#MODIFIED ON: 10/21/2016            

#COMMIT: checking missing files for region 5 with check_missing function 

in_dir_mosaic <- "/data/project/layers/commons/NEX_data/climateLayers/out/reg5/mosaics/mosaic"

out_suffix <- "global_assessment_reg5_10102016"

l_dates <- c("19990101","19990102","19990103","19990104","19990105") 

test_missing <- check_missing(lf=lf_raster, 

                              pattern_str=NULL,

                              in_dir=".", #this is not used if lf is given

                              date_start="1984101",

                              date_end="20141231",

                              item_no=13,

                              out_suffix="",

                              num_cores=num_cores,

                              out_dir=".")

plot_and_animate_raster_time_series(lf_raster=lf_raster,

                                    NAvalue=NA_flag_val, 

                                    item_no=13,

                                    region_name=region_name,

                                    var_name=var_name,

                                    metric_name=metric_name,

                                    frame_speed=frame_speed,

                                    animation_format=animation_format,

                                    zlim_val=NULL,

                                    plot_figure=F,

                                    generate_animation=T,

                                    num_cores=num_cores,

                                    out_suffix=out_suffix,

                                    out_dir=out_dir)

############ Now accuracy

#### PLOT ACCURACY METRICS: First test ####

##this will be cleaned up later:

in_dir_mosaic_RMSE <- "/data/project/layers/commons/NEX_data/climateLayers/out/reg6/mosaicsRMSE/mosaic"

pattern_str <-"*.tif"

in_dir_mosaic <- in_dir_mosaic_RMSE

lf_raster_rmse <- list.files(path=in_dir_mosaic,pattern=pattern_str,recursive=F,full.names=T)

lf_raster <- lf_raster_rmse

r_stack <- stack(lf_raster,quick=T) #this is very fast now with the quick option!

#save(r_mosaic,file="r_mosaic.RData")

NAvalue(r_stack)

plot(r_stack,y=6,zlim=c(0,8000)) #this is not rescaled

lf_mosaic_list <- lf_raster

list_dates_produced_RMSE <-  mclapply(1:2,

                                 FUN=extract_date,

                                 x=lf_mosaic_list,

                                 item_no=15,

                                 mc.preschedule=FALSE,

                                 mc.cores = 2)  

item_no <-15

list_dates_produced_RMSE <- unlist(mclapply(1:length(lf_raster),

                                       FUN=extract_date,

                                       x=lf_raster,

                                       item_no=item_no,

                                       mc.preschedule=FALSE,

                                       mc.cores = num_cores))                         

list_dates_produced_date_val <- as.Date(strptime(list_dates_produced_RMSE,"%Y%m%d"))

month_str <- format(list_dates_produced_date_val, "%b") ## Month, char, abbreviated

year_str <- format(list_dates_produced_date_val, "%Y") ## Year with century

day_str <- as.numeric(format(list_dates_produced_date_val, "%d")) ## numeric month

df_raster_rmse <- data.frame(lf=basename(lf_raster),

                          date=list_dates_produced_date_val,

                          month_str=month_str,

                          year=year_str,

                          day=day_str,

                          dir=dirname(lf_mosaic_list))

df_raster_fname <- file.path(out_dir,paste0("df_raster_rmse",out_suffix,".txt"))

write.table(df_raster,file= df_raster_fname,sep=",",row.names = F) 

r_stack_subset <- subset(r_stack,1:11)

l_dates <- list_dates_produced_date_val[1:11]

#undebug(plot_raster_mosaic)

out_suffix_str <- paste0("rmse_",out_suffix)

zlim_val <- NULL

##Need to add title option!!

list_param_plot_raster_mosaic <- list(l_dates,r_stack_subset,NA_flag_val,out_dir,out_suffix_str,

                                      region_name,variable_name, zlim_val)

names(list_param_plot_raster_mosaic) <- c("l_dates","r_mosaiced_scaled","NA_flag_val_mosaic","out_dir","out_suffix",

                                          "region_name","variable_name","zlim_val")

lf_mosaic_plot_fig <- lapply(1:2,

                               FUN=plot_raster_mosaic,

                               list_param=list_param_plot_raster_mosaic)         

### Now run for the full time series

#13.26 Western time: start

l_dates <- list_dates_produced_date_val

r_stack_subset <- r_stack

zlim_val <- NULL

list_param_plot_raster_mosaic <- list(l_dates,r_stack_subset,NA_flag_val,out_dir,out_suffix,

                                      region_name,variable_name, zlim_val)

names(list_param_plot_raster_mosaic) <- c("l_dates","r_mosaiced_scaled","NA_flag_val_mosaic","out_dir","out_suffix",

                                          "region_name","variable_name","zlim_val")

#started at 20.16 on 10/10/2016, finished 22.39

lf_mosaic_plot_fig <- mclapply(1:length(l_dates),

                               FUN=plot_raster_mosaic,

                               list_param=list_param_plot_raster_mosaic,

                               mc.preschedule=FALSE,

                               mc.cores = num_cores)  

if(is.null(zlim_val)){

  out_suffix_movie <- paste("min_max_",out_suffix,sep="")

}else{

  zlim_val_str <- paste(zlim_val,sep="_",collapse="_")

  out_suffix_movie <- paste(zlim_val_str,"_",out_suffix,sep="")

}

#r_stack_subset <- subset(r_stack,1:11)

#l_dates <- list_dates_produced_date_val[1:11]

filenames_figures_mosaic_test <- "list_figures_animation_test_reg6.txt"

write.table(unlist(lf_mosaic_plot_fig[1:11]),filenames_figures_mosaic_test,row.names = F,col.names = F,quote = F)

filenames_figures_mosaic <- paste0("list_figures_animation_",out_suffix_movie,".txt")

write.table(unlist(lf_mosaic_plot_fig),filenames_figures_mosaic,row.names = F,col.names = F,quote = F)

#now generate movie with imageMagick

frame_speed <- 60

animation_format <- ".gif"

out_suffix_str <- out_suffix

out_suffix_movie <- paste0("rmse_",out_suffix_movie)

#started: 

generate_animation_from_figures_fun(filenames_figures= unlist(lf_mosaic_plot_fig[1:11]),

                                    frame_speed=frame_speed,

                                    format_file=animation_format,

                                    out_suffix=out_suffix_str,

                                    out_dir=out_dir,

                                    out_filename_figure_animation="test2_reg6_animation.gif")

#started 6.43 Western time on Oct 11 and 7.19

generate_animation_from_figures_fun(filenames_figures= filenames_figures_mosaic,

                                    frame_speed=frame_speed,

                                    format_file=animation_format,

                                    out_suffix=out_suffix_movie,

                                    out_dir=out_dir,

                                    out_filename_figure_animation=NULL)