#DATE MODIFIED: 12/12/2013            

diff_date_rast_pred_fun <- function(i,list_param){

  index <- i #index date

  list_raster_obj_files <- list_param$list_raster_obj_files

  methods_name <- list_param$methods_name

  y_var_name <- list_param$y_var_name

  ref_mod <- list_param$ref_mod

  alt_mod <- list_param$alt_mod

  NA_flag_val <- list_param$NA_flag_val

  file_format <- list_param$file_format

  out_dir <- list_param$out_dir

  out_prefix <- list_param$out_prefix

  #index<-244 #index corresponding to Sept 1

  #lf_list<-lapply(list_raster_obj_files[c("gam_daily","gam_CAI","gam_fss")],

  #                             FUN=function(x){x<-load_obj(x);x$method_mod_obj[[index]][[y_var_name]]})  

  lf_list<-lapply(list_raster_obj_files[methods_name],

                               FUN=function(x){x<-load_obj(x);x$method_mod_obj[[index]][[y_var_name]]})  

  diff_pred_list <- vector("list",length=length(lf_list))

  for (i in 1:length(lf_list)){

    interpolation_method <- methods_name[i]

    r_diff <- raster(lf_list[[i]][[ref_mod]]) - raster(lf_list[[i]][[alt_mod]])

    data_name <-paste(index,"_",y_var_name,"_diff_",ref_mod,"_",alt_mod,sep="")

    raster_name <-file.path(out_dir,paste(interpolation_method,"_",data_name,out_prefix,file_format, sep=""))

    diff_pred_list[[i]] <-raster_name 

    writeRaster(r_diff, filename=raster_name,NAflag=NA_flag_val,bylayer=FALSE,bandorder="BSQ",overwrite=TRUE)  #Writing the data in a raster file format...  

  }

  return(unlist(diff_pred_list))

}

#Extract statistic by zones...make this general by changing names?

extract_diff_by_landcover <- function(r_stack_diff,s_raster,LC_subset,LC_names,avl){

  rclmat<-matrix(avl,ncol=3,byrow=TRUE)

  LC_s <- subset(s_raster,LC_subset)

  LC_s_rec <-reclassify(LC_s,rclmat)

  names(LC_s_rec)<- LC_names

  #plot(LC_s)  

  #plot average difference per class of forest and LC2

  list_avg_diff <- vector("list",length=nlayers(r_stack_diff))

  list_sd_diff <- vector("list",length=nlayers(r_stack_diff))

  for (i in 1:nlayers(r_stack_diff)){

    rast_diff  <- subset(r_stack_diff,i)

    list_avg <- vector("list",length=nlayers(LC_s_rec))

    list_sd <- vector("list",length=nlayers(LC_s_rec))

    for(k in 1:nlayers(LC_s_rec)){

      LC_rec <- subset(LC_s_rec,k)

      list_avg[[k]] <- zonal(rast_diff,z=LC_rec,stat="mean",na.rm=TRUE)[,2]

      list_sd[[k]]  <- zonal(rast_diff,z=LC_rec,stat="sd",na.rm=TRUE)[,2]

    }

    zones_avg <- do.call(cbind,list_avg) 

    zones_sd <- do.call(cbind,list_sd) 

    colnames(zones_avg)<- LC_names

    colnames(zones_sd)<-LC_names

    list_avg_diff[[i]] <- zones_avg

    list_sd_diff[[i]] <- zones_sd    

  }

  list_zones <- list(avg=list_avg_diff,sd=list_sd_diff)

  return(list_zones)

}

## Utilit function to quickly write out a stack or brick of rasterlayer to disk using names of layers

# Note that each layers are written individually, default NA value and format is provided

write_out_raster_fun <-function(r_stack,out_suffix,out_dir,NA_flag_val=-9999,file_format=".rst"){

  for(i in 1:nlayers(r_stack)){

    list_raster_name <- vector("list",length=nlayers(r_stack))

    r<-subset(r_stack,i)

    raster_name <- paste(names(r_stack)[i],"_",out_suffix,file_format,sep="")

    writeRaster(r, NAflag=NA_flag_val,filename=file.path(out_dir,raster_name)

                   ,bylayer=FALSE,bandorder="BSQ",overwrite=TRUE)

    list_raster_name[[i]] <- file.path(out_dir,raster_name) 

  }

  return(unlist(list_raster_name))

}