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Revision b1260ae5

Added by Benoit Parmentier over 8 years ago

adding valid range option to master script mosaicing

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climate/research/oregon/interpolation/master_script_stage_7.R
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#AUTHOR: Benoit Parmentier                                                                        


  		




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#CREATED ON: 01/01/2016  


  		




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#MODIFIED ON: 04/20/2016  


  		




  
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#MODIFIED ON: 04/23/2016  


  		




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#PROJECT: NCEAS INPLANT: Environment and Organisms                                                                           


  		




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#First source these files:


  		




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


  		




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script_path <- "/nobackupp8/bparmen1/env_layers_scripts" #path to script


  		




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function_mosaicing_functions <- "global_run_scalingup_mosaicing_function_04202016b.R" #PARAM12


  		




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function_mosaicing <-"global_run_scalingup_mosaicing_04202016b.R"


  		




  
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function_mosaicing_functions <- "global_run_scalingup_mosaicing_function_04222016b.R" #PARAM12


  		




  
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function_mosaicing <-"global_run_scalingup_mosaicing_04222016.R"


  		




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


  		




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


  		




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


  		




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


  		




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#tmp_files <- FALSE #arg 18, param 18


  		




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#use_int <- TRUE #, param 19, use int32 for output layers mosaiced


  		




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#scaling <- 100 #, param 20, 


  		




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


  		




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


  		




  
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#values_range <- c(-100,100)


  		




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


  		




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


  		




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


  		




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


  		




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out_suffix <- "reg4" #PARAM 4, arg 4


  		




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


  		




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out_suffix_str <- region_name #PARAM 4, CONST 3


  		




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


  		




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create_out_dir_param <- TRUE #PARAM 6, arg 6


  		




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


  		




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day_start <- "19910101" #PARAM 12 arg 12


  		




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day_end <- "19910103" #PARAM 13 arg 13


  		




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


  		




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


  		




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


  		




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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


  		




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


  		




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


  		




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tmp_files <- FALSE #arg 18, param 18


  		




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use_int <- TRUE #, param 19, use int32 for output layers mosaiced


  		




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scaling <- 100 #, param 20, 


  		




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


  		




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


  		




  
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values_range <- c(-100,100) #args 21, if NULL don't screen values


  		




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#path_assessment <- NOT USED "/nobackupp6/aguzman4/climateLayers/out/reg4/assessment/output_reg4_1991" #PARAM 14a, arg 14


  		




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


  		




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


  		




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#Rscript /nobackupp8/bparmen1/env_layers_scripts/master_script_stage_7_04202016.R TMAX /nobackupp6/aguzman4/climateLayers/out/ reg4 reg4 /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_reg4.tif /nobackupp6/aguzman4/climateLayers/out/reg4/assessment/output_reg4_1991/df_assessment_files_reg4_1991_reg4_1991.txt python var_pred FALSE TRUE 100 


  		




  
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#Rscript /nobackupp8/bparmen1/env_layers_scripts/master_script_stage_7_04202016.R TMAX /nobackupp6/aguzman4/climateLayers/out/ reg4 reg4 /nobackupp8/bparmen1/climateLayers/out/reg4 TRUE 1991 6 1e+07 use_edge_weights rmse 19910101 19910103 /nobackupp8/bparmen1/NEX_data/regions_input_files/mask_reg4_bool.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


  		




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############################


  		




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#layers_option <- c("var_pred") #options are:


  		




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#res_training, res_testing,ac_training, ac_testing, var_pred


  		




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tmp_files <- args[18] #PARAM 18


  		




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use_int <- args[19] #PARAM 19 #use integer 32 for layers outputs


  		




  
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data_type <- args[19] #PARAM 19 #use integer 32 for layers outputs


  		




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scaling <- args[20] #PARAM 19 #use integer 32 for layers outputs


  		




  
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values_range <-  args[21] #Param 21, args 21


  		




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#tmp_files <- FALSE


  		




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interpolation_method <- c("gam_CAI") #PARAM21


  		




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proj_str<- CRS_WGS84 #PARAM 24 #check this parameter


  		




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file_format <- ".tif" #PARAM 25


  		




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NA_value <- -9999 #PARAM 26


  		




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NA_flag_val <- NA_value #PARAM 27


  		




  
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#NA_value <- -32768 #PARAM 26


  		




  
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NA_flag_val <- NA_value #PARAM 26


  		




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use_autokrige <- F #PARAM 28


  		




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#proj_str <- CRS_locs_WGS84 #PARAM 29


  		




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#python script and gdal on NEX NASA:


  		




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##30 parameters passed


  		




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list_param_run_mosaicing_prediction <- list(in_dir,y_var_name,interpolation_method,region_name,


  		




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                 mosaicing_method,out_suffix,out_suffix_str,metric_name,pred_mod_name,var_pred, out_dir,


  		




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                 create_out_dir_param,day_to_mosaic_range,year_predicted,proj_str,file_format,NA_value,num_cores,


  		




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                 use_autokrige,infile_mask,df_assessment_files_name,mosaic_python,


  		




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                 python_bin,algorithm,match_extent,list_models,layers_option,tmp_files,use_int,scaling)


  		




  
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                 create_out_dir_param,day_to_mosaic_range,year_predicted,proj_str,file_format,NA_value,


  		




  
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                 num_cores,use_autokrige,infile_mask,df_assessment_files_name,mosaic_python,


  		




  
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                 python_bin,algorithm,match_extent,list_models,layers_option,tmp_files,data_type,scaling,values_range)


  		




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param_names <- c("in_dir","y_var_name","interpolation_method","region_name",


  		




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                 "mosaicing_method","out_suffix","out_suffix_str","metric_name","pred_mod_name","var_pred","out_dir",


  		




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                 "create_out_dir_param","day_to_mosaic_range","year_predicted","proj_str","file_format","NA_value","num_cores",


  		




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                 "use_autokrige","infile_mask","df_assessment_files_name","mosaic_python",


  		




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                 "python_bin","algorithm","match_extent","list_models","layers_option","tmp_files","use_int","scaling")


  		




  
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                 "create_out_dir_param","day_to_mosaic_range","year_predicted","proj_str","file_format","NA_value",


  		




  
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                 "num_cores","use_autokrige","infile_mask","df_assessment_files_name","mosaic_python",


  		




  
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                 "python_bin","algorithm","match_extent","list_models","layers_option","tmp_files","data_type","scaling","values_range")


  		




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names(list_param_run_mosaicing_prediction) <- param_names


  		




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#list_param_run_mosaicing_prediction


  		




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#debug(run_mosaicing_prediction_fun)


  		












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