Revision 3959e686
Added by Adam Wilson about 12 years ago
| climate/procedures/MOD06_L2_process.r | ||
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| 220 | 220 |
system(paste("r.mapcalc <<EOF
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COT_denom=",paste("!isnull(COT2_",1:nfs,")",sep="",collapse="+"),"
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| 222 | 222 |
COT_numer=",paste("if(isnull(COT2_",1:nfs,"),0,COT2_",1:nfs,")",sep="",collapse="+"),"
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COT_daily=COT_numer/COT_denom
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COT_daily=int((COT_numer/COT_denom)*100)
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CER_denom=",paste("!isnull(CER2_",1:nfs,")",sep="",collapse="+"),"
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| 225 | 225 |
CER_numer=",paste("if(isnull(CER2_",1:nfs,"),0,CER2_",1:nfs,")",sep="",collapse="+"),"
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CER_daily=CER_numer/CER_denom
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CLD_daily=max(",paste("if(isnull(CM_cloud_",1:nfs,"),0,CM_cloud_",1:nfs,")",sep="",collapse=","),")
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CER_daily=int(100*(CER_numer/CER_denom))
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CLD_daily=int((max(",paste("if(isnull(CM_cloud_",1:nfs,"),0,CM_cloud_",1:nfs,")",sep="",collapse=","),"))*100)
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EOF",sep="")) |
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#### Write the files to a geotiff |
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execGRASS("r.out.gdal",input="CER_daily",output=paste(outdir,"/CER_",date,".tif",sep=""),nodata=-999,flags=c("quiet"))
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execGRASS("r.out.gdal",input="COT_daily",output=paste(outdir,"/COT_",date,".tif",sep=""),nodata=-999,flags=c("quiet"))
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execGRASS("r.out.gdal",input="CLD_daily",output=paste(outdir,"/CLD_",date,".tif",sep=""),nodata=99,flags=c("quiet"))
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# execGRASS("r.out.gdal",input="CER_daily",output=paste(outdir,"/CER_",date,".tif",sep=""),nodata=-999,flags=c("quiet"))
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# execGRASS("r.out.gdal",input="COT_daily",output=paste(outdir,"/COT_",date,".tif",sep=""),nodata=-999,flags=c("quiet"))
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# execGRASS("r.out.gdal",input="CLD_daily",output=paste(outdir,"/CLD_",date,".tif",sep=""),nodata=99,flags=c("quiet"))
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### Write the files to a netcdf file |
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## create image group to facilitate export as multiband netcdf |
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execGRASS("i.group",group="mod06",input=c("CER_daily","COT_daily","CLD_daily")) ; print("")
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ncfile=paste(outdir,"/MOD06_",date,".nc",sep="") |
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execGRASS("r.out.gdal",input="mod06",output=ncfile,type="Int16",nodata=-32768,flags=c("quiet"),createopt=c("WRITE_GDAL_TAGS=YES","WRITE_LONLAT=NO"),format="netCDF")
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system(paste("/nasa/nco/3.9.8/bin/ncecat -O -u time ",ncfile," ",ncfile,sep=""))
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system(paste("/nasa/nco/3.9.8/bin/ncap -O -s 'time[time]=",as.integer(fs$date[fs$dateid==date]-as.Date("2000-01-01")),"'",ncfile," ",ncfile))
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system(paste("/nasa/nco/3.9.8/bin/ncatted -a calendar,time,c,c,\"standard\" -a long_name,time,c,c,\"time\" -a units,time,c,c,\"days since 2000-01-01 12:00:00\"",ncfile))
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system(paste("/nasa/nco/3.9.8/bin/ncrename -v Band1,CER -v Band2,COT -v Band3,CLD",ncfile))
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system(paste("/nasa/nco/3.9.8/bin/ncatted -a scale_factor,CER,o,d,0.001 -a missing_value,CER,o,d,-32768 -a long_name,CER,o,c,\"Effective Radius\"",ncfile))
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system(paste("/nasa/nco/3.9.8/bin/ncatted -a scale_factor,COT,o,d,0.001 -a missing_value,CER,o,d,-32768 -a long_name,COT,o,c,\"Optical Thickness\"",ncfile))
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system(paste("/nasa/nco/3.9.8/bin/ncatted -a scale_factor,CLD,o,d,0.001 -a missing_value,CER,o,d,-32768 -a long_name,CLD,o,c,\"Cloud Mask\"",ncfile))
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### delete the temporary files |
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unlink_.gislock() |
| 237 | 252 |
system("/nobackupp1/awilso10/software/grass-6.4.3svn/etc/clean_temp")
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| climate/procedures/Pleiades.R | ||
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| 11 | 11 |
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cat(paste("
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#PBS -S /bin/bash |
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#PBS -l select=64:ncpus=4:mpiprocs=4:model=wes
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#PBS -l select=32:ncpus=4:mpiprocs=4:model=wes
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####old PBS -l select=64:ncpus=4:mpiprocs=4:model=wes |
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####### old: select=48:ncpus=8:mpiprocs=8:model=neh |
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#PBS -l walltime=10:00:00
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#PBS -l walltime=1:00:00 |
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#PBS -j oe |
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#PBS -m e |
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#PBS -V |
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####PBS -W group_list=s1007 |
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###PBS -q devel
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###PBS -o log/log_^array_index^
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#PBS -q devel |
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#PBS -o log/log_^array_index^ |
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#PBS -o log/log_DataCompile |
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#PBS -M adam.wilson@yale.edu |
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#PBS -N MOD06 |
| ... | ... | |
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export R_LIBS=\"/u/awilso10/R/x86_64-unknown-linux-gnu-library/2.15/\" |
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export TMPDIR=/nobackupp1/awilso10/mod06/tmp |
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## load modules |
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module load gcc mpi-sgi/mpt.2.06r6 hdf4 udunits R |
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module load gcc mpi-sgi/mpt.2.06r6 hdf4 udunits R nco
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## Run the script! |
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TMPDIR=$TMPDIR Rscript --verbose --vanilla /u/awilso10/environmental-layers/climate/procedures/MOD06_L2_process.r |
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exit 0 |
| ... | ... | |
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#system("qsub MOD06_process")
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## work in interactive mode |
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#system("qsub -I -lselect=1:ncpus=2:model=wes -q devel")
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#system("qsub -I -l walltime=1:00:00 -lselect=1:ncpus=2:model=wes -q devel")
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## check progress |
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system("qstat -u awilso10")
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| ... | ... | |
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### copy the files back to Yale |
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system("scp 2_daily/* adamw@acrobates.eeb.yale.edu:/data/personal/adamw/projects/interp/")
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list.files("2_daily")
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system("scp 2_daily/* adamw@acrobates.eeb.yale.edu:/data/personal/adamw/projects/interp/data/modis/Venezuela")
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system("scp /tmp/Rtmp6I6tFn/MOD06_L2.A2000061.1615.051.2010273184629.hdf adamw@acrobates.eeb.yale.edu:/data/personal/adamw/projects/interp/data/modis/Venezuela")
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system("scp 2_daily/MOD06_20000410.nc adamw@acrobates.eeb.yale.edu:/data/personal/adamw/projects/interp/data/modis/Venezuela")
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system("scp /tmp/Rtmp6I6tFn/MOD06_L2.A2000061.1615.051.2010273184629.hdf adamw@acrobates.eeb.yale.edu:/data/personal/adamw/projects/interp/")
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list.files(" /tmp/Rtmp6I6tFn")
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Also available in: Unified diff
Updated MOD06 process to output NetCDF files instead of geotif for faster post-processing