Revision 331e163a
Added by Benoit Parmentier over 8 years ago
| 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: 04/24/2016
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#MODIFIED ON: 05/01/2016
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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_04232016.R" #PARAM12
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function_mosaicing <-"global_run_scalingup_mosaicing_04222016.R"
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function_mosaicing_functions <- "global_run_scalingup_mosaicing_function_05012016.R" #PARAM12
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function_mosaicing <-"global_run_scalingup_mosaicing_05012016.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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#The 20 arguments are passed directly from Rscript: |
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### Use the following values to run code from the shell: |
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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_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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#year_predicted <- 1991 #PARAM 7, arg 7 |
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#num_cores <- 6 #PARAM 8, arg 8 |
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#max_mem = 1e+07 #param 9, arg 9 |
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#mosaicing_method <- "use_edge_weights" #PARAM10, arg 10 |
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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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#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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#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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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_1999" #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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year_predicted <- 1999 #PARAM 7, arg 7 |
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num_cores <- 6 #PARAM 8, arg 8 |
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max_mem = 1e+07 #param 9, arg 9 |
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mosaicing_method <- "use_edge_weights" #PARAM10, arg 10 |
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metric_name <- "rmse" #RMSE, MAE etc. #PARAM 11, arg 11 |
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day_start <- "19990701" #PARAM 12 arg 12 |
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day_end <- "19990703" #PARAM 13 arg 13 |
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infile_mask <- "/nobackupp8/bparmen1/NEX_data/regions_input_files/r_mask_LST_reg4.tif" #PARAM 14, arg 14 |
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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 |
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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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#layers_option <- c("ac_testing") #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, keep temp files if TRUE |
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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 <- "-100,100" |
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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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python_bin <- "/nobackupp6/aguzman4/climateLayers/sharedModules2/bin" #PARAM 30 |
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#python script and gdal on Atlas NCEAS |
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#mosaic_python <- "/data/project/layers/commons/NEX_data/sharedCode" #PARAM 30 |
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#python_bin <- "/usr/bin" #PARAM 30 |
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#python_bin <- "/usr/bin" #PARAM 30 #Atlas
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match_extent <- "FALSE" #PARAM 31 #try without matching!!! |
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#for residuals... |
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list_models <- NULL #PARAM 32 |
Also available in: Unified diff
running stage 7 mosaicing for region 4 on 1999 for poster NASA biodiversity conference