#MODIFIED ON: 05/08/2015            

mosaic_m_raster_list<-function(j,list_param){

  #This functions returns a subset of tiles from the modis grid.

  #Arguments: modies grid tile,list of tiles

  #Output: spatial grid data frame of the subset of tiles

  #Note that rasters are assumed to be in the same projection system!!

  #modified for global mosaic...still not working right now...

  #rast_list<-vector("list",length(mosaic_list))

  #for (i in 1:length(mosaic_list)){  

  # read the individual rasters into a list of RasterLayer objects

  # this may be changed so that it is not read in the memory!!!

  #parse output...

  #j<-list_param$j

  mosaic_list<-list_param$mosaic_list

  out_path<-list_param$out_path

  out_names<-list_param$out_rastnames

  file_format <- list_param$file_format

  NA_flag_val <- list_param$NA_flag_val

  out_suffix <- list_param$out_suffix

  ## Start

  if(class(mosaic_list[[j]])=="list"){

    m_list <- unlist(mosaic_list[[j]])

  }else{

    m_list <- mosaic_list[[j]]

  }

  input.rasters <- lapply(m_list, raster) #create raster image for each element of the list

  #inMemory(input.rasters[[1]])

  #note that input.rasters are not stored in memory!!

  mosaiced_rast<-input.rasters[[1]]

  for (k in 2:length(input.rasters)){

    mosaiced_rast<-mosaic(mosaiced_rast,input.rasters[[k]], tolerance=1,fun=mean)

    #mosaiced_rast<-mosaic(mosaiced_rast,raster(input.rasters[[k]]), fun=mean)

  }

  data_name<-paste("mosaiced_",sep="") #can add more later...

  #raster_name<-paste(data_name,out_names[j],".tif", sep="")

  raster_name<-paste(data_name,out_names[j],file_format, sep="")

  writeRaster(mosaiced_rast, NAflag=NA_flag_val,filename=file.path(out_path,raster_name),overwrite=TRUE)  

  #Writing the data in a raster file format...  

  rast_list<-file.path(out_path,raster_name)

  ## The Raster and rgdal packages write temporary files on the disk when memory is an issue. This can potential build up

  ## in long  loops and can fill up hard drives resulting in errors. The following  sections removes these files 

  ## as they are created in the loop. This code section  can be transformed into a "clean-up function later on

  ## Start remove

  #tempfiles<-list.files(tempdir(),full.names=T) #GDAL transient files are not removed

  #files_to_remove<-grep(out_suffix,tempfiles,value=T) #list files to remove

  #if(length(files_to_remove)>0){

  #  file.remove(files_to_remove)

  #}

  #now remove temp files from raster package located in rasterTmpDir

  removeTmpFiles(h=0) #did not work if h is not set to 0

  ## end of remove section

  return(rast_list)

}

#list_r_weights <- lapply(1:length(weights_obj_list), FUN=function(i,x){raster(x[[i]]$r_weights)},x=weights_obj_list)

#list_r_weights_prod <- lapply(1:length(weights_obj_list), FUN=function(i,x){raster(x[[i]]$r_weights_prod)},x=weights_obj_list)

list_r_weights <- lapply(1:length(weights_obj_list), FUN=function(i,x){x[[i]]$r_weights},x=weights_obj_list)

list_r_weights_prod <- lapply(1:length(weights_obj_list), FUN=function(i,x){x[[i]]$r_weights_prod},x=weights_obj_list)

list_args_weights <- list_r_weights

list_args_weights_prod <- list_r_weights_prod

mosaic_list_var <- list(list_r_weights)

#out_rastnames_var <- l_out_rastnames_var[[i]]

out_rastnames_var <- c("reg2_mosaic_weights.tif")

#list_param_mosaic <- list(list_r_weights,out_dir,outrastnames,file_format,NA_flag_val,out_suffix)

file_format <- ".tif"

NA_flag_val <- -9999

j<-1 #date index for loop

list_param_mosaic<-list(j,mosaic_list_var,out_rastnames_var,out_dir,file_format,NA_flag_val)

names(list_param_mosaic)<-c("j","mosaic_list","out_rastnames","out_path","file_format","NA_flag_val")

debug(mosaic_m_raster_list)

mosaic_m_raster_list(1,list_param_mosaic)

#list_var_mosaiced <- mclapply(1:2,FUN=mosaic_m_raster_list,list_param=list_param_mosaic,mc.preschedule=FALSE,mc.cores = 2)

list_var_mosaiced <- mclapply(1,FUN=mosaic_m_raster_list,list_param=list_param_mosaic,mc.preschedule=FALSE,mc.cores = 1)

#list_var_mosaiced <- mclapply(1:1,FUN=mosaic_m_raster_list,list_param=list_param_mosaic,mc.preschedule=FALSE,mc.cores = 1)

#list_var_mosaiced <- mclapply(1:365,FUN=mosaic_m_raster_list,list_param=list_param_mosaic,mc.preschedule=FALSE,mc.cores = 2)

outrastnames <- "reg2_mosaic_weights.tif"

list_param_mosaic <- list(list_r_weights,out_dir,outrastnames,file_format,NA_flag_val,out_suffix)

#mosaic_list<-list_param$mosaic_list

#out_path<-list_param$out_path

#  out_names<-list_param$out_rastnames

#  file_format <- list_param$file_format

#  NA_flag_val <- list_param$NA_flag_val

#  out_suffix <- list_param$out_suffix