Revision b6e392da
Added by Adam Wilson almost 12 years ago
| climate/procedures/Pleiades.R | ||
|---|---|---|
| 1 | 1 |
#### Script to facilitate processing of MOD06 data |
| 2 | 2 |
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| 3 | 3 |
setwd("/nobackupp1/awilso10/mod06")
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| 4 |
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| 4 | 5 |
library(rgdal) |
| 5 | 6 |
library(raster) |
| 6 | 7 |
|
| ... | ... | |
| 9 | 10 |
tb$tile=paste("h",sprintf("%02d",tb$ih),"v",sprintf("%02d",tb$iv),sep="")
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| 10 | 11 |
save(tb,file="modlandTiles.Rdata") |
| 11 | 12 |
|
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## delete temporary log file that can grow to GB |
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system("rm /nobackupp1/awilso10/software/heg/TOOLKIT_MTD/runtime/LogStatus")
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tile="h11v08" # Venezuela |
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tile="h11v07" # Venezuela coast |
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tile="h09v04" # Oregon |
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| 12 | 20 |
outdir="2_daily" #directory for separate daily files |
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outdir2="3_summary" #directory for combined daily files and summarized files |
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outdir=paste("daily/",tile,"/",sep="") #directory for separate daily files
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if(!file.exists(outdir)) dir.create(outdir) |
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outdir2="summary" #directory for combined daily files and summarized files |
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if(!file.exists(outdir2)) dir.create(outdir2) |
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| 14 | 25 |
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| 15 | 26 |
## load a MOD11A1 file to define grid |
| 16 | 27 |
gridfile=list.files("/nobackupp4/datapool/modis/MOD11A1.005/2006.01.27/",pattern=paste(tile,".*hdf$",sep=""),full=T)[1]
|
| ... | ... | |
| 20 | 31 |
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| 21 | 32 |
### get list of files to process |
| 22 | 33 |
datadir="/nobackupp4/datapool/modis/MOD06_L2.005/" |
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datadir="/nobackupp1/awilso10/mod06/data" #for data downloaded from |
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| 23 | 35 |
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fs=data.frame(path=list.files(datadir,full=T,recursive=T,pattern="hdf"),stringsAsFactors=F) |
| 25 | 37 |
fs$file=basename(fs$path) |
| ... | ... | |
| 38 | 50 |
|
| 39 | 51 |
#### Generate submission file |
| 40 | 52 |
## identify which have been completed |
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done=alldates%in%substr(list.files(outdir),7,14)
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table(done)
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notdone=alldates[!done] #these are the dates that still need to be processed
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#fdone=system(paste("ssh -q lou2 \"ls ",pdir," | grep \"nc$\"\"",sep=""),intern=T)
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fdone=list.files(outdir,pattern="nc$")
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done=alldates%in%substr(fdone,14,21)
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if(exists("fdly")){
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notdone=notdone[notdone%in%fdly$dateid[is.na(fdly$npar)]] |
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if(exists("fdly")){ #update using table from below
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done[alldates%in%fdly$dateid[is.na(fdly$npar)]]=F |
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} |
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table(done) |
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notdone=alldates[!done] #these are the dates that still need to be processed |
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| 48 | 63 |
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tile="h11v08" #can move this to submit script if needed |
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| 50 | 64 |
script="/u/awilso10/environmental-layers/climate/procedures/MOD06_L2_process.r" |
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write.table(paste("--verbose ",script," --date ",notdone," --tile \"",tile,"\"",sep=""),file="notdone.txt",row.names=F,col.names=F,quote=F)
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#write.table(paste("--verbose ",script," date=",notdone[1:30],sep=""),file="notdone.txt",row.names=F,col.names=F,quote=F)
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#write.table(notdone[1:30],file="notdone.txt",row.names=F,col.names=F,quote=F) |
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write.table(paste("--verbose ",script," --date ",notdone," --verbose T --tile \"",tile,"\"",sep=""),file=paste(tile,"_notdone.txt",sep=""),row.names=F,col.names=F,quote=F)
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| 54 | 67 |
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| 55 | 68 |
save(fs,alldates,gridfile,td,file="allfiles.Rdata") |
| 56 | 69 |
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## run script |
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#cat(paste("
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##! /bin/bash |
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#source ~/moduleload |
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#source ~/.bashrc |
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#Rscript --verbose --vanilla /u/awilso10/environmental-layers/climate/procedures/MOD06_L2_process.r date=$1 |
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#Rscript --verbose --vanilla rtest |
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#",sep=""),file="MOD06_process2") |
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#system("chmod +x MOD06_process2")
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#cat(paste("
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#library(rgdal) |
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#GDALinfo |
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#",sep=""),file="rtest") |
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## Submission script |
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#cat(paste("
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##PBS -S /bin/bash |
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##PBS -l select=2:ncpus=16:model=san |
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####PBS -l select=4:ncpus=8:model=neh |
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###PBS -l select=1:ncpus=12:model=wes |
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######## old: select=48:ncpus=8:mpiprocs=8:model=neh |
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##PBS -l walltime=2:00:00 |
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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 -q devel |
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##PBS -o log/log_^array_index^ |
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##PBS -o log/log_DataCompile.log |
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##PBS -M adam.wilson@yale.edu |
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##PBS -N MOD06 |
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## cd to working directory |
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#cd /nobackupp1/awilso10/mod06 |
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## set some memory limits |
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# ulimit -d 1500000 -m 1500000 -v 1500000 #limit memory usage |
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# source /usr/local/lib/global.profile |
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# source /u/awilso10/.bashrc |
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# source /u/awilso10/moduleload |
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### export a few important variables |
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# export NNODES=32 |
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# export R_LIBS=\"/u/awilso10/R/x86_64-unknown-linux-gnu-library/2.15/\" |
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### Run the script! |
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## current version not parallelizing across nodes! |
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# TMPDIR=$TMPDIR Rscript --verbose --vanilla /u/awilso10/environmental-layers/climate/procedures/MOD06_L2_process.r date=20000403 |
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#WORKLIST=notdone.txt |
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##EXE=\"Rscript\" |
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#EXE="./MOD06_process2" |
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#LOG=log/log_DataCompile.log |
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#MQUEUE=/nobackupp4/pvotava/software/share/mqueue-eg/mqueue/mqueue |
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#TMPDIR=$TMPDIR mpiexec -np $NNODES $MQUEUE -l $WORKLIST -p $EXE -v -v -v --random-starts 2-4 --work-analyze #> $LOG |
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#exit 0 |
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#",sep=""),file="MOD06_process") |
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### simplified qsub script |
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### qsub script |
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cat(paste("
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#PBS -S /bin/bash |
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#PBS -l select=48:ncpus=8:mpiprocs=8
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#PBS -l select=40:ncpus=8:mpiprocs=8
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##PBS -l select=2:ncpus=4:mpiprocs=4 |
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#PBS -l walltime=02:00:00
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#PBS -l walltime=2:00:00 |
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#PBS -j n |
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#PBS -m be |
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#PBS -N mod06 |
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#PBS -q devel |
| 127 | 80 |
#PBS -V |
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CORES=384
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CORES=320
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HDIR=/u/armichae/pr/ |
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source $HDIR/etc/environ.sh |
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source /u/awilso10/.bashrc |
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IDIR=/nobackupp1/awilso10/mod06/ |
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##WORKLIST=$HDIR/var/run/pxrRgrs/work.txt |
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WORKLIST=$IDIR/notdone.txt |
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WORKLIST=$IDIR/",tile,"_notdone.txt
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EXE=Rscript |
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LOGSTDOUT=$IDIR/log/log.stdout |
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LOGSTDERR=$IDIR/log/log.stderr |
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mpiexec -np $CORES pxargs -a $WORKLIST -p $EXE -v -v -v --work-analyze 1> $LOGSTDOUT 2> $LOGSTDERR |
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"),file="mod06_qsub")
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",sep=""),file=paste(tile,"_mod06_qsub",sep=""))
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### Check the file |
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system("cat mod06_qsub")
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system(paste("cat ",tile,"_mod06_qsub",sep=""))
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#system("cat ~/environmental-layers/climate/procedures/MOD06_L2_process.r")
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## check queue status |
| ... | ... | |
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system("/u/scicon/tools/bin/qtop.pl 492352")
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## Submit it (and keep the pid)! |
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system("qsub mod06_qsub")
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system("/u/scicon/tools/bin/pdsh_gdb -j 568835 -d tmp -s -u awilso10")
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system(paste("qsub ",tile,"_mod06_qsub",sep=""))
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## work in interactive mode |
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# system("qsub -I -l walltime=2:00:00 -lselect=2:ncpus=16:model=san -q devel")
|
| ... | ... | |
| 161 | 113 |
system(paste("/u/scicon/tools/bin/qps ",568835))
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| 162 | 114 |
system(paste("qstat -t -x",pid))
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system("qstat devel ")
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#system("qstat | grep awilso10")
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#################################### |
| 168 | 118 |
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## move to permanent storage on lou? |
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# system(paste("scp -r ",ncfile," ",pdir,sep=""))
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file.remove( |
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list.files(pattern="filetable[.]temp|GetAttrtemp|core[.]|MCFWrite[.]temp") |
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) |
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|
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################################################################################ |
| 171 | 126 |
## now generate the climatologies |
| 172 | 127 |
fdly=data.frame( |
| 173 | 128 |
path=list.files(outdir,pattern="nc$",full=T), |
| 174 | 129 |
file=list.files(outdir,pattern="nc$")) |
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fdly$dateid=substr(fdly$file,7,14)
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fdly$date=as.Date(substr(fdly$file,7,14),"%Y%m%d")
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fdly$dateid=substr(fdly$file,14,21)
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fdly$date=as.Date(substr(fdly$file,14,21),"%Y%m%d")
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| 177 | 132 |
fdly$month=format(fdly$date,"%m") |
| 178 | 133 |
fdly$year=format(fdly$date,"%Y") |
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nrow(fdly) |
|
| 179 | 135 |
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## check validity (via npar and ntime) of nc files |
| 181 | 137 |
for(i in 1:nrow(fdly)){
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# fdly$ntime[i]<-as.numeric(system(paste("cdo sinfo ",fdly$path[i]),intern=T))
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fdly$ntime[i]<-as.numeric(system(paste("cdo -s ntime ",fdly$path[i]),intern=T))
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fdly$npar[i]<-as.numeric(system(paste("cdo -s npar ",fdly$path[i]),intern=T))
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print(i) |
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fdly$fyear[i]<-as.numeric(system(paste("cdo -s showyear ",fdly$path[i]),intern=T))
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fdly$fmonth[i]<-as.numeric(system(paste("cdo -s showmon ",fdly$path[i]),intern=T))
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fdly$fvar[i]<-system(paste("cdo -s showvar ",fdly$path[i]),intern=T)
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print(paste(i," out of ",nrow(fdly)," for year ", fdly$fyear[i])) |
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} |
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### table of problematic files |
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table(is.na(fdly$npar)) |
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table(fdly$fmonth) |
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table(fdly$fvar) |
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fdly[is.na(fdly$npar),] |
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## delete files that fail check? |
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delete=T |
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if(delete) {
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drop=is.na(fdly$npar)|fdly$fvar!=" CER COT CLD" |
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file.remove(as.character(fdly$path[drop])) |
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fdly=fdly[!drop,] |
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| 185 | 159 |
} |
| 186 | 160 |
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| 187 | 161 |
## Combine all days within years into a single file (can't mergetime all days at once because this opens too many files) |
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ncopath="/nasa/sles11/nco/4.0.8/gcc/mpt/bin/" |
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library(multicore) |
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## create temporary directory to put intermediate files (will be deleted when R quits) |
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| 188 | 167 |
tsdir=paste(tempdir(),"/summary",sep="") |
| 189 | 168 |
dir.create(tsdir) |
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lapply(unique(fdly$year),function(y){
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system(paste("cdo -O mergetime ",paste(fdly$path[!is.na(fdly$npar)&fdly$year==y],collapse=" ")," ",tsdir,"/MOD09_",tile,"_",y,"_daily.nc",sep=""))
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print(paste("Finished merging daily files for year",y))
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}) |
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## Combine the year-by-year files into a single daily file |
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system(paste("cdo -O mergetime ",paste(list.files(tsdir,full=T,pattern="daily[.]nc$"),collapse=" ")," ",outdir2,"/MOD09_",tile,"_daily.nc",sep=""))
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system(paste("cdo -O monmean ",outdir2,"/MOD09_",tile,"_daily.nc ",outdir2,"/",tile,"_monmean.nc",sep=""))
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system(paste("cdo -O ymonmean ",outdir2,"/MOD09_",tile,"_daily.nc ",outdir2,"/",tile,"_ymonmean.nc",sep=""))
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system(paste("cdo -O ymonstd ",outdir2,"/MOD09_",tile,"_daily.nc ",outdir2,"/",tile,"_ymonstd.nc",sep=""))
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## create a file of daily scenes for each year |
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#mclapply(unique(fdly$year),function(y){
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# system(paste("cdo -O mergetime ",paste(fdly$path[!is.na(fdly$npar)&fdly$year==y],collapse=" ")," ",tsdir,"/MOD06_",tile,"_",y,"_daily.nc",sep=""))
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# print(paste("Finished merging daily files for year",y))
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#},mc.cores=5) |
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## merge all daily files to create a single file with all dates |
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system(paste(ncopath,"ncrcat -O ",outdir,"/*nc ",outdir2,"/MOD06_",tile,"_daily.nc",sep="")) |
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############################## |
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## Combine the year-by-year files into a single daily file in the summary directory (for archiving) |
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#system(paste("cdo -O mergetime ",paste(list.files(tsdir,full=T,pattern="daily[.]nc$"),collapse=" ")," ",outdir2,"/MOD06_",tile,"_daily.nc",sep=""))
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system(paste(ncopath,"ncatted ", |
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" -a units,time,o,c,\"days since 2000-1-1 0:0:0\" ", |
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" -a title,global,o,c,\"MODIS Cloud Product (MOD06) Daily Timeseries\" ", |
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" -a institution,global,o,c,\"Yale University\" ", |
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" -a source,global,o,c,\"MODIS Cloud Product (MOD06)\" ", |
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" -a comment,global,o,c,\"Compiled by Adam M. Wilson (adam.wilson@yale.edu)\" ", |
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outdir2,"/MOD06_",tile,"_daily.nc",sep="")) |
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#system(paste("cdo -O monmean ",outdir2,"/MOD06_",tile,"_daily.nc ",tsdir,"/MOD06_",tile,"_monmean.nc",sep=""))
|
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############################# |
|
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## Generate the Climatologies |
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myear=as.integer(max(fdly$year)) #this year will be used in all dates of monthly climatologies (and day will = 15) |
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|
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## Monthly means |
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system(paste("cdo -O sorttimestamp -setyear,",myear," -setday,15 -ymonmean ",outdir2,"/MOD06_",tile,"_daily.nc ",tsdir,"/MOD06_",tile,"_ymonmean.nc",sep=""))
|
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|
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## Monthly standard deviation |
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system(paste("cdo -O sorttimestamp -setyear,",myear," -setday,15 -ymonstd ",outdir2,"/MOD06_",tile,"_daily.nc ",tsdir,"/MOD06_",tile,"_ymonstd.nc",sep=""))
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system(paste(ncopath,"ncrename -v CER,CER_sd -v CLD,CLD_sd -v COT,COT_sd ",tsdir,"/MOD06_",tile,"_ymonstd.nc",sep="")) |
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system(paste(ncopath,"ncatted ", |
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" -a long_name,CER_sd,o,c,\"Cloud Particle Effective Radius (standard deviation of daily observations)\" ", |
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" -a long_name,CLD_sd,o,c,\"Cloud Mask (standard deviation of daily observations)\" ", |
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" -a long_name,COT_sd,o,c,\"Cloud Optical Thickness (standard deviation of daily observations)\" ", |
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tsdir,"/MOD06_",tile,"_ymonstd.nc",sep="")) |
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|
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## cer > 20 |
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system(paste("cdo -O sorttimestamp -setyear,",myear," -setday,15 -ymonmean -gtc,20 -selvar,CER ",outdir2,"/MOD06_",tile,"_daily.nc ",tsdir,"/MOD06_",tile,"_ymoncer20.nc",sep=""))
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system(paste(ncopath,"ncrename -v CER,CER20 ",tsdir,"/MOD06_",tile,"_ymoncer20.nc",sep="")) |
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system(paste(ncopath,"ncatted ", |
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" -a long_name,CER20,o,c,\"Proportion of Days with Cloud Particle Effective Radius > 20um\" ", |
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" -a units,CER20,o,c,\"Proportion\" ", |
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tsdir,"/MOD06_",tile,"_ymoncer20.nc",sep="")) |
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|
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## number of observations |
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system(paste("cdo -O sorttimestamp -setyear,",myear," -setday,15 -nint -mulc,100 -ymonmean -eqc,9999 -setmisstoc,9999 -selvar,CER,CLD ",outdir2,"/MOD06_",tile,"_daily.nc ",tsdir,"/MOD06_",tile,"_ymonmiss.nc",sep=""))
|
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system(paste(ncopath,"ncrename -v CER,CER_pmiss -v CLD,CLD_pmiss ",tsdir,"/MOD06_",tile,"_ymonmiss.nc",sep="")) |
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system(paste(ncopath,"ncatted ", |
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" -a long_name,CER_pmiss,o,c,\"Proportion of Days with missing data for CER\" ", |
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" -a long_name,CLD_pmiss,o,c,\"Proportion of Days with missing data for CLD\" ", |
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" -a scale_factor,CER_pmiss,o,d,0.01 ", |
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" -a units,CER_pmiss,o,c,\"Proportion\" ", |
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" -a scale_factor,CLD_pmiss,o,d,0.01 ", |
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" -a units,CLD_pmiss,o,c,\"Proportion\" ", |
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tsdir,"/MOD06_",tile,"_ymonmiss.nc",sep="")) |
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|
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## append variables to a single file |
|
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system(paste(ncopath,"ncks -O ",tsdir,"/MOD06_",tile,"_ymonmean.nc ",tsdir,"/MOD06_",tile,"_ymon.nc",sep="")) |
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system(paste(ncopath,"ncks -A ",tsdir,"/MOD06_",tile,"_ymonstd.nc ",tsdir,"/MOD06_",tile,"_ymon.nc",sep="")) |
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system(paste(ncopath,"ncks -A ",tsdir,"/MOD06_",tile,"_ymoncer20.nc ",tsdir,"/MOD06_",tile,"_ymon.nc",sep="")) |
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system(paste(ncopath,"ncks -A ",tsdir,"/MOD06_",tile,"_ymonmiss.nc ",tsdir,"/MOD06_",tile,"_ymon.nc",sep="")) |
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|
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## append sinusoidal grid from one of input files as CDO doesn't transfer all attributes |
|
| 236 |
system(paste(ncopath,"ncks -A -v sinusoidal ",list.files(tsdir,full=T,pattern="daily[.]nc$")[1]," ",tsdir,"/MOD06_",tile,"_ymon.nc",sep="")) |
|
| 237 |
|
|
| 238 |
## invert latitude so it plays nicely with gdal |
|
| 239 |
system(paste(ncopath,"ncpdq -O -a -y ",tsdir,"/MOD06_",tile,"_ymon.nc ",outdir2,"/MOD06_",tile,".nc",sep="")) |
|
| 240 |
|
|
| 241 |
## update attributes |
|
| 242 |
system(paste(ncopath,"ncatted ", |
|
| 243 |
#" -a standard_parallel,sinusoidal,o,c,\"0\" ", |
|
| 244 |
#" -a longitude_of_central_meridian,sinusoidal,o,c,\"0\" ", |
|
| 245 |
#" -a latitude_of_central_meridian,sinusoidal,o,c,\"0\" ", |
|
| 246 |
" -a units,time,o,c,\"days since 2000-1-1 0:0:0\" ", |
|
| 247 |
" -a title,global,o,c,\"MODIS Cloud Product (MOD06) Climatology\" ", |
|
| 248 |
" -a institution,global,o,c,\"Yale University\" ", |
|
| 249 |
" -a source,global,o,c,\"MODIS Cloud Product (MOD06)\" ", |
|
| 250 |
" -a comment,global,o,c,\"Compiled by Adam M. Wilson (adam.wilson@yale.edu)\" ", |
|
| 251 |
outdir2,"/MOD06_",tile,".nc",sep="")) |
|
| 252 |
|
|
| 200 | 253 |
|
| 201 | 254 |
print("Finished! %%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%")
|
| 202 | 255 |
## quit R |
| ... | ... | |
| 206 | 259 |
################################################################# |
| 207 | 260 |
|
| 208 | 261 |
### copy the files back to Yale |
| 209 |
list.files("2_daily")
|
|
| 210 |
system(paste("scp ",outdir2,"/*_ymonmean.nc adamw@acrobates.eeb.yale.edu:/data/personal/adamw/projects/interp/data/modis/Venezuela/summary",sep=""))
|
|
| 262 |
system(paste("scp ",outdir2,"/MOD06_",tile,".nc adamw@acrobates.eeb.yale.edu:/data/personal/adamw/projects/interp/data/modis/mod06/summary",sep=""))
|
|
| 211 | 263 |
|
| 212 | 264 |
system("scp /tmp/Rtmp6I6tFn/MOD06_L2.A2000061.1615.051.2010273184629.hdf adamw@acrobates.eeb.yale.edu:/data/personal/adamw/projects/interp/data/modis/Venezuela")
|
| 213 | 265 |
system("scp 2_daily/MOD06_20000410.nc adamw@acrobates.eeb.yale.edu:/data/personal/adamw/projects/interp/data/modis/Venezuela")
|
Also available in: Unified diff
Identified problem in handling of missing values of MOD06 product. In some areas limiting quality control to the highest quality results in ~90% NAs.