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### Script to compile the monthly cloud data from earth engine into a netcdf file for further processing
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setwd("~/acrobates/adamw/projects/cloud")
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library(raster)
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library(doMC)
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registerDoMC(10)
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tempdir="tmp"
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if(!file.exists(tempdir)) dir.create(tempdir)
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## Get list of available files
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df=data.frame(path=list.files("data/mod09",pattern="*.tif$",full=T),stringsAsFactors=F)
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df[,c("region","year","month")]=do.call(rbind,strsplit(basename(df$path),"_|[.]"))[,c(2,3,4)]
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df$date=as.Date(paste(df$year,"_",df$month,"_15",sep=""),"%Y_%m_%d")
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table(df$year,df$month)
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## drop some if not complete
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df=df[df$year<=2006,]
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## Loop over existing months to build composite netcdf files
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foreach(date=unique(df$date)) %dopar% {
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## get date
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print(date)
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## Define output and check if it already exists
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ncfile=paste(tempdir,"/mod09_",date,".nc",sep="")
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if(file.exists(ncfile)) next
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## merge regions to a new netcdf file
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system(paste("gdal_merge.py -o ",ncfile," -of netCDF -ot Byte -n 0 ",paste(df$path[df$date==date],collapse=" ")))
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system(paste("ncecat -O -u time ",ncfile," ",ncfile,sep=""))
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## create temporary nc file with time information to append to MOD06 data
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cat(paste("
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netcdf time {
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dimensions:
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time = 1 ;
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variables:
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int time(time) ;
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time:units = \"days since 2000-01-01 00:00:00\" ;
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time:calendar = \"gregorian\";
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time:long_name = \"time of observation\";
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data:
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time=",as.integer(date-as.Date("2000-01-01")),";
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}"),file=paste(tempdir,"/",date,"_time.cdl",sep=""))
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system(paste("ncgen -o ",tempdir,"/",date,"_time.nc ",tempdir,"/",date,"_time.cdl",sep=""))
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system(paste("ncks -A ",tempdir,"/",date,"_time.nc ",ncfile,sep=""))
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## add other attributes
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system(paste("ncrename -v Band1,CF ",ncfile,sep=""))
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system(paste("ncatted ",
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" -a units,CF,o,c,\"Proportion Days Cloudy\" ",
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" -a missing_value,CF,o,b,255 ",
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" -a _FillValue,CF,d,, ",
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" -a valid_range,CF,o,b,\"0,100\" ",
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" -a long_name,CF,o,c,\"Proportion cloudy days (%)\" ",
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ncfile,sep=""))
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## add the fillvalue attribute back (without changing the actual values)
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system(paste("ncatted -a _FillValue,CF,o,b,255 ",ncfile,sep=""))
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if(as.numeric(system(paste("cdo -s ntime ",ncfile),intern=T))<1) {
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print(paste(ncfile," has no time, deleting"))
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file.remove(ntime)
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}
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print(paste(basename(ncfile)," Finished"))
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}
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### merge all the tiles to a single global composite
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#system(paste("ncdump -h ",list.files(tempdir,pattern="mod09.*.nc$",full=T)[10]))
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system(paste("cdo -O mergetime ",paste(list.files(tempdir,pattern="mod09.*.nc$",full=T),collapse=" ")," data/mod09.nc"))
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### generate the monthly mean and sd
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system(paste("cdo -O merge -ymonmean data/mod09.nc -chname,CF,CF_sd -ymonstd data/mod09.nc -chname,CF,CF_annual -timmean data/mod09.nc data/mod09_clim.nc"))
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74
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