Project

General

Profile

« Previous | Next » 

Revision 34e2c563

Added by Benoit Parmentier over 8 years ago

testing code with new flag value and masking file

View differences:

climate/research/oregon/interpolation/master_script_stage_7.R
14 14 

  		




  15
  15
  
    
#AUTHOR: Benoit Parmentier                                                                        


  		




  16
  16
  
    
#CREATED ON: 01/01/2016  


  		




  17
  
  
    
#MODIFIED ON: 04/23/2016  


  		




  
  17
  
    
#MODIFIED ON: 04/24/2016  


  		




  18
  18
  
    
#PROJECT: NCEAS INPLANT: Environment and Organisms                                                                           


  		




  19
  19
  
    

  		




  20
  20
  
    
#First source these files:


  		




  ......




  63
  63
  
    

  		




  64
  64
  
    
#script_path <- "/home/parmentier/Data/IPLANT_project/env_layers_scripts"


  		




  65
  65
  
    
script_path <- "/nobackupp8/bparmen1/env_layers_scripts" #path to script


  		




  66
  
  
    
function_mosaicing_functions <- "global_run_scalingup_mosaicing_function_04222016b.R" #PARAM12


  		




  
  66
  
    
function_mosaicing_functions <- "global_run_scalingup_mosaicing_function_04232016.R" #PARAM12


  		




  67
  67
  
    
function_mosaicing <-"global_run_scalingup_mosaicing_04222016.R"


  		




  68
  68
  
    
source(file.path(script_path,function_mosaicing)) #source all functions used in this script 


  		




  69
  69
  
    
source(file.path(script_path,function_mosaicing_functions)) #source all functions used in this script 


  		




  ......




  117
  117
  
    
#scaling <- 100 #, param 20, if null use 1


  		




  118
  118
  
    
#values_range <- c(-100,100)


  		




  119
  119
  
    

  		




  120
  
  
    
var <- "TMAX" # variable being interpolated #param 1, arg 1


  		




  121
  
  
    
in_dir <- "/nobackupp6/aguzman4/climateLayers/out/" #PARAM2,arg 2


  		




  122
  
  
    
region_name <- "reg4" #PARAM 3, arg 3 #reg4 South America, Africa reg5,Europe reg2, North America reg1, Asia reg3


  		




  123
  
  
    
out_suffix <- "reg4_1991" #PARAM 4, arg 4


  		




  124
  
  
    
out_suffix_str <- region_name #PARAM 4, CONST 3


  		




  125
  
  
    
out_dir <- "/nobackupp8/bparmen1/climateLayers/out/reg4" #PARAM 5,arg 5 use this location for now


  		




  126
  
  
    
create_out_dir_param <- TRUE #PARAM 6, arg 6


  		




  127
  
  
    
year_predicted <- 1991 #PARAM 7, arg 7


  		




  128
  
  
    
num_cores <- 6 #PARAM 8, arg 8         


  		




  129
  
  
    
max_mem = 1e+07 #param 9, arg 9


  		




  130
  
  
    
mosaicing_method <- "use_edge_weights" #PARAM10, arg 10


  		




  131
  
  
    
metric_name <- "rmse" #RMSE, MAE etc. #PARAM 11, arg 11


  		




  132
  
  
    
day_start <- "19910101" #PARAM 12 arg 12


  		




  133
  
  
    
day_end <- "19910103" #PARAM 13 arg 13


  		




  134
  
  
    
#infile_mask <- "/nobackupp8/bparmen1/NEX_data/regions_input_files/r_mask_reg4.tif" #PARAM 14, arg 14


  		




  135
  
  
    
infile_mask <- "/nobackupp8/bparmen1/NEX_data/regions_input_files/r_mask_LST.tif"


  		




  136
  
  
    
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


  		




  137
  
  
    
algorithm <- "python" #PARAM 16 #if R use mosaic function for R, if python use modified gdalmerge script from Alberto Guzmann


  		




  138
  
  
    
layers_option <- c("var_pred") #arg 17 ,param 17, options are:#res_training, res_testing,ac_training, ac_testing, var_pred


  		




  139
  
  
    
tmp_files <- FALSE #arg 18, param 18


  		




  140
  
  
    
data_type <- "Int16" #, param 19, use int32 for output layers mosaiced


  		




  141
  
  
    
scaling <- 100 #, param 20, if NULL don't rescale values


  		




  142
  
  
    
values_range <- c(-100,100) #args 21, if NULL don't screen values


  		




  
  120
  
    
# var <- "TMAX" # variable being interpolated #param 1, arg 1


  		




  
  121
  
    
# in_dir <- "/nobackupp6/aguzman4/climateLayers/out/" #PARAM2,arg 2


  		




  
  122
  
    
# region_name <- "reg4" #PARAM 3, arg 3 #reg4 South America, Africa reg5,Europe reg2, North America reg1, Asia reg3


  		




  
  123
  
    
# out_suffix <- "reg4_1991" #PARAM 4, arg 4


  		




  
  124
  
    
# out_suffix_str <- region_name #PARAM 4, CONST 3


  		




  
  125
  
    
# out_dir <- "/nobackupp8/bparmen1/climateLayers/out/reg4" #PARAM 5,arg 5 use this location for now


  		




  
  126
  
    
# create_out_dir_param <- TRUE #PARAM 6, arg 6


  		




  
  127
  
    
# year_predicted <- 1991 #PARAM 7, arg 7


  		




  
  128
  
    
# num_cores <- 6 #PARAM 8, arg 8         


  		




  
  129
  
    
# max_mem = 1e+07 #param 9, arg 9


  		




  
  130
  
    
# mosaicing_method <- "use_edge_weights" #PARAM10, arg 10


  		




  
  131
  
    
# metric_name <- "rmse" #RMSE, MAE etc. #PARAM 11, arg 11


  		




  
  132
  
    
# day_start <- "19910101" #PARAM 12 arg 12


  		




  
  133
  
    
# day_end <- "19910103" #PARAM 13 arg 13


  		




  
  134
  
    
# #infile_mask <- "/nobackupp8/bparmen1/NEX_data/regions_input_files/r_mask_reg4.tif" #PARAM 14, arg 14


  		




  
  135
  
    
# infile_mask <- "/nobackupp8/bparmen1/NEX_data/regions_input_files/r_mask_LST.tif"


  		




  
  136
  
    
# 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


  		




  
  137
  
    
# algorithm <- "python" #PARAM 16 #if R use mosaic function for R, if python use modified gdalmerge script from Alberto Guzmann


  		




  
  138
  
    
# layers_option <- c("var_pred") #arg 17 ,param 17, options are:#res_training, res_testing,ac_training, ac_testing, var_pred


  		




  
  139
  
    
# tmp_files <- FALSE #arg 18, param 18


  		




  
  140
  
    
# data_type <- "Int16" #, param 19, use int32 for output layers mosaiced


  		




  
  141
  
    
# scaling <- 100 #, param 20, if NULL don't rescale values


  		




  
  142
  
    
# values_range <- "-100,100" #args 21, if NULL don't screen values


  		




  
  143
  
    
#NA_flag_val <- -32768 #should be here


  		




  
  144
  
    

  		




  143
  145
  
    

  		




  144
  146
  
    
#path_assessment <- NOT USED "/nobackupp6/aguzman4/climateLayers/out/reg4/assessment/output_reg4_1991" #PARAM 14a, arg 14


  		




  145
  147
  
    

  		




  146
  148
  
    
### Testing several years on the bridge before running jobs on nodes with qsub


  		




  147
  149
  
    
#Use the following command to run as script via the shell on the bridge 


  		




  148
  
  
    
#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


  		




  
  150
  
    
#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


  		




  149
  151
  
    

  		




  150
  152
  
    
############################


  		




  151
  153
  
    

  		




  ......




  222
  224
  
    
var_pred <- "res_mod1" #used in residuals mapping #PARAM 23


  		




  223
  225
  
    
proj_str<- CRS_WGS84 #PARAM 24 #check this parameter


  		




  224
  226
  
    
file_format <- ".tif" #PARAM 25


  		




  225
  
  
    
NA_value <- -9999 #PARAM 26


  		




  226
  
  
    
#NA_value <- -32768 #PARAM 26


  		




  
  227
  
    
#NA_value <- -9999 #PARAM 26


  		




  
  228
  
    
NA_value <- -32768 #PARAM 26


  		




  227
  229
  
    
NA_flag_val <- NA_value #PARAM 26


  		




  228
  230
  
    
use_autokrige <- F #PARAM 28


  		




  229
  231
  
    
#proj_str <- CRS_locs_WGS84 #PARAM 29


  		




  ......




  253
  255
  
    
  day_to_mosaic_range <- NULL


  		




  254
  256
  
    
}


  		




  255
  257
  
    

  		




  
  258
  
    
#parse input value range


  		




  
  259
  
    
values_range <- as.numeric(unlist(strsplit(values_range,",")))


  		




  
  260
  
    
scaling <- as.numeric(scaling)


  		




  
  261
  
    

  		




  256
  262
  
    
#browser()


  		




  257
  263
  
    

  		




  258
  264
  
    
#rasterOptions(maxmemory=1e+07,timer=TRUE)


  		




  ......




  284
  290
  
    
}


  		




  285
  291
  
    

  		




  286
  292
  
    
#runs in 42 minutes for 3 dates but note that beyond date 1, the process is about 11 minutes or so.


  		




  287
  
  
    

  		




  
  293
  
    
#19h09


  		




  288
  294
  
    
###############   END OF SCRIPT   ###################


  		




  289
  295
  
    
#####################################################


  		




  290
  296
  
    

  		












Also available in:  Unified diff