Revision c24e32a8
Added by Adam Wilson about 11 years ago
| climate/procedures/MOD35_Climatology.r | ||
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## Update attributes |
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system(paste(ncopath,"ncatted ", |
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" -a valid_min,PClear,o,b,0 ", |
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" -a valid_max,PClear,o,b,100 ", |
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#" -a valid_range,PClear,o,b,\"0,255\" ", |
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#" -a missing_value,PClear,o,b,255 ", |
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#" -a _FillValue,PClear,d,b,255 ", |
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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 (MOD35) Daily Timeseries\" ", |
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" -a institution,global,o,c,\"Yale University\" ", |
| ... | ... | |
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## subset dates |
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## due to bug (?) in CDO tools, only 10 years of data can be processed at a time or strange areas of NAs appear. |
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datesubset="-seldate,2002-01-01,2012-01-01"
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datesubset="-seldate,2000-01-01,2011-12-31"
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## Monthly means |
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if(verbose) print("Calculating the monthly means")
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system(paste("cdo -O sorttimestamp -setyear,",myear," -setday,15 -mulc,-1 -subc,100 -ymonmean ",outdir2,"/MOD35_",tile,"_daily.nc ",tsdir,"/MOD35_",tile,"_ymonmean.nc",sep=""),wait=T)
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#system(paste("cdo -v -O selindexbox,1,100,1100,1200 ",outdir2,"/MOD35_",tile,"_daily.nc ",tsdir,"/MOD35_",tile,"_dailysmall.nc",sep=""),wait=T)
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#system(paste("cdo -v -O sorttimestamp -setyear,",myear," -setday,15 -mulc,-1 -subc,100 -ymonmean ",outdir2,"/MOD35_",tile,"_dailysmall.nc ",tsdir,"/MOD35_",tile,"_ymonmean.nc",sep=""),wait=T)
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system(paste("cdo -O -b I8 -v sorttimestamp -setyear,",myear," -setday,15 -mulc,-1 -subc,100 -ymonmean ",outdir2,"/MOD35_",tile,"_daily.nc ",tsdir,"/MOD35_",tile,"_ymonmean.nc",sep=""),wait=T)
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system(paste(ncopath,"ncrename -v PClear,PCloud ",tsdir,"/MOD35_",tile,"_ymonmean.nc",sep="")) |
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system(paste(ncopath,"ncatted ", |
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" -a long_name,PCloud,o,c,\"Mean Probability of Cloud\" ", |
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" -a missing_value,PCloud,o,b,255 ", |
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" -a _FillValue,PCloud,d,b,255 ", |
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tsdir,"/MOD35_",tile,"_ymonmean.nc",sep="")) |
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system(paste("cdo -O sorttimestamp -setyear,",myear," -setday,15 -mulc,-1 -subc,100 -ymonmean ",outdir2,"/MOD35_",tile,"_daily.nc ",tsdir,"/MOD35_",tile,"_ymonmean.nc",sep=""),wait=T)
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system(paste("cdo -O sorttimestamp -setyear,",myear," -setday,15 -mulc,-1 -subc,100 -monmean ",outdir2,"/MOD35_",tile,"_daily.nc ",tsdir,"/MOD35_",tile,"_monmean.nc",sep=""),wait=T)
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## Monthly Mean |
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#months=c("01","02","03","04","05","06","07","08","09","10","11","12")
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# month="02" |
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#ymonmean=function(month){
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# tfile=paste(tempdir(),"/",tile,"_",month,"_",Sys.getpid(),".txt",sep="") |
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# write.table(paste(fdly$path[fdly$month==month],collapse=" "),tfile,col.names=F,row.names=F,quote=F) |
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# system(paste("cat ",tfile," | ",ncopath,"ncra -O -o ",tsdir,"/MOD35_",tile,"_",month,".nc",sep=""))
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# system(paste("cdo -O -setyear,",myear," -setmon,",month," -setday,15 -mulc,-1 -subc,100 ",tsdir,"/MOD35_",tile,"_",month,".nc ",tsdir,"/MOD35_",tile,"_",month,"b.nc",sep=""))
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# system(paste(ncopath,"ncrename -v PClear,PCloud ",tsdir,"/MOD35_",tile,"_",month,"b.nc",sep="")) |
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# system(paste(ncopath,"ncatted ", |
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#" -a long_name,PCloud,o,c,\"Mean Probability of Cloud\" ", |
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#" -a missing_value,PCloud,o,b,255 ", |
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#" -a _FillValue,PCloud,d,b,255 ", |
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#tsdir,"/MOD35_",tile,"_",month,"b.nc",sep="")) |
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#} |
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#mclapply(months,ymonmean) |
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## merge to a single file |
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# system(paste("cdo -O -b I8 -v -mergetime ",paste(tsdir,"/MOD35_",tile,"_",months,"b.nc ",sep="",collapse=" ")," ",tsdir,"/MOD35_",tile,"_ymonmean.nc",sep=""))
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system(paste("cdo -O sorttimestamp -setyear,",myear," -mulc,-1 -subc,100 -ydrunmean,30 ",datesubset," ",outdir2,"/MOD35_",tile,"_daily.nc ",tsdir,"/MOD35_",tile,"_ydrunmean30.nc",sep=""),wait=T)
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#system(paste("cdo -v -O selindexbox,1,100,1100,1200 ",outdir2,"/MOD35_",tile,"_daily.nc ",tsdir,"/MOD35_",tile,"_dailysmall.nc",sep=""),wait=T)
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#system(paste("cdo -v -O sorttimestamp -setyear,",myear," -setday,15 -mulc,-1 -subc,100 -ymonmean ",outdir2,"/MOD35_",tile,"_dailysmall.nc ",tsdir,"/MOD35_",tile,"_ymonmean.nc",sep=""),wait=T)
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#system(paste("cdo -O sorttimestamp -setyear,",myear," -setday,15 -mulc,-1 -subc,100 -timmean -selmon,2 ",datesubset," ",outdir2,"/MOD35_",tile,"_daily.nc ",tsdir,"/MOD35_",tile,"_ymonmean.nc",sep=""),wait=T)
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#system(paste("cdo -O sorttimestamp -setyear,",myear," -setday,15 -mulc,-1 -subc,100 -monmean ",outdir2,"/MOD35_",tile,"_daily.nc ",tsdir,"/MOD35_",tile,"_monmean.nc",sep=""),wait=T)
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#system(paste("cdo -O sorttimestamp -setyear,",myear," -mulc,-1 -subc,100 -ydrunmean,30 ",datesubset," ",outdir2,"/MOD35_",tile,"_daily.nc ",tsdir,"/MOD35_",tile,"_ydrunmean30.nc",sep=""),wait=T)
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#system(paste("scp ",tsdir,"/MOD35_",tile,"_ymonmean.nc adamw@acrobates.eeb.yale.edu:/data/personal/adamw/projects/interp/data/modis/mod35/",sep=""))
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#system(paste("scp summary/MOD35_",tile,".nc adamw@acrobates.eeb.yale.edu:/data/personal/adamw/projects/interp/data/modis/mod35/",sep=""))
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#system(paste("ncdump -h ",tsdir,"/MOD35_",tile,"_ymonmean.nc ",sep=""))
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system(paste(ncopath,"ncrename -v PClear,PCloud ",tsdir,"/MOD35_",tile,"_ymonmean.nc",sep="")) |
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system(paste(ncopath,"ncatted ", |
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" -a long_name,PCloud,o,c,\"Mean Probability of Cloud\" ", |
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tsdir,"/MOD35_",tile,"_ymonmean.nc",sep="")) |
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## Monthly standard deviation |
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if(verbose) print("Calculating the monthly SD")
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system(paste("cdo -O sorttimestamp -setyear,",myear," -setday,15 -ymonstd ",outdir2,"/MOD35_",tile,"_daily.nc ",tsdir,"/MOD35_",tile,"_ymonstd.nc",sep=""))
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system(paste("cdo -O -b I8 sorttimestamp -setyear,",myear," -setday,15 -ymonstd ",outdir2,"/MOD35_",tile,"_daily.nc ",tsdir,"/MOD35_",tile,"_ymonstd.nc",sep=""))
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system(paste(ncopath,"ncrename -v PClear,PCloud_sd ",tsdir,"/MOD35_",tile,"_ymonstd.nc",sep="")) |
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system(paste(ncopath,"ncatted ", |
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" -a long_name,PCloud_sd,o,c,\"Standard Deviation of p(cloud)\" ", |
| ... | ... | |
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## frequency of cloud days p(clear<90%) |
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if(verbose) print("Calculating the proportion of cloudy and probably cloudy days")
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system(paste("cdo -O sorttimestamp -setyear,",myear," -setday,15 -ymonmean -mulc,100 -lec,90 -selvar,PClear ",outdir2,"/MOD35_",tile,"_daily.nc ",tsdir,"/MOD35_",tile,"_ymoncld01.nc",sep=""))
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system(paste("cdo -O -b I8 sorttimestamp -setyear,",myear," -setday,15 -ymonmean -mulc,100 -lec,90 -selvar,PClear ",outdir2,"/MOD35_",tile,"_daily.nc ",tsdir,"/MOD35_",tile,"_ymoncld01.nc",sep=""))
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system(paste(ncopath,"ncrename -v PClear,CF ",tsdir,"/MOD35_",tile,"_ymoncld01.nc",sep="")) |
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system(paste(ncopath,"ncatted ", |
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" -a long_name,CF,o,c,\"Cloud Frequency: Proportion of Days with probability of clear < 90%\" ", |
| ... | ... | |
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## number of observations |
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if(verbose) print("Calculating the number of missing variables")
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system(paste("cdo -O sorttimestamp -setyear,",myear," -setday,15 -ymonmean -mulc,100 -eqc,9999 -setmisstoc,9999 -selvar,PClear ",outdir2,"/MOD35_",tile,"_daily.nc ",tsdir,"/MOD35_",tile,"_ymonmiss.nc",sep=""))
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system(paste("cdo -O -b I8 sorttimestamp -setyear,",myear," -setday,15 -ymonmean -mulc,100 -eqc,9999 -setmisstoc,9999 -selvar,PClear ",outdir2,"/MOD35_",tile,"_daily.nc ",tsdir,"/MOD35_",tile,"_ymonmiss.nc",sep=""))
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system(paste(ncopath,"ncrename -v PClear,Pmiss ",tsdir,"/MOD35_",tile,"_ymonmiss.nc",sep="")) |
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system(paste(ncopath,"ncatted ", |
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" -a long_name,Pmiss,o,c,\"Proportion of Days with missing data\" ", |
Also available in: Unified diff
Fixed the 'missing stripes' problem in the climatology script. Source of problem was related to the _FillValue attribute being incorrectly set to a short integer when the data was saved as byte. Changing both the attribute and the data to type 'byte' appears to have fixed the problem.