Revision e4e30b86
Added by Adam Wilson over 11 years ago
| climate/procedures/MOD35_Climatology.r | ||
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### path to NCO |
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ncopath="/nasa/sles11/nco/4.0.8/gcc/mpt/bin/" |
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### Vector of variables that must be in file or they will be deleted. |
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### Formated as output from system(paste("cdo -s showvar ",fdly$path[i]),intern=T)
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#finalvars=" CER COT CLD" |
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################################################################################ |
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## Get list of all daily files |
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if(verbose) print(paste("Checking daily output in preparation for generating climatology:",tile))
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| ... | ... | |
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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,"/MOD35_",tile,"_daily.nc",sep="")) |
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system(paste("ncdump -h ",outdir2,"/MOD35_",tile,"_daily.nc",sep=""))
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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) Summaries\" ", |
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" -a institution,global,o,c,\"Yale University\" ", |
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" -a source,global,o,c,\"MODIS Collection 6 Cloud Mask (MOD35)\" ", |
| ... | ... | |
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## Overall Means |
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if(verbose) print(paste("Calculating the overall mean:",tile))
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system(paste("cdo -O -b I8 -v sorttimestamp -setyear,",myear," -setmon,1 -setday,1 -mulc,-1 -subc,100 -timmean -selyear,2009 ",outdir2,"/MOD35_",tile,"_daily.nc ",outdir2,"/MOD35_",tile,"_2009mean.nc",sep=""),wait=T)
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system(paste(ncopath,"ncrename -v PClear,PCloud ",outdir2,"/MOD35_",tile,"_2009mean.nc",sep=""))
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system(paste("cdo -O -b I8 -v sorttimestamp -setyear,",myear," -setmon,1 -setday,1 -mulc,100 -timmean -lec,1 ",outdir2,"/MOD35_",tile,"_daily.nc ",outdir2,"/MOD35_",tile,"_mean.nc",sep=""),wait=T)
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system(paste(ncopath,"ncrename -v CMday,CFday -v CMnight,CFnight ",outdir2,"/MOD35_",tile,"_mean.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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outdir2,"/MOD35_",tile,"_2009mean.nc",sep="")) |
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" -a long_name,CFday,o,c,\"Daytime Cloud Frequency\" ", |
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" -a missing_value,CFday,o,b,255 ", |
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" -a _FillValue,CFday,d,b,255 ", |
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" -a long_name,CFnight,o,c,\"Nighttime Cloud Frequency\" ", |
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" -a missing_value,CFnight,o,b,255 ", |
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" -a _FillValue,CFnight,d,b,255 ", |
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outdir2,"/MOD35_",tile,"_mean.nc",sep="")) |
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## Monthly means |
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if(verbose) print(paste("Calculating the monthly means:",tile))
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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("cdo -O -b I8 sorttimestamp -setyear,",myear," -setday,15 -mulc,100 -ymonmean -lec,1 ",outdir2,"/MOD35_",tile,"_daily.nc ",tsdir,"/MOD35_",tile,"_ymonmean.nc",sep=""),wait=T)
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system(paste(ncopath,"ncrename -v CMday,CFday -v CMnight,CFnight ",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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" -a long_name,CFday,o,c,\"Daytime Cloud Frequency\" ", |
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" -a units,CFday,o,c,\"Proportion (%)\" ", |
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" -a missing_value,CFday,o,b,255 ", |
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" -a _FillValue,CFday,d,b,255 ", |
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" -a long_name,CFnight,o,c,\"Nighttime Cloud Frequency\" ", |
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" -a units,CFnight,o,c,\"Proportion (%)\" ", |
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" -a missing_value,CFnight,o,b,255 ", |
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" -a _FillValue,CFnight,d,b,255 ", |
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tsdir,"/MOD35_",tile,"_ymonmean.nc",sep="")) |
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| ... | ... | |
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## Monthly standard deviation |
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if(verbose) print(paste("Calculating the monthly SD:",tile))
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system(paste("cdo -O -b I8 sorttimestamp -setyear,",myear," -setday,15 -ymonstd -mulc,-1 -subc,100 -monmean ",
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system(paste("cdo -O -b I8 sorttimestamp -setyear,",myear," -setday,15 -ymonstd -mulc,100 -monmean -lec,1 ",
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outdir2,"/MOD35_",tile,"_daily.nc ", |
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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,"ncrename -v CMday,CFday_sd -v CMnight,CFnight_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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" -a long_name,CFnight_sd,o,c,\"Standard Deviation of monthly nighttime cloud frequency\" ", |
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" -a long_name,CFday_sd,o,c,\"Standard Deviation of monthly daytime cloud frequency\" ", |
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tsdir,"/MOD35_",tile,"_ymonstd.nc",sep="")) |
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## frequency of cloud days p(clear<90%) |
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if(verbose) print(paste("Calculating the proportion of cloudy and probably cloudy days:",tile))
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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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" -a units,CF,o,c,\"Proportion (%)\" ", |
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tsdir,"/MOD35_",tile,"_ymoncld01.nc",sep="")) |
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#if(verbose) print(paste("Calculating the proportion of cloudy and probably cloudy days:",tile))
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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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#" -a units,CF,o,c,\"Proportion (%)\" ",
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#tsdir,"/MOD35_",tile,"_ymoncld01.nc",sep=""))
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## number of observations |
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if(verbose) print(paste("Calculating the number of missing variables:",tile))
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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("cdo -O -b I8 sorttimestamp -setyear,",myear," -setday,15 -ymonmean -mulc,100 -eqc,9999 -setmisstoc,9999 ",outdir2,"/MOD35_",tile,"_daily.nc ",tsdir,"/MOD35_",tile,"_ymonmiss.nc",sep=""))
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system(paste(ncopath,"ncrename -v CMday,CFday_pmiss -v CMnight,CFnight_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\" ", |
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" -a units,Pmiss,o,c,\"Proportion (%)\" ", |
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" -a long_name,CFday_pmiss,o,c,\"Proportion of Days with missing data\" ", |
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" -a units,CFday_pmiss,o,c,\"Proportion (%)\" ", |
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" -a long_name,CFnight_pmiss,o,c,\"Proportion of Days with missing data\" ", |
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" -a units,CFnight_pmiss,o,c,\"Proportion (%)\" ", |
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tsdir,"/MOD35_",tile,"_ymonmiss.nc",sep="")) |
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## TODO: fix projection information so GDAL can read it correctly. |
| ... | ... | |
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if(verbose) print(paste("Append all monthly climatologies into a single file:",tile))
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system(paste(ncopath,"ncks -O ",tsdir,"/MOD35_",tile,"_ymonmean.nc ",tsdir,"/MOD35_",tile,"_ymon.nc",sep="")) |
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system(paste(ncopath,"ncks -A ",tsdir,"/MOD35_",tile,"_ymonstd.nc ",tsdir,"/MOD35_",tile,"_ymon.nc",sep="")) |
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system(paste(ncopath,"ncks -A ",tsdir,"/MOD35_",tile,"_ymoncld01.nc ",tsdir,"/MOD35_",tile,"_ymon.nc",sep="")) |
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#system(paste(ncopath,"ncks -A ",tsdir,"/MOD35_",tile,"_ymoncld01.nc ",tsdir,"/MOD35_",tile,"_ymon.nc",sep=""))
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system(paste(ncopath,"ncks -A ",tsdir,"/MOD35_",tile,"_ymonmiss.nc ",tsdir,"/MOD35_",tile,"_ymon.nc",sep="")) |
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## append sinusoidal grid from one of input files as CDO doesn't transfer all attributes |
Also available in: Unified diff
updated swtif error checking to use r.neighbor instead of r.mapcalc. Submitted job for northern block of tiles