in_dir_mosaic <- "/data/project/layers/commons/NEX_data/climateLayers/out/reg6/mosaics/mosaic"

## using predictions

var_name <- "dailyTmax"

debug(plot_and_animate_raster_time_series)

metric_name <- "var_pred" #use RMSE if accuracy

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,

                                    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)

## Create function here:

plot_and_animate_raster_time_series <- function(lf_raster,NAvalue, item_no,region_name,var_name,metric_name,frame_speed,animation_format,zlim_val,plot_figure,generate_animation,num_cores,out_suffix,out_dir){

  #Function to generate figures and animation for a list of raster

  #

  #

  #INPUTS

  #1) lf_raster,

  #2) NAvalue

  #3) item_no

  #4) region_name,

  #5) var_name

  #6) metric_name

  #7) frame_speed

  #8) animation_format

  #9) zlim_val

  #10) plot_figure

  #11) generate_animation

  #12) num_cores

  #13) out_suffix

  #14) out_dir

  #OUTPUTS

  #

  #

  lf_mosaic_list <- lf_raster

  variable_name <- var_name

  if(plot_figure==T){

    #item_no <- 13

    list_dates_produced <- 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, "%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 <- 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_", out_suffix, ".txt"))

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

    ############### PART5: Make raster stack and display maps #############

    #### Extract corresponding raster for given dates and plot

    r_stack_subset <- subset(r_stack, 1:11)

    l_dates <- list_dates_produced_date_val[1:11]

    #undebug(plot_raster_mosaic)

    zlim_val <- NULL

    ### 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")

    lf_mosaic_plot_fig <- mclapply(1:length(l_dates[1:11]),

                                   FUN = plot_raster_mosaic,

                                   list_param = list_param_plot_raster_mosaic,

                                   mc.preschedule = FALSE,

                                   mc.cores = num_cores)

    ##start at 14.12

    ##finished at 16.47

    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)

  }

  ### Part 2 generate movie

  if(generate_animation==TRUE){

    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 <- 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

    #started

    #debug(generate_animation_from_figures_fun)

    out_filename_figure_animation <- 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 17.36 Western time on Oct 10 and 18.18

     out_filename_figure_animation <- 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)

  }

  ## prepare object to return

  figure_animation_obj <- list(filenames_figures_mosaic,out_filename_figure_animation)

  names(figure_animation_obj) <- c("filenames_figures_mosaic","out_filename_figure_animation")

  return(figure_animation_obj)

}