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

####  Extract MOD35 C6 processing path

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

library(multicore)

library(raster)

library(spgrass6)

##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/Npp_1km_C5.1_mean_00_to_06.tif",sep=""))

## 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",

#  "Quality_Assurance",       "QA"),

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

## establish sudo priveleges to run swtif

system("sudo ls")

mclapply(files,function(file){

  tempfile=paste(tempdir(),"/",basename(file),sep="")

#  tempfile2=paste("gridded/",sub("hdf","tif",basename(tempfile)),sep="")

  tempfile2=paste(tempdir(),"/",sub("hdf","tif",basename(tempfile)),sep="")

  outfile=paste("gridded2/",sub("hdf","tif",basename(tempfile)),sep="")

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

  ## 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 = ( 90 -180 )

SPATIAL_SUBSET_LR_CORNER = ( -90 180 )

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,"

END

",sep="")

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

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

    file.remove(list.files(tempdir(),pattern=basename(file),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 ; echo $$)",sep=""),intern=T,ignore.stderr=F)

  ## convert to land path

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

#  za=raster(paste("HDF4_EOS:EOS_GRID:\"",tempfile,"\":mod35:Quality_Assurance_1",sep=""))

  ## add projection information - ellipsoid should be wgs84

  projection(d)=projection(glb)

  extent(d)=alignExtent(d,extent(glb))

                                        #  d=readAll(d)

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

  calc(d,fun=getlc,filename=outfile,options=c("COMPRESS=LZW", "LEVEL=9","PREDICTOR=2"),datatype="INT1U",overwrite=T)

  ### warp it to align all pixels

  system(paste("gdalwarp -overwrite -tap -tr 0.008333333 0.008333333 -co COMPRESS=LZW -co LEVEL=9 -co PREDICTOR=2 -s_srs \"",projection(glb),"\" ",tempfile2," ",outfile,sep=""))

#  getqa=function(x) {(x%/%2^1) %% 2^3}

#  za=calc(za,fun=getqa)#,filename=outfile,options=c("COMPRESS=LZW", "LEVEL=9","PREDICTOR=2"),datatype="INT1U",overwrite=T)

  ## resample to line up with glb so we can use mosaic later

## delete temporary files

  file.remove(tempfile,tempfile2)

  return(c(file,1))

})

## 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])

#  origin(raster(gfiles[5]))

  system(paste("gdalinfo ",gfiles[1]," | grep Origin"))

  system(paste("gdalinfo ",gfiles[2]," | grep Origin"))

  system(paste("gdalinfo ",gfiles[3]," | grep Origin"))

system(paste("gdalwarp -tap -tr 0.008333333 0.008333333 -s_srs \"",projection(glb),"\" ",gfiles[1]," test1.tif"))

system(paste("gdalwarp -tap -tr 0.008333333 0.008333333 -s_srs \"",projection(glb),"\" ",gfiles[2]," test2.tif"))

  system(paste("gdalinfo test1.tif | grep Origin"))

  system(paste("gdalinfo test2.tif | grep Origin"))

system(paste("pkmosaic ",paste("-i",gfiles[1:2],collapse=" ")," -o MOD35_path2.tif  -m 6 -v -t 255"))

system(paste("pkmosaic ",paste("-i",c("test1.tif","test2.tif"),collapse=" ")," -o MOD35_path2.tif  -m 6 -v -max 10 -ot Byte"))

  ## 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.tif  -m 6 -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))

system(paste("pkmosaic ",bb," -co COMPRESS=LZW -co PREDICTOR=2 ",paste("-i",list.files("gridded",full=T,pattern="tif$"),collapse=" ")," -o h11v08_path_pkmosaic.tif  -m 6 -v -t 255 -t 0 &"))

                                        #  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")