#MODIFIED ON: 02/07/2016            

  script_path <- "/home/parmentier/Data/IPLANT_project/env_layers_scripts"

  function_assessment_part2_functions <- "global_run_scalingup_assessment_part2_functions_01032016.R"

  source(file.path(script_path,function_assessment_part2_functions)) #source all functions used in this script 

  list_param_run_assessment_plotting$in_dir_list_filename #PARAM 0

  list_outfiles <- vector("list", length=23) #collect names of output files, this should be dynamic?

  list_outfiles_names <- vector("list", length=23) #collect names of output files

  ##As a first quick set up for the meeting 01/27 just read in from the in_dir_list

  list_tb_fname <- list.files(path=file.path(in_dir,in_dir_list),"tb_diagnostic_v_NA_.*._run_global_analyses_pred_.*._reg4.txt",full.names=T)

  list_df_fname <- list.files(path=file.path(in_dir,in_dir_list),"df_tile_processed_.*._run_global_analyses_pred_.*._reg4.txt",full.names=T)

  list_summary_metrics_v_fname <- list.files(path=file.path(in_dir,in_dir_list),"summary_metrics_v2_NA_.*._run_global_analyses_pred_.*._reg4.txt",full.names=T)

  tb <-  read.table(list_tb[1],stringsAsFactors=F,sep=",")

  df_assessment_files <- read.table(df_assessment_files_name,stringsAsFactors=F,sep=",")

  #df_assessment_files, note that in_dir indicate the path of the textfiles

  summary_metrics_v <- read.table(file.path(in_dir,basename(df_assessment_files$files[1])),sep=",")

  tb <- read.table(file.path(in_dir, basename(df_assessment_files$files[2])),sep=",")

  tb_s <- read.table(file.path(in_dir, basename(df_assessment_files$files[4])),sep=",")

  tb_month_s <- read.table(file.path(in_dir,basename(df_assessment_files$files[3])),sep=",")

  pred_data_month_info <- read.table(file.path(in_dir, basename(df_assessment_files$files[10])),sep=",")

  pred_data_day_info <- read.table(file.path(in_dir, basename(df_assessment_files$files[11])),sep=",")

  df_tile_processed <- read.table(file.path(in_dir, basename(df_assessment_files$files[12])),sep=",")

  #summary_metrics_v

  #tb_all <- tb

  #summary_metrics_v_all <- summary_metrics_v 

  #table(summary_metrics_v_all$reg)

  #table(summary_metrics_v$reg)

  #table(tb_all$reg)

  #table(tb$reg)

  list_shp_reg_files <- as.character(basename(list_df[[1]]$shp_files)) #this could be the solution!!

  #unique(summaty_metrics$tile_id)

  #text(lat-shp,)

  #union(list_shp_reg_files[[1]],list_shp_reg_files[[2]])

#### CURRENT ERROR ON NEX

# #comments                                                                     #figure_no    #region   #models       

# tile processed for the region                                           figure_1           reg4        NA

# boxplot with outlier                                                        figure_2a          reg4        mod1

# boxplot with outlier                                                        figure_2a          reg4        mod_kr

# boxplot scaling by tiles                                                   figure_2b          reg4        mod1

# boxplot scaling by tiles                                                   figure_2b          reg4        mod_kr

# boxplot overall region with outliers                              figure_3a          reg4        NA

# boxplot overall region with scaling                               figure_3b          reg4        NA

# Barplot of metrics ranked by tile                                  Figure_5            

# boxplot overall region with scaling                               figure_3b          reg4        NA

# Barplot of metrics ranked by tile                                  Figure_5            

# Barplot of metrics ranked by tile                                  Figure_5

# Average metrics map centroids                                  Figure_6

# Average metrics map centroids                                  Figure_6

# Number of missing day threshold1 map centroids                                    Figure_7a

# Number of missing day threshold1 map centroids                                    Figure_7a

# Number of missing day threshold1 map centroids                                    Figure_7a

# Number of missing day threshold1 map centroids                                    Figure_7a

# number_daily_predictions_per_model                                                        Figure_7b

# histogram number_daily_predictions_per_models                                    Figure_7c

# boxplot_overall_separated_by_region_with_oultiers_                              Figure 8a

# boxplot_overall_separated_by_region_with_scaling                                 Figure 8b

# Browse[3]> c

# Error in text.default(coordinates(pt)[1], coordinates(pt)[2], labels = i,  : 

#                         X11 font -adobe-helvetica-%s-%s-*-*-%d-*-*-*-*-*-*-*, face 2 at size 16 could not be loaded

#                       In addition: Warning message:

#                         In polypath(x = mcrds[, 1], y = mcrds[, 2], border = border, col = col,  :

#                                       Path drawing not available for this device

# Browse[2]>   for(i in 1:length(threshold_missing_day)){

# +     

# +     #summary_metrics_v$n_missing <- summary_metrics_v$n == 365

# +     #summary_metrics_v$n_missing <- summary_metrics_v$n < 365

# +     summary_metrics_v$n_missing <- summary_metrics_v$n < threshold_missing_day[i]

# +     summary_metrics_v_subset <- subset(summary_metrics_v,model_name=="mod1")

# +     

# +     #res_pix <- 1200

# +     res_pix <- 960

# +     

# +     col_mfrow <- 1

# +     row_mfrow <- 1

# +     fig_filename <- paste("Figure7a_ac_metrics_map_centroids_tile_",model_name[j],"_","missing_day_",threshold_missing_day[i],

# +                        "_",out_suffix,".png",sep="")

# +     png(filename=paste("Figure7a_ac_metrics_map_centroids_tile_",model_name[j],"_","missing_day_",threshold_missing_day[i],

# +                        "_",out_suffix,".png",sep=""),

# +         width=col_mfrow*res_pix,height=row_mfrow*res_pix)

# +     

# +     model_name[j]

# +     

# +     p_shp <- layer(sp.polygons(reg_layer, lwd=1, col='black'))

# +     #title("(a) Mean for 1 January")

# +     p <- bubble(summary_metrics_v_subset,"n_missing",main=paste("Missing per tile and by ",model_name[j]," for ",

# +                                                                 threshold_missing_day[i]))

# +     p1 <- p+p_shp

# +     try(print(p1)) #error raised if number of missing values below a threshold does not exist

# +     dev.off()

# +     

# +     list_outfiles[[counter_fig+i]] <- fig_filename

# +   }

# debug at /nobackupp8/bparmen1/env_layers_scripts/global_run_scalingup_assessment_part2_01042016.R#272: i

# Browse[3]>   counter_fig <- counter_fig+length(threshold_missing_day) #currently 4 days...

# Browse[3]> c

# Error in grid.Call.graphics(L_setviewport, pvp, TRUE) : 

#   non-finite location and/or size for viewport

#Error in grid.Call.graphics(L_setviewport, vp, TRUE) : 

#  non-finite location and/or size for viewport