="$2"; shift ;;
136+
-- ) shift; break ;;
137+
* ) break ;;
138+
esac
139+
shift
140+
done
141+
142+
if [ $# -ne $MANDATORY_ARGS ] ; then
143+
echoerr "Mandatory argument is missing."; help
144+
else
145+
IBASE="$1" # basename (with extension)
146+
CALC="$2" # GDAL calc expression
61147
fi
62148

63-
64-
INP=$1
65-
OUT=$2
66-
IBASE=$3
67-
OBASE=$4
68-
IBAND=$5
69-
CALC=$6
70-
RES=$7
71-
72-
73-
if [ ! -r $INP ]; then
74-
echo "$INP is not existing/readable"
75-
exit
149+
debug "input dir: $DINP"
150+
debug "output dir: $DOUT"
151+
debug "input base: $IBASE"
152+
debug "output base: $OBASE"
153+
debug "input layer: $LAYER"
154+
debug "output res: $RES"
155+
debug "expression: $CALC"
156+
debug "njobs: $NJOB"
157+
158+
if [ ! -r $DINP ]; then
159+
echoerr "$DINP is not existing/readable"; help
76160
fi
77161

78-
if [ ! -w $OUT ]; then
79-
echo "$INP is not existing/writeable"
80-
exit
162+
if [ ! -w $DOUT ]; then
163+
echoerr "$DOUT is not existing/writeable"; help
81164
fi
82165

83-
if [ ! -r $INP/datacube-definition.prj ]; then
84-
echo "$OUT/datacube-definition.prj is not existing/readable"
85-
exit
166+
if [ ! -r $DINP/datacube-definition.prj ]; then
167+
echoerr "$DINP/datacube-definition.prj is not existing/readable"; help
86168
fi
87169

88-
if [ ! -r $OUT/datacube-definition.prj ]; then
170+
if [ -r $DOUT/datacube-definition.prj ]; then
171+
DIFF=$(diff "$DINP/datacube-definition.prj" "$DOUT/datacube-definition.prj")
172+
NUM=$(echo $DIFF | wc -w)
173+
if [ $NUM -gt 0 ]; then
174+
echoerr "input and output datacubes do not match"; help
175+
fi
176+
else
89177
echo "copying datacube-definition.prj"
90-
cp $INP/datacube-definition.prj $OUT/datacube-definition.prj
178+
cp "$DINP/datacube-definition.prj" "$DOUT/datacube-definition.prj"
179+
fi
180+
181+
if [ $OBASE == "DEFAULT" ]; then
182+
CORE=${IBASE%%.*} # corename from input file
183+
FOUT="$CORE""_procmask.tif"
184+
else
185+
CORE=${OBASE%%.*} # corename from user parameters
186+
FOUT="$CORE.tif"
91187
fi
92188

93-
# force tif extension
94-
OBASE=$(basename $OBASE)
95-
OBASE=${OBASE%%.*}
96-
OBASE=$OBASE".tif"
189+
debug "output file: $FOUT"
97190

191+
# main thing -----------------------------------------------------------------------------
98192

99193
NOW=$PWD
100-
cd $INP
194+
cd $DINP
101195

102196
# list with input images
103-
TEMP=temp-force-procmask.txt
197+
TEMP="$DOUT/temp-force-procmask.txt"
104198

105-
ls X*/$IBASE > $TEMP
199+
ls X*/$IBASE > "$TEMP"
106200

107-
if [ $(cat $TEMP | wc -l) -lt 1 ]; then
108-
echo "could not find any instance of $IBASE in $INP"
109-
rm $TEMP
110-
exit
201+
if [ $(cat "$TEMP" | wc -l) -lt 1 ]; then
202+
echoerr "could not find any instance of $IBASE in $DINP"
203+
rm "$TEMP"
204+
help
111205
fi
112206

113207
# tile /chunk size
114-
TILESIZE=$(head -n 6 $OUT/datacube-definition.prj | tail -1 )
115-
CHUNKSIZE=$(head -n 7 $OUT/datacube-definition.prj | tail -1 )
208+
TILESIZE=$(head -n 6 $DOUT/datacube-definition.prj | tail -1 )
209+
CHUNKSIZE=$(head -n 7 $DOUT/datacube-definition.prj | tail -1 )
116210

117211
# block size
118212
XBLOCK=$(echo $TILESIZE $RES | awk '{print int($1/$2)}')
119213
YBLOCK=$(echo $CHUNKSIZE $RES | awk '{print int($1/$2)}')
120214

121-
export OUT=$OUT
122-
export OBASE=$OBASE
123-
export IBAND=$IBAND
215+
export DOUT=$DOUT
216+
export FOUT=$FOUT
217+
export LAYER=$LAYER
124218
export CALC=$CALC
125219
export XBLOCK=$XBLOCK
126220
export YBLOCK=$YBLOCK
127221

128-
parallel -a $TEMP --eta mask {}
222+
$PARALLEL_EXE -j $NJOB -a $TEMP --eta mask {}
129223

130224
rm $TEMP
131225

132226
cd $PWD
133227

228+
exit 0

0 commit comments

Comments
 (0)