#MODIFIED ON: 06/12/2016  

## Comments: dealing with flags and datatype in output mosaics

function_mosaicing_functions <- "global_run_scalingup_mosaicing_function_06122016.R" #PARAM12

function_mosaicing <-"global_run_scalingup_mosaicing_06122016.R"

var <- "TMAX" # variable being interpolated #param 1, arg 1

in_dir <- "/nobackupp6/aguzman4/climateLayers/out/" #PARAM2,arg 2

region_name <- "reg4" #PARAM 3, arg 3 #reg4 South America, Africa reg5,Europe reg2, North America reg1, Asia reg3

out_suffix <- "reg4_1999" #PARAM 4, arg 4

out_suffix_str <- region_name #PARAM 4, CONST 3

out_dir <- "/nobackupp8/bparmen1/climateLayers/out/reg4" #PARAM 5,arg 5 use this location for now

create_out_dir_param <- TRUE #PARAM 6, arg 6

year_predicted <- 1999 #PARAM 7, arg 7

num_cores <- 6 #PARAM 8, arg 8         

max_mem = 1e+07 #param 9, arg 9

mosaicing_method <- "use_edge_weights" #PARAM10, arg 10

#metric_name <- "rmse" # "mae", "r" for MAE, R etc.; can also be ns or nv? #PARAM 11, arg 11

metric_name <- "n"

#metric_name <- "mae"

#day_start <- "19990701" #PARAM 12 arg 12

#day_end <- "19990703" #PARAM 13 arg 13

day_start <- "19990107" #PARAM 12 arg 12

day_end <- "19990108" #PARAM 13 arg 13

infile_mask <- "/nobackupp8/bparmen1/NEX_data/regions_input_files/r_mask_LST_reg4.tif" #PARAM 14, arg 14

df_assessment_files_name <- "/nobackupp6/aguzman4/climateLayers/out/reg4/assessment/output_reg4_1999/df_assessment_files_reg4_1999_reg4_1999.txt"  # data.frame with all files used in assessmnet, PARAM 15

algorithm <- "python" #PARAM 16 #if R use mosaic function for R, if python use modified gdalmerge script from Alberto Guzmann

#layers_option <- c("var_pred") #arg 17 ,param 17, options are:#res_training, res_testing,ac_training, ac_testing, var_pred

layers_option <- c("ac_training") #arg 17 ,param 17, options are:#res_training, res_testing,ac_training, ac_testing, var_pred

#layers_option <- c("res_training") # #arg 17 ,param 17, options are:#res_training, res_testing,ac_training, ac_testing, var_pred

#layers_option <- c("res_testing") #arg 17 ,param 17, options are:#res_training, res_testing,ac_training, ac_testing, var_pred

#layers_option <- c("ac_testing") #arg 17 ,param 17, options are:#res_training, res_testing,ac_training, ac_testing, var_pred

tmp_files <- TRUE #arg 18, param 18, keep temp files if TRUE

data_type <- "Int16" #, param 19, use int32 for output layers mosaiced

scaling <- 100 #, param 20, if null use 1

values_range <- "-100,100"

NA_flag_val <- -32768 #should be here

# out_suffix <- "reg4_1991" #PARAM 4, arg 4

# year_predicted <- 1991 #PARAM 7, arg 7

# metric_name <- "rmse" #RMSE, MAE etc. #PARAM 11, arg 11

# day_start <- "19910101" #PARAM 12 arg 12

# day_end <- "19910103" #PARAM 13 arg 13

# #infile_mask <- "/nobackupp8/bparmen1/NEX_data/regions_input_files/r_mask_reg4.tif" #PARAM 14, arg 14

# infile_mask <- "/nobackupp8/bparmen1/NEX_data/regions_input_files/r_mask_LST.tif"

# df_assessment_files_name <- "/nobackupp6/aguzman4/climateLayers/out/reg4/assessment/output_reg4_1991/df_assessment_files_reg4_1991_reg4_1991.txt"  # data.frame with all files used in assessmnet, PARAM 15

# algorithm <- "python" #PARAM 16 #if R use mosaic function for R, if python use modified gdalmerge script from Alberto Guzmann

# layers_option <- c("var_pred") #arg 17 ,param 17, options are:#res_training, res_testing,ac_training, ac_testing, var_pred

# tmp_files <- FALSE #arg 18, param 18

# data_type <- "Int16" #, param 19, use int32 for output layers mosaiced

# scaling <- 100 #, param 20, if NULL don't rescale values

# values_range <- "-100,100" #args 21, if NULL don't screen values

### Testing several years on the bridge before running jobs on nodes with qsub

#Use the following command to run as script via the shell on the bridge 

#Rscript /nobackupp8/bparmen1/env_layers_scripts/master_script_stage_7_04232016.R TMAX /nobackupp6/aguzman4/climateLayers/out/ reg4 reg4_1991 /nobackupp8/bparmen1/climateLayers/out/reg4 TRUE 1991 6 1e+07 use_edge_weights rmse 19910101 19910103 /nobackupp8/bparmen1/NEX_data/regions_input_files/r_mask_LST.tif /nobackupp6/aguzman4/climateLayers/out/reg4/assessment/output_reg4_1991/df_assessment_files_reg4_1991_reg4_1991.txt python var_pred FALSE Int16 100 -100,100