f=list.files(pattern="*.hdf")

Sys.setenv(GEOL_AS_GCPS = "PARTIAL")

system(paste("gdalinfo",f[1]))

GDALinfo("HDF4_EOS:EOS_SWATH:\"MOD35_L2.A2000100.1445.006.2012252024758.hdf\":mod35:Cloud_Mask")

system("gdalinfo HDF4_EOS:EOS_SWATH:\"MOD35_L2.A2000100.1445.006.2012252024758.hdf\":mod35:Cloud_Mask | tail -n 200")

system("gdalwarp -overwrite -geoloc -order 2 -r near -s_srs \"EPSG:4326\" HDF4_EOS:EOS_SWATH:\"MOD35_L2.A2000100.1445.006.2012252024758.hdf\":mod35:Cloud_Mask cloudmask.tif")

system("gdalwarp -overwrite -r near -s_srs \"EPSG:4326\" HDF4_EOS:EOS_SWATH:\"MOD35_L2.A2000100.1445.006.2012252024758.hdf\":mod35:Cloud_Mask:1 cloudmask2.tif")

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

###  R code to aquire and process MOD35_L2 cloud data from the MODIS platform

# Redirect all warnings to stderr()

#options(warn = -1)

#write("2) write() to stderr", stderr())

#write("2) write() to stdout", stdout())

#warning("2) warning()")

## import commandline arguments

library(getopt)

## load libraries

require(reshape)

require(geosphere)

require(raster)

require(rgdal)

require(spgrass6)

require(RSQLite)

## get options

opta <- getopt(matrix(c(

                        'date', 'd', 1, 'character',

                        'tile', 't', 1, 'character',

                        'verbose','v',1,'logical',

                        'help', 'h', 0, 'logical'

                        ), ncol=4, byrow=TRUE))

if ( !is.null(opta$help) )

  {

       prg <- commandArgs()[1];

          cat(paste("Usage: ", prg,  " --date | -d <file> :: The date to process\n", sep=""));

          q(status=1);

     }

## default date and tile to play with  (will be overwritten below when running in batch)

date="20010410"

tile="h11v08"

platform="pleiades" 

verbose=T

## now update using options if given

date=opta$date  

tile=opta$tile 

verbose=opta$verbose  #print out extensive information for debugging?

outdir=paste("daily/",tile,"/",sep="")  #directory for separate daily files

## get year and doy from date

year=format(as.Date(date,"%Y%m%d"),"%Y")

doy=format(as.Date(date,"%Y%m%d"),"%j")

if(platform=="pleiades"){

  ## location of MOD06 files

  datadir=paste("/nobackupp4/datapool/modis/MOD06_L2.005/",year,"/",doy,"/",sep="")

  ## path to some executables

  ncopath="/nasa/sles11/nco/4.0.8/gcc/mpt/bin/"

  swtifpath="/nobackupp1/awilso10/software/heg/bin/swtif"

  ## path to swath database

  db="/nobackupp4/pvotava/DB/export/swath_geo.sql.sqlite3.db"

  ## specify working directory

  setwd("/nobackupp1/awilso10/mod06")

  gisBase="/u/armichae/pr/grass-6.4.2/"

  ## path to MOD11A1 file for this tile to align grid/extent

  gridfile=list.files("/nobackupp4/datapool/modis/MOD11A1.005/2006.01.27",pattern=paste(tile,".*[.]hdf$",sep=""),recursive=T,full=T)[1]

  td=readGDAL(paste("HDF4_EOS:EOS_GRID:\"",gridfile,"\":MODIS_Grid_Daily_1km_LST:Night_view_angl",sep=""))

  projection(td)="+proj=sinu +lon_0=0 +x_0=0 +y_0=0 +a=6371007.181 +b=6371007.181 +units=m +no_defs +datum=WGS84 +ellps=WGS84 "

}

if(platform=="litoria"){  #if running on local server, use different paths

  ## specify working directory

  setwd("~/acrobates/projects/interp")

  gisBase="/usr/lib/grass64"

   ## location of MOD06 files

  datadir="~/acrobates/projects/interp/data/modis/mod35"

  ## path to some executables

  ncopath=""

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

  ## path to swath database

  db="/home/adamw/acrobates/projects/interp/data/modis/mod06/swath_geo.sql.sqlite3.db"

  ## get grid file

  td=raster(paste("~/acrobates/projects/interp/data/modis/mod06/summary/MOD06_",tile,".nc",sep=""),varname="CER")

  projection(td)="+proj=sinu +lon_0=0 +x_0=0 +y_0=0 +a=6371007.181 +b=6371007.181 +units=m +no_defs +datum=WGS84 +ellps=WGS84 "

}

### print some status messages

if(verbose) print(paste("Processing tile",tile," for date",date))

## load tile information and get bounding box

load(file="modlandTiles.Rdata")

tile_bb=tb[tb$tile==tile,] ## identify tile of interest

upleft=paste(tile_bb$lat_max,tile_bb$lon_min) #northwest corner

lowright=paste(tile_bb$lat_min,tile_bb$lon_max) #southeast corner

## 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)

## vector of variables expected to be in final netcdf file.  If these are not present, the file will be deleted at the end.

finalvars=c("CLD","CLD2")

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

##find swaths in region from sqlite database for the specified date/tile

if(verbose) print("Accessing swath ID's from database")

con=dbConnect("SQLite", dbname = db)

fs=dbGetQuery(con,paste("SELECT * from swath_geo

            WHERE east>=",tile_bb$lon_min," AND

                  west<=",tile_bb$lon_max," AND

                  north>=",tile_bb$lat_min," AND

                  south<=",tile_bb$lat_max," AND

                  year==",format(as.Date(date,"%Y%m%d"),"%Y")," AND

                  day==",as.numeric(format(as.Date(date,"%Y%m%d"),"%j"))

  ))

con=dbDisconnect(con)

fs$id=substr(fs$id,7,19)

## find the swaths on disk (using datadir)

swaths=list.files(datadir,pattern=paste(fs$id,collapse="|"),recursive=T,full=T)

if(verbose) print(paste(nrow(fs)," swath IDs recieved from database and ",length(swaths)," found on disk"))

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

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

### Use the HEG tool to grid all available swath data for this date-tile

for(file in swaths){

  ## Function to generate hegtool parameter file for multi-band HDF-EOS file

  print(paste("Starting file",basename(file)))

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

  ## 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

OUTPUT_PIXEL_SIZE_X=1000

OUTPUT_PIXEL_SIZE_Y=1000

SPATIAL_SUBSET_UL_CORNER = ( ",upleft," )

SPATIAL_SUBSET_LR_CORNER = ( ",lowright," )

#RESAMPLING_TYPE =",ifelse(grepl("Flag|Mask|Quality",vars),"NN","CUBIC"),"

RESAMPLING_TYPE =NN

OUTPUT_PROJECTION_TYPE = SIN

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 = ",outfile,"

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

  log=system(paste("(",swtifpath," -p ",tempdir(),"/",basename(file),"_MODparms.txt -d ; echo $$)",sep=""),intern=T,ignore.stderr=T)

  ## clean up temporary files in working directory

#  file.remove(list.files(pattern=

#              paste("filetable.temp_",

#              as.numeric(log[length(log)]):(as.numeric(log[length(log)])+3),sep="",collapse="|")))  #Look for files with PID within 3 of parent process

  if(verbose) print(log)

  print(paste("Finished gridding ", file))

}  #end looping over swaths

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

## confirm at least one file for this date is present.  If not, quit.

outfiles=paste(tempdir(),"/",basename(swaths),sep="")

if(!any(file.exists(outfiles))) {

  print(paste("########################################   No gridded files for region exist for tile",tile," on date",date))

  q("no",status=0)

}

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

## Process the gridded files to align exactly with MODLAND tile and produce a daily summary of multiple swaths

## Identify output file

  ncfile=paste(outdir,"/MOD06_",tile,"_",date,".nc",sep="")  #this is the 'final' daily output file

## function to convert binary to decimal to assist in identifying correct values

## this is helpful when defining QA handling below, but isn't used in processing

## b2d=function(x) sum(x * 2^(rev(seq_along(x)) - 1)) #http://tolstoy.newcastle.edu.au/R/e2/help/07/02/10596.html

## for example:

## b2d(c(T,T))

  ## set Grass to overwrite

  Sys.setenv(GRASS_OVERWRITE=1)

  Sys.setenv(DEBUG=1)

  Sys.setenv(GRASS_GUI="txt")

### Extract various SDSs from a single gridded HDF file and use QA data to throw out 'bad' observations

## make temporary working directory

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

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

  ## create output directory if needed

  if(!file.exists(dirname(ncfile))) dir.create(dirname(ncfile),recursive=T)

  ## set up temporary grass instance for this PID

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

  initGRASS(gisBase=gisBase,gisDbase=tf,SG=as(td,"SpatialGridDataFrame"),override=T,location="mod06",mapset="PERMANENT",home=tf,pid=Sys.getpid())

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

  ## Define region by importing one MOD11A1 raster.

  print("Import one MOD11A1 raster to define grid")

  if(platform=="pleiades") execGRASS("r.in.gdal",input=paste("HDF4_EOS:EOS_GRID:\"",gridfile,"\":MODIS_Grid_Daily_1km_LST:Night_view_angl",sep=""),

            output="modisgrid",flags=c("quiet","overwrite","o"))

   if(platform=="litoria")

  execGRASS("r.in.gdal",input=paste("NETCDF:\"/home/adamw/acrobates/projects/interp/data/modis/mod06/summary/MOD06_",tile,".nc\":CER",sep=""),output="modisgrid",flags=c("overwrite","o"))

system("g.region rast=modisgrid save=roi --overwrite",ignore.stdout=F,ignore.stderr=F)

system("g.region rast=modisgrid.1 save=roi --overwrite",ignore.stdout=F,ignore.stderr=F)

## Identify which files to process

tfs=basename(swaths)

## drop swaths that did not produce an output file (typically due to not overlapping the ROI)

tfs=tfs[tfs%in%list.files(tempdir())]

#tfs=list.files(tempdir(),pattern="temp.*hdf")

nfs=length(tfs)

if(verbose) print(paste(nfs,"swaths available for processing"))

## loop through scenes and process QA flags

  for(i in 1:nfs){

     file=paste(tempdir(),"/",tfs[i],sep="")

     ## Cloud Mask

     execGRASS("r.in.gdal",input=paste("HDF4_EOS:EOS_GRID:\"",file,"\":mod35:Cloud_Mask_0",sep=""),

              output=paste("CM1_",i,sep=""),flags=c("overwrite","o")) ; print("")

    ## extract cloudy and 'probably/confidently clear' pixels

    system(paste("r.mapcalc <<EOF

                CM_cloud_",i," =  ((CM1_",i," / 2^0) % 2) == 1  &&  ((CM1_",i," / 2^1) % 2^2) == 0 

                CM_clear_",i," =  ((CM1_",i," / 2^0) % 2) == 1  &&  ((CM1_",i," / 2^1) % 2^2) >=  2 

                CM_path_",i," =   ((CM1_",i," / 2^6) % 2^2) 

                CM_cloud2_",i," = ((CM1_",i," / 2^1) % 2^2) 

EOF",sep=""))

    ## QA

     execGRASS("r.in.gdal",input=paste("HDF4_EOS:EOS_GRID:\"",file,"\":mod35:Quality_Assurance_0",sep=""),

             output=paste("QA_",i,sep=""),flags=c("overwrite","o")) ; print("")

   ## QA_CER

#   system(paste("r.mapcalc <<EOF

#                 QA_COT_",i,"=   ((QA_",i," / 2^0) % 2^1 )==1

#                 QA_COT2_",i,"=  ((QA_",i," / 2^1) % 2^2 )>=2

#                 QA_COT3_",i,"=  ((QA_",i," / 2^3) % 2^2 )==0

#                 QA_CER_",i,"=   ((QA_",i," / 2^5) % 2^1 )==1

#                 QA_CER2_",i,"=  ((QA_",i," / 2^6) % 2^2 )>=2

#EOF",sep="")) 

#                 QA_CWP_",i,"=   ((QA_",i," / 2^8) % 2^1 )==1

#                 QA_CWP2_",i,"=  ((QA_",i," / 2^9) % 2^2 )==3

 } #end loop through sub daily files

#### Now generate daily averages (or maximum in case of cloud flag)

  system(paste("r.mapcalc <<EOF

         CLD_daily=int((max(",paste("if(isnull(CM_cloud_",1:nfs,"),-9999,CM_cloud_",1:nfs,")",sep="",collapse=","),"))) 

         CLD2_daily=int((min(",paste("if(isnull(CM_cloud2_",1:nfs,"),-9999,CM_cloud2_",1:nfs,")",sep="",collapse=","),"))) 

EOF",sep=""))

execGRASS("r.null",map="CLD_daily",setnull="-9999")

execGRASS("r.null",map="CLD2_daily",setnull="-9999")

  ### Write the files to a netcdf file

  ## create image group to facilitate export as multiband netcdf

    execGRASS("i.group",group="mod06",input=c("CLD_daily","CLD2_daily")) ; print("")

  if(file.exists(ncfile)) file.remove(ncfile)  #if it exists already, delete it

  execGRASS("r.out.gdal",input="mod06",output=ncfile,type="Int16",nodata=-32768,flags=c("quiet"),

#      createopt=c("FORMAT=NC4","ZLEVEL=5","COMPRESS=DEFLATE","WRITE_GDAL_TAGS=YES","WRITE_LONLAT=NO"),format="netCDF")  #for compressed netcdf

      createopt=c("FORMAT=NC","WRITE_GDAL_TAGS=YES","WRITE_LONLAT=NO"),format="netCDF")

  system(paste(ncopath,"ncecat -O -u time ",ncfile," ",ncfile,sep=""))

## create temporary nc file with time information to append to MOD06 data

  cat(paste("

    netcdf time {

      dimensions:

        time = 1 ;

      variables:

        int time(time) ;

      time:units = \"days since 2000-01-01 00:00:00\" ;

      time:calendar = \"gregorian\";

      time:long_name = \"time of observation\"; 

    data:

      time=",as.integer(as.Date(date,"%Y%m%d")-as.Date("2000-01-01")),";

    }"),file=paste(tempdir(),"/time.cdl",sep=""))

system(paste("ncgen -o ",tempdir(),"/time.nc ",tempdir(),"/time.cdl",sep=""))

system(paste(ncopath,"ncks -A ",tempdir(),"/time.nc ",ncfile,sep=""))

## add other attributes

  system(paste(ncopath,"ncrename -v Band1,CLD -v Band2,CLD2 ",ncfile,sep=""))

  system(paste(ncopath,"ncatted -a scale_factor,CLD,o,d,1 -a units,CLD,o,c,\"none\" -a missing_value,CLD,o,d,-32768 -a long_name,CLD,o,c,\"Cloud Mask\" ",ncfile,sep=""))

system(paste(ncopath,"ncatted -a scale_factor,CLD2,o,d,1 -a units,CLD2,o,c,\"none\" -a missing_value,CLD2,o,d,-32768 -a long_name,CLD2,o,c,\"Cloud Mask Flag\" ",ncfile,sep=""))

                                        #  system(paste(ncopath,"ncatted -a sourcecode,global,o,c,",script," ",ncfile,sep=""))

### delete the temporary files 

  unlink_.gislock()

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

## Confirm that the file has the correct attributes, otherwise delete it

ntime=as.numeric(system(paste("cdo -s ntime ",ncfile),intern=T))

## confirm it has all 'final variables as specified above"

fvar=all(finalvars%in%strsplit(system(paste("cdo -s showvar ",ncfile),intern=T)," ")[[1]])

  if(ntime!=1|!fvar) {

      print(paste("FILE ERROR:  tile ",tile," and date ",date," was not outputted correctly, deleting... "))

      file.remove(ncfile)

    }

  ## print out some info

print(paste(" ###################################################################               Finished ",date,

"################################################################"))

## delete old files

system("cleartemp")

## quit

q("no",status=0)