############################

####  Extract MOD35 C6 processing path

library(raster)

library(spgrass6)

stitch=paste("sudo MRTDATADIR=\"/usr/local/heg/2.12/data\" PGSHOME=/usr/local/heg/2.12/TOOLKIT_MTD PWD=/home/adamw /usr/local/heg/2.12b/bin/swtif")

## Link to MOD35 Swath data

dir.create("swath")

if(getdata)

  system(paste("wget -S --recursive --no-parent --no-directories -N -P swath --accept \"hdf\" --accept \"002|003|004\" ",url))

## make global extent

glb=t

glb=extend(glb,extent(-180,180,-90,90))

files=paste(getwd(),"/",list.files("swath",pattern="hdf$",full=T),sep="")[1:5000]

## vars to process

vars=as.data.frame(matrix(c(

  "Sensor_Zenith",        "SZ",   "CUBIC", 1),

  byrow=T,ncol=4,dimnames=list(1:2,c("variable","varid","method","band"))),stringsAsFactors=F)

## global bounding box

   proj4string(gpp)=projection(glb)

  outfile=paste(tempdir(),"/",var$varid,"_",basename(file),sep="")  #gridded path

INPUT_FILENAME=",file,"

OBJECT_NAME=mod35

BAND_NUMBER = ",var$band,"

OUTPUT_PIXEL_SIZE_Y=0.008333333

SPATIAL_SUBSET_LR_CORNER = ( ",bbox(gpp)[2,1]," ",bbox(gpp)[1,2]," )

RESAMPLING_TYPE =",var$method,"

OUTPUT_PROJECTION_PARAMETERS = ( 0.0 0.0 0.0 0.0 0.0 0.0 0.0 0.0 0.0 0.0 0.0 0.0 0.0 0.0 0.0 )

ELLIPSOID_CODE = WGS84

OUTPUT_TYPE = HDFEOS

",sep="")

   cat( c(hdr,grp)   , file=paste(tempdir(),"/",basename(file),"_MODparms.txt",sep=""))

   ## now run the swath2grid tool

   ## write the gridded file

   print(paste("Starting",file))

}  

   setwd(tempdir())

   bfile=sub(".hdf","",basename(file))

   tempfile2_path=paste(tempdir(),"/",bfile,".tif",sep="")  #gridded/masked/processed path

   outfile=paste(outdir,"/",bfile,".tif",sep="")  #final file

#######

## run swtif for each band

   lapply(1:nrow(vars),function(i) swtif(file,vars[i,]))

   if(!file.exists(paste(tempdir(),"/CM_",basename(file),sep=""))) {

     return(c(file,0))

   }

   ## convert to land path

   sz=raster(paste(tempdir(),"/SZ_",basename(file),sep=""))

   NAvalue(sz)=-9999

### warp them to align all pixels

   system(paste("gdalwarp -overwrite -srcnodata 255 -dstnodata 255 -tap -tr 0.008333333 0.008333333 -co COMPRESS=LZW -co ZLEVEL=9 -co PREDICTOR=2 -s_srs \"",projection(t),"\" ",tempfile2_path," ",outfile,sep=""))

   ## delete temporary files

   file.remove(list.files(tempdir(),pattern=bfile,full=T))

   return(c(file,1))

 }

## check gdal can read all of them

check=do.call(rbind,mclapply(gfiles,function(file){

    gd=system(paste("gdalinfo ",file,sep=""),intern=T)

    if(any(grepl("Corner",gd))) return(1)

    else return(0)

}))

###########

  tf=paste(tempdir(),"/grass", Sys.getpid(),"/", sep="")  #temporar

  if(!file.exists(tf)) dir.create(tf)

  ## set up temporary grass instance for this PID

  gisBase="/usr/lib/grass64"

  print(paste("Set up temporary grass session in",tf))

  initGRASS(gisBase=gisBase,gisDbase=tf,SG=as(glb,"SpatialGridDataFrame"),override=T,location="mod35",mapset="PERMANENT",home=tf,pid=Sys.getpid())

  system(paste("g.proj -c proj4=\"",projection(glb),"\"",sep=""),ignore.stdout=T,ignore.stderr=T)

## read in NPP grid to serve as grid

  execGRASS("r.in.gdal",input=t@file@name,output="grid")

  system("g.region rast=grid n=90 s=-90 save=roi --overwrite",ignore.stdout=F,ignore.stderr=F)

## get files already imported - only important if more tifs were written after an initial import

imported=basename(gfiles)%in%system("g.mlist type=rast pattern=MOD*",intern=T)

table(imported)

## read in all tifs

    print(f)

nbreaks=100

bins=cut(1:5000,nbreaks)

ts=system("g.mlist type=rast pattern=MOD*.tif",intern=T)  #files to process

execGRASS("r.series",input=paste(ts[bins==levels(bins)[i]],sep="",collapse=","),output=paste("path",i,sep="_"),method="mode",range=c(0,5),flags=c("verbose","overwrite"),Sys_wait=T)

##  Get mode of each chunk

execGRASS("r.series",input=paste(system("g.mlist type=rast pattern=path*",intern=T),sep="",collapse=","),output="MOD35_path",method="mode",range=c(0,5),flags=c("verbose","overwrite"))

## fill in missing data (due to gridding artifacts) very near poles with water (north) and land (south)

system("r.mapcalc \"MOD35_patha=if(isnull(MOD35_path)&y()>-84.31,0,MOD35_path)\"")

system("r.mapcalc \"MOD35_pathb=if(isnull(MOD35_patha)&y()<-84.31,3,MOD35_patha)\"")

## add colors

## update metadata

tags=c("TIFFTAG_IMAGEDESCRIPTION='Collection 5 MOD35 Processing Path (0=Water,1=Coast,2=Desert,3=Land)'",

  "TIFFTAG_DOCUMENTNAME='Collection 5 MOD35 Processing Path'",

  "TIFFTAG_DATETIME='20130901'",

  "TIFFTAG_ARTIST='Adam M. Wilson (adam.wilson@yale.edu)'")

system(paste("/usr/local/src/gdal-1.10.0/swig/python/scripts/gdal_edit.py ",getwd(),"/C5MOD35_ProcessPath.tif ",paste("-mo ",tags,sep="",collapse=" "),sep=""))

### delete the temporary files 

  unlink_.gislock()

  system(paste("rm -frR ",tf,sep=""))