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

####  Extract MOD35 C6 processing path

setwd("~/acrobates/adamw/projects/interp/data/modis/mod35")

library(multicore)

library(raster)

library(spgrass6)

library(rgeos)

##download 3 days of modis swath data:

url="ftp://ladsweb.nascom.nasa.gov/allData/51/MOD35_L2/2012/"

dir.create("swath")

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

### make global raster that aligns with MODLAND tiles

## get MODLAND tile to serve as base

#system("wget http://e4ftl01.cr.usgs.gov/MOLT/MOD13A3.005/2000.02.01/MOD13A3.A2000032.h00v08.005.2006271174446.hdf")

#t=raster(paste("HDF4_EOS:EOS_GRID:\"",getwd(),"/MOD13A3.A2000032.h00v08.005.2006271174446.hdf\":MOD_Grid_monthly_1km_VI:1 km monthly NDVI",sep=""))

t=raster(paste("../MOD17/MOD17A3_Science_NPP_mean_00_12.tif",sep=""))

projection(t)

## make global extent

pmodis="+proj=sinu +lon_0=0 +x_0=0 +y_0=0 +a=6371007.181 +b=6371007.181 +units=m +no_defs"

glb=t

#values(glb)=NA

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

#glb=raster(glb,crs="+proj=longlat +datum=WGS84",nrows=42500,ncols=85000)

#extent(glb)=alignExtent(projectRaster(glb,crs=projection(t),over=T),t)

#res(glb)=c(926.6254,926.6264)

#projection(glb)=pmodis

## confirm extent

#projectExtent(glb,crs="+proj=longlat +datum=WGS84")

#### Grid and mosaic the swath data

stitch="sudo MRTDATADIR=\"/usr/local/heg/data\" PGSHOME=/usr/local/heg/TOOLKIT_MTD PWD=/home/adamw /usr/local/heg/bin/swtif"

files=paste(getwd(),"/",list.files("swath",pattern="hdf$",full=T),sep="")

## vars to process

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

  "Cloud_Mask",              "CM",

  "Sensor_Azimuth",       "ZA",

  "Sensor_Zenith",        "SZ"),

  byrow=T,ncol=2,dimnames=list(1:3,c("variable","varid"))),stringsAsFactors=F)

## global bounding box

   gbb=cbind(c(-180,-180,180,180,-180),c(-85,85,85,-85,-85))

   gpp = SpatialPolygons(list(Polygons(list(Polygon(gbb)),1)))

   proj4string(gpp)=projection(glb)

getpath<- function(file){  

   setwd(tempdir())

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

   tempfile_path=paste(tempdir(),"/path_",basename(file),sep="")  #gridded path

   tempfile_sz=paste(tempdir(),"/sz_",basename(file),sep="")  # gridded sensor zenith

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

   outfile=paste("~/acrobates/adamw/projects/interp/data/modis/mod35/gridded/",bfile,".tif",sep="")  #final file

   if(file.exists(outfile)) return(c(file,0))

   ## get bounding coordinates

   glat=as.numeric(do.call(c,strsplit(sub("GRINGPOINTLATITUDE=","",system(paste("gdalinfo ",file," | grep GRINGPOINTLATITUDE"),intern=T)),split=",")))

   glon=as.numeric(do.call(c,strsplit(sub("GRINGPOINTLONGITUDE=","",system(paste("gdalinfo ",file," | grep GRINGPOINTLONGITUDE"),intern=T)),split=",")))

   bb=cbind(c(glon,glon[1]),c(glat,glat[1]))

   pp = SpatialPolygons(list(Polygons(list(Polygon(bb)),1)))

   proj4string(pp)=projection(glb)

   ppc=gIntersection(pp,gpp)

   ppc=gBuffer(ppc,width=0.3)  #buffer a little to remove gaps between images

   ## First write the parameter file (careful, heg is very finicky!)

   hdr=paste("NUM_RUNS = ",length(vars$varid),"|MULTI_BAND_HDFEOS:",length(vars$varid),sep="")

   grp=paste("

BEGIN

INPUT_FILENAME=",file,"

OBJECT_NAME=mod35

FIELD_NAME=",vars$variable,"|

BAND_NUMBER = ",1:length(vars$varid),"

OUTPUT_PIXEL_SIZE_X=0.008333333

OUTPUT_PIXEL_SIZE_Y=0.008333333

SPATIAL_SUBSET_UL_CORNER = ( ",bbox(ppc)[2,2]," ",bbox(ppc)[1,1]," )

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

OUTPUT_OBJECT_NAME = mod35|

RESAMPLING_TYPE =NN

OUTPUT_PROJECTION_TYPE = GEO

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 )

# OUTPUT_PROJECTION_PARAMETERS = ( 6371007.181 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 )

# projection parameters from http://landweb.nascom.nasa.gov/cgi-bin/QA_WWW/newPage.cgi?fileName=sn_gctp

ELLIPSOID_CODE = WGS84

OUTPUT_TYPE = HDFEOS

OUTPUT_FILENAME= ",tempfile_path,"

END

",sep="")

   ## if any remnants from previous runs remain, delete them

   if(length(list.files(tempdir(),pattern=bfile)>0))

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

   ## write it to a file

   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))

   system(paste("(",stitch," -p ",tempdir(),"/",basename(file),"_MODparms.txt -d)",sep=""),intern=F)#,ignore.stderr=F)

##############  Now run the 5km summary

   ## First write the parameter file (careful, heg is very finicky!)

   hdr=paste("NUM_RUNS = ",nrow(vars[-1,]),"|MULTI_BAND_HDFEOS:",nrow(vars[-1,]),sep="")

   grp=paste("

BEGIN

INPUT_FILENAME=",file,"

OBJECT_NAME=mod35

FIELD_NAME=",vars$variable[-1],"|

BAND_NUMBER = ",1,"

OUTPUT_PIXEL_SIZE_X=0.008333333

#0.0416666

OUTPUT_PIXEL_SIZE_Y=0.008333333

#0.0416666

SPATIAL_SUBSET_UL_CORNER = ( ",bbox(ppc)[2,2]," ",bbox(ppc)[1,1]," )

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

#OUTPUT_OBJECT_NAME = mod35|

RESAMPLING_TYPE =NN

OUTPUT_PROJECTION_TYPE = GEO

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 )

#OUTPUT_PROJECTION_PARAMETERS = ( 6371007.181 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 )

# projection parameters from http://landweb.nascom.nasa.gov/cgi-bin/QA_WWW/newPage.cgi?fileName=sn_gctp

ELLIPSOID_CODE = WGS84

OUTPUT_TYPE = HDFEOS

OUTPUT_FILENAME= ",tempfile_sz,"

END

",sep="")

   ## write it to a file

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

   ## now run the swath2grid tool

   ## write the gridded file

   print(paste("Starting",file))

   system(paste("(",stitch," -p ",tempdir(),"/",basename(file),"_MODparms_angle.txt -d)",sep=""),intern=F,ignore.stderr=F)

####### import to R for processing

   if(!file.exists(tempfile_path)) {

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

     return(c(file,0))

   }

   ## convert to land path

   d=raster(paste("HDF4_EOS:EOS_GRID:\"",tempfile_path,"\":mod35:Cloud_Mask_0",sep=""))

   sz=raster(paste("HDF4_EOS:EOS_GRID:\"",tempfile_sz,"\":mod35:Sensor_Zenith",sep=""))

   NAvalue(sz)=0

   ## resample sensor angles to 1km grid and mask paths with angles >=30

#   sz2=resample(sz,d,method="ngb",file=sub("hdf","tif",tempfile_sz),overwrite=T)

   getlc=function(x,y) {ifelse(y==0|y>40,NA,((x%/%2^6) %% 2^2))}

   path=  overlay(d,sz,fun=getlc,filename=tempfile2_path,options=c("COMPRESS=LZW", "LEVEL=9","PREDICTOR=2"),datatype="INT1U",overwrite=T)

### 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))

 }

## establish sudo priveleges to run swtif

system("sudo ls"); mclapply(files,getpath,mc.cores=10)

## check gdal can read all of them

gfiles=list.files("gridded",pattern="tif$",full=T)

length(gfiles)

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)

}))

table(check)

file.remove(gfiles[check==0])

## use new gdal

system(paste("/usr/local/gdal-1.10.0/bin/gdalwarp -wm 900 -overwrite -co COMPRESS=LZW -co PREDICTOR=2 -multi -r mode gridded/*.tif MOD35_path_gdalwarp.tif"))

#  origin(raster(gfiles[5]))

  ## try with pktools

  ## global

system(paste("pkmosaic -co COMPRESS=LZW -co PREDICTOR=2 ",paste("-i",list.files("gridded",full=T,pattern="tif$"),collapse=" ")," -o MOD35_path_pkmosaic_max.tif  -m 2 -v -t 255 -t 0 &"))

#bb="-ulx -180 -uly 90 -lrx 180 -lry -90"

#bb="-ulx -180 -uly 90 -lrx 170 -lry 80"

bb="-ulx -72 -uly 11 -lrx -59 -lry -1"

#expand.grid(x=seq(-180,170,by=10),y=seq(-90,80))

gf2=  grep("2012009[.]03",gfiles,value=T)

system(paste("pkmosaic ",bb," -co COMPRESS=LZW -co PREDICTOR=2 ",paste("-i",gf2,collapse=" ")," -o h11v08_path_pkmosaic.tif -ot Byte -m 7 -v -t 255"))

                                        #  bounding box?  

###########

### Use GRASS to import all the tifs and calculat the mode

## make temporary working directory

  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

  for(f in gfiles[!imported])  execGRASS("r.in.gdal",input=f,output=basename(f),flags="o")

## calculate mode

execGRASS("r.series",input=paste(system("g.mlist type=rast pattern=MOD*",intern=T)[1:1000],sep="",collapse=","),output="MOD35_path",method="mode",range=c(1,5),flags=c("verbose","overwrite"))

## add colors

execGRASS("r.colors",map="MOD35_path",rules="MOD35_path_grasscolors.txt")

## write to disk

execGRASS("r.out.gdal",input="MOD35_path",output=paste(getwd(),"/MOD35_ProcessPath_C5.tif",sep=""),type="Byte",createopt="COMPRESS=LZW,LEVEL=9,PREDICTOR=2")

### delete the temporary files 

  unlink_.gislock()

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

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

cols=c("blue","lightblue","tan","green")

  ###  Merge them into a geotiff

    system(paste("gdal_merge.py -v -n 255 -o MOD35_ProcessPath.tif -co \"COMPRESS=LZW\" -co \"PREDICTOR=2\" `ls -d -1 gridded/*.tif`",sep=""))

## connect to raster to extract land-cover bit

library(raster)

d=raster("CM.tif")

getlc=function(x) {(x/2^6) %% 2^2}

calc(d,fun=getlc,filename="CM_LC.tif")