Revision 4f171339
Added by Adam M. Wilson almost 11 years ago
| climate/procedures/MOD35_Explore.r | ||
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## explore the MOD35 data downloaded and gridded by the DAAC |
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setwd("~/acrobates/adamw/projects/interp/data/modis/mod35")
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setwd("/Users/adamw/GoogleDrive/Work/presentations/20130426_NASAMeeting/data")
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library(raster) |
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library(rasterVis) |
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library(rgdal) |
| ... | ... | |
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## get % cloudy |
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v5=stack(brick("../mod06/summary/MOD06_h11v08_ymoncld01.nc",varname="CLD01"))
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v5=stack(brick("summary/MOD06_h11v08_ymoncld01.nc",varname="CLD01"))
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projection(v5)="+proj=sinu +lon_0=0 +x_0=0 +y_0=0 +a=6371007.181 +b=6371007.181 +units=m +no_defs" |
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v6=stack(brick("summary/MOD35_h11v08.nc",varname="PCloud"))
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projection(v6)="+proj=sinu +lon_0=0 +x_0=0 +y_0=0 +a=6371007.181 +b=6371007.181 +units=m +no_defs" |
| ... | ... | |
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v5m=mean(v5) |
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## worldclim |
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wc=brick("summary/worldclim_h11v08.tif")
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names(wc)=paste("WC",1:12,sep="_")
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projection(wc)="+proj=sinu +lon_0=0 +x_0=0 +y_0=0 +a=6371007.181 +b=6371007.181 +units=m +no_defs" |
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wcsp=projectRaster(wc,crs="+proj=longlat +datum=WGS84 +no_defs +ellps=WGS84 +towgs84=0,0,0") |
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wcsp=readAll(wcsp) |
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wcsp=setZ(wcsp,paste("2011-",1:12,"-15",sep=""))
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## landcover |
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lulc=raster("~/acrobatesroot/jetzlab/Data/environ/global/landcover/MODIS/MCD12Q1_IGBP_2005_v51.tif")
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lulc=raster("~/acrobatesroot/jetzlab/Data/environ/global/landcover/MODIS/MCD12Q1_IGBP_2005_v51.tif")
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projection(lulc)="+proj=sinu +lon_0=0 +x_0=0 +y_0=0 +a=6371007.181 +b=6371007.181 +units=m +no_defs" |
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lulc=crop(lulc,v6) |
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| ... | ... | |
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### load WORLDCLIM elevation |
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dem=raster("../../tiles/h11v08/dem_h11v08.tif",format="GTiff")
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projection(dem)="+proj=sinu +lon_0=0 +x_0=0 +y_0=0 +a=6371007.181 +b=6371007.181 +units=m +no_defs" |
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dem=raster("summary/dem_h11v08.tif",format="GTiff")
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dif=v6-v5 |
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names(dif)=month.name |
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| ... | ... | |
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### compare MOD43 and MOD17 products |
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## MOD17 |
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mod17=raster("../MOD17/Npp_1km_C5.1_mean_00_to_06.tif",format="GTiff")
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mod17=crop(projectRaster(mod17,v6,method="bilinear"),v6) |
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NAvalue(mod17)=32767 |
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#mod17=raster("../MOD17/Npp_1km_C5.1_mean_00_to_06.tif",format="GTiff")
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#mod17=crop(projectRaster(mod17,v6,method="bilinear"),v6)
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#NAvalue(mod17)=32767
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mod17qc=raster("../MOD17/Npp_QC_1km_C5.1_mean_00_to_06.tif",format="GTiff")
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mod17qc=raster("summary/Npp_QC_1km_C5.1_mean_00_to_06.tif",format="GTiff")
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mod17qc=crop(projectRaster(mod17qc,v6,method="bilinear"),v6) |
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mod17qc[mod17qc<0|mod17qc>100]=NA |
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## MOD43 via earth engine |
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mod43=raster("../mod43/3b21aa90cc657523ff31e9559f36fb12.EVI_MEAN.tif",format="GTiff")
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mod43=crop(projectRaster(mod43,v6,method="bilinear"),v6) |
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#mod43=raster("../mod43/3b21aa90cc657523ff31e9559f36fb12.EVI_MEAN.tif",format="GTiff")
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#mod43=crop(projectRaster(mod43,v6,method="bilinear"),v6)
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mod43qc=raster("../mod43/3b21aa90cc657523ff31e9559f36fb12.Percent_Cloudy.tif",format="GTiff")
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mod43qc=raster("summary/3b21aa90cc657523ff31e9559f36fb12.Percent_Cloudy.tif",format="GTiff")
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mod43qc=crop(projectRaster(mod43qc,v6,method="bilinear"),v6) |
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mod43qc[mod43qc<0|mod43qc>100]=NA |
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| ... | ... | |
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modprod=stack(mod17qc,mod43qc) |
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names(modprod)=c("MOD17","MOD43")
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### |
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### worldclim and interpolation |
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m7=raster("summary/h11v08_pred_2_8.nc",varname="ppt")
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m7=readAll(m7) |
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m7=m7*30 |
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pred=stack(subset(wc,2),subset(m7,2)) |
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names(pred)=c("WorldClim","MOD35 Precipitation")
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n=100 |
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at=seq(0,100,len=n) |
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cols=grey(seq(0,1,len=n)) |
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cols=rainbow(n) |
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bgyr=colorRampPalette(c("blue","green","yellow","red"))
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gbg=colorRampPalette(c(grey(.2),"grey","blue")) |
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cols=bgyr(n) |
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#levelplot(lulcf,margin=F,layers="LULC") |
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compare=stack(v5,v6) |
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m=3 |
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mcompare=stack(subset(v5,m),subset(v6,m)) |
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names(compare)=paste(rep(c("C5","C6"),each=12),1:12,sep="_")
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mdiff=subset(v5,m)-subset(v6,m) |
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names(mcompare)=c("Collection_5","Collection_6")
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names(mdiff)=c("Collection_5-Collection_6")
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library(Cairo) |
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(trellis.par.get()) |
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trellis.par.set(par.ylab.text=list(cex=5)) |
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CairoPDF("output/mod35compare.pdf",width=11,height=8.5)
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pdf("output/mod35compare.pdf",width=11,height=8.5, fontsize=18)
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#CairoPNG("output/mod35compare_%d.png",units="in", width=11,height=8.5,pointsize=4000,dpi=1200,antialias="subpixel")
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levelplot(mcompare,col.regions=cols,at=at,margin=F,sub="Frequency of MOD35 Clouds in March") |
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levelplot(mcompare,col.regions=cols,at=at,margin=F,sub="Cloud Frequency (%) from MOD35 in March") |
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## show all months c5 vs c6 |
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levelplot(compare,col.regions=cols,at=at,margin=F,sub="C5 and C6 MOD35 Comparison", |
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layout=c(12,2),as.table=T) |
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#levelplot(dif,col.regions=bgyr(20),margin=F) |
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levelplot(mdiff,col.regions=bgyr(100),at=seq(mdiff@data@min,mdiff@data@max,len=100),margin=F) |
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boxplot(as.matrix(subset(dif,subset=1))~forest,varwidth=T,notch=T);abline(h=0) |
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#boxplot(as.matrix(subset(dif,subset=1))~forest,varwidth=T,notch=T);abline(h=0)
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levelplot(modprod,main="Missing Data (%) in MOD17 (NPP) and MOD43 (BRDF Reflectance)", |
| ... | ... | |
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sub="Tile H11v08 (Venezuela)",col.regions=cols,at=at, |
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xlim=c(-7300000,-6670000),ylim=c(0,600000)) |
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levelplot(v5m,main="Missing Data (%) in MOD17 (NPP) and MOD43 (BRDF Reflectance)", |
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sub="Tile H11v08 (Venezuela)",col.regions=cols,at=at, |
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xlim=c(-7200000,-6670000),ylim=c(0,400000),margin=F) |
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levelplot(subset(v5v6compare,1:2),main="Proportion Cloudy Days (%) in Collection 5 and 6 MOD35", |
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levelplot(subset(v5v6compare,1:2),main="Mean Annual Proportion Cloudy Days (%) in Collection 5 and 6 MOD35", |
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sub="Tile H11v08 (Venezuela)",col.regions=cols,at=at, |
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margin=F) |
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levelplot(subset(v5v6compare,1:2),main="Proportion Cloudy Days (%) in Collection 5 and 6 MOD35", |
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levelplot(subset(v5v6compare,1:2),main="Mean Annual Proportion Cloudy Days (%) in Collection 5 and 6 MOD35",
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sub="Tile H11v08 (Venezuela)",col.regions=cols,at=at, |
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xlim=c(-7200000,-6670000),ylim=c(0,400000),margin=F) |
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| ... | ... | |
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sub="Tile H11v08 (Venezuela)",col.regions=cols,at=at, |
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xlim=c(-7500000,-7200000),ylim=c(700000,1000000),margin=F) |
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levelplot(pred,main="Comparison of WorldClim with Cloud-Informed interpolation", |
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sub="Tile H11v08 (Venezuela)",col.regions=grey(seq(0,1,len=n)),at=quantile(as.numeric(as.matrix(pred)),na.rm=T,seq(0,1,len=n))) |
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levelplot(pred,main="Comparison of WorldClim with Cloud-Informed interpolation", |
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sub="Tile H11v08 (Venezuela)",col.regions=cols,at=quantile(as.numeric(as.matrix(pred)),na.rm=T,seq(0,1,len=n))) |
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levelplot(pred,main="Comparison of WorldClim with Cloud-Informed interpolation", |
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sub="Tile H11v08 (Venezuela)",col.regions=cols,at=seq(0,360,len=n)) |
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p.strip <- list(cex=1.5, lines=2, fontface='bold') |
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ckey <- list(labels=list(cex=2), height=1) |
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x.scale <- list(cex=1.5, alternating=1) |
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y.scale <- list(cex=1.5, alternating=1) |
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levelplot(pred,main="Comparison of WorldClim with Cloud-Informed interpolation", |
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sub="Tile H11v08 (Venezuela)",col.regions=cols,at=c(seq(-2,150,len=n*.75),seq(150.1,360,len=n*.25)), |
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xlim=c(-7700000,-6700000),ylim=c(350000,1100000) , scales=list(x=x.scale,y=y.scale),par.strip.text=p.strip,colorkey=ckey, |
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layout=c(2,1)) |
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dev.off() |
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| ... | ... | |
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#### export KML timeseries |
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wd="/Users/adamw/GoogleDrive/Work/presentations/20130426_NASAMeeting/data/" |
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library(plotKML) |
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tile="h11v08" |
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file=paste("summary/MOD35_",tile,".nc",sep="")
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system(paste("gdalwarp -overwrite -multi -ot INT16 -r cubicspline -srcnodata 255 -dstnodata 255 -s_srs '+proj=sinu +lon_0=0 +x_0=0 +y_0=0 +a=6371007.181 +b=6371007.181 +units=m +no_defs' -t_srs 'EPSG:4326' NETCDF:",file,":PCloud MOD35_",tile,".tif",sep=""))
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system(paste("gdalwarp -overwrite -multi -r cubicspline -srcnodata 255 -dstnodata 255 -s_srs '+proj=sinu +lon_0=0 +x_0=0 +y_0=0 +a=6371007.181 +b=6371007.181 +units=m +no_defs' -t_srs 'EPSG:4326' NETCDF:",file,":PCloud MOD35_",tile,".tif",sep=""))
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v6sp=brick(paste("MOD35_",tile,".tif",sep=""))
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v6sp=brick(paste("summary/MOD35_",tile,".tif",sep=""))
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v6sp=readAll(v6sp) |
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## wasn't working with line below, perhaps Z should just be text? not date? |
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v6sp=setZ(v6sp,as.Date(paste("2011-",1:12,"-15",sep="")))
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v6sp=setZ(v6sp,paste("2011-",1:12,"-15",sep=""))
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names(v6sp)=month.name |
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kml_open("output/mod35.kml")
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setwd(paste(wd,"/kml/mod35",sep="")) |
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kmlf="mod35.kml" |
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kml_open(file.name=kmlf) |
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kml_layer.RasterBrick(v6sp, |
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plot.legend = TRUE, dtime = "", tz = "GMT", |
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z.lim = c(0,100),colour_scale = get("colour_scale_numeric", envir = plotKML.opts))
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z.lim = c(0,100),colour_scale = gbg(20),
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# home_url = get("home_url", envir = plotKML.opts),
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# metadata = NULL, html.table = NULL, |
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# altitudeMode = "clampToGround", balloon = FALSE,
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altitudeMode = "clampToGround", balloon = FALSE,folder.name=kmlfl,legend.file="mod35_legend.png"
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) |
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logo = "http://static.tumblr.com/t0afs9f/KWTm94tpm/yale_logo.png" |
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kml_screen(image.file = logo, position = "UL", sname = "YALE logo",size=c(.1,.1)) |
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kml_close("mod35.kml")
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kml_compress("mod35.kml",files=c(paste(month.name,".png",sep=""),"obj_legend.png"),zip="/usr/bin/zip")
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#logo = "yale_logo.png" |
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#kml_screen(image.file = logo, position = "UL", sname = "YALE logo",size=c(.1,.1)) |
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kml_close(file.name=kmlf) |
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#kml_compress(file.name=kmlf,files=c(paste(month.name,".png",sep=""),"obj_legend.png"),zip="/usr/bin/zip") |
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### worldclim |
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setwd(paste(wd,"/kml/wc",sep="")) |
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kmlf="worldclim.kml" |
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kml_open(file.name=kmlf) |
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kml_layer.RasterBrick(wcsp, |
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plot.legend = TRUE, dtime = "", tz = "GMT", |
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z.lim = c(0,650),colour_scale = gbg(100), |
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# home_url = get("home_url", envir = plotKML.opts),
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# metadata = NULL, html.table = NULL, |
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altitudeMode = "clampToGround", balloon = FALSE |
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) |
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kml_close(file.name=kmlf) |
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#kml_compress(file.name=kmlf,files=c(paste("WC_",1:12,".png",sep=""),"obj_legend.png"),zip="/usr/bin/zip")
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setwd(wd) |
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Also available in: Unified diff
Old code