Revision 81318fd0
Added by Benoit Parmentier almost 9 years ago
| climate/research/oregon/interpolation/global_run_scalingup_mosaicing_function.R | ||
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#Different options to explore mosaicing are tested. This script only contains functions. |
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#AUTHOR: Benoit Parmentier |
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#CREATED ON: 04/14/2015 |
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#MODIFIED ON: 10/27/2015
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#MODIFIED ON: 11/09/2015
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#Version: 1 |
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#PROJECT: Environmental Layers project |
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#COMMENTS: first commit of function script to test mosaicing using 1500x4500km and other tiles |
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#### end of function |
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mosaic_python_merge <- function(module_path,module_name,input_file,out_mosaic_name){
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#out_mosaic_name <- r_weights_sum_raster_name <- file.path(out_dir,paste("r_weights_sum_m_",method_str,"_weighted_mean_",out_suffix,".tif",sep=""))
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cmd_str <- paste("python", file.path(module_path,module_name),
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"--config GDAL_CACHEMAX=1500", |
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"--overwrite=TRUE", |
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paste("-o",out_mosaic_name,sep=" "),
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paste("--optfile", input_file,sep=" "))
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system(cmd_str) |
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#list(out_mosaic_name,cmd_str) |
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return(out_mosaic_name) |
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} |
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create_weights_fun <- function(i, list_param){
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#This function generates weights from a point location on a raster layer. |
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#Note that the weights are normatlized on 0-1 scale using max and min values. |
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if(mosaic_method%in%c("use_linear_weights","use_sine_weights","use_edge_weights")){
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lf_files <- unlist(list_weights) |
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##Maching resolution is probably only necessary for the r mosaic function |
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#MOdify later to take into account option R or python... |
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list_param_raster_match <- list(lf_files,rast_ref,file_format,python_bin,out_suffix,out_dir) |
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names(list_param_raster_match) <- c("lf_files","rast_ref","file_format","python_bin","out_suffix","out_dir_str")
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#debug(raster_match) |
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#r_test <- raster(raster_match(1,list_param_raster_match)) |
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list_weights_m <- mclapply(1:length(lf_files),FUN=raster_match,list_param=list_param_raster_match,mc.preschedule=FALSE,mc.cores = num_cores) |
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lf_files <- unlist(list_weights_prod) |
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list_param_raster_match <- list(lf_files,rast_ref,file_format,python_bin,out_suffix,out_dir) |
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names(list_param_raster_match) <- c("lf_files","rast_ref","file_format","python_bin","out_suffix","out_dir_str")
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#num_cores <-11 |
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list_weights_prod_m <- mclapply(1:length(lf_files),FUN=raster_match,list_param=list_param_raster_match,mc.preschedule=FALSE,mc.cores = num_cores) |
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##################### |
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###### PART 4: compute the weighted mean with the mosaic function ##### |
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if(algorithm=="python"){
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#The file to do the merge is /nobackupp6/aguzman4/climateLayers/sharedCode/gdal_merge_sum.py. Sample call below. |
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#python /nobackupp6/aguzman4/climateLayers/sharedCode/gdal_merge_sum.py --config GDAL_CACHEMAX=1500 --overwrite=TRUE -o outputname.tif --optfile input.txt |
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#lf_day_to_mosaic <- list_weights_m |
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#lf_day_to_mosaic <- unlist(lf_day_to_mosaic) |
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#write.table(lf_day_to_mosaic,file=file.path(out_dir,paste("list_to_mosaics_",day_to_mosaic[i],".txt",sep="")))
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#filename_list_mosaics <- file.path(out_dir,paste("list_to_mosaics_",day_to_mosaic[i],".txt",sep=""))
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filename_list_mosaics_weights_m <- file.path(out_dir,paste("list_to_mosaics_","weights_m_",mosaic_method,"_",out_suffix,".txt",sep=""))
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filename_list_mosaics_prod_weights_m <- file.path(out_dir,paste("list_to_mosaics_","prod_weights_m_",mosaic_method,"_",out_suffix,".txt",sep=""))
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filename_list_mosaics_weights_m <- file.path(out_dir,paste("list_to_mosaics_","weights_",mosaic_method,"_",out_suffix,".txt",sep=""))
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filename_list_mosaics_prod_weights_m <- file.path(out_dir,paste("list_to_mosaics_","prod_weights_",mosaic_method,"_",out_suffix,".txt",sep=""))
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#writeLines(unlist(list_weights_m),con=filename_list_mosaics_weights_m) #weights files to mosaic |
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#writeLines(unlist(list_weights_prod_m),con=filename_list_mosaics_prod_weights_m) #prod weights files to mosaic |
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writeLines(unlist(list_weights_m),con=filename_list_mosaics_weights_m) #weights files to mosaic
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writeLines(unlist(list_weights_prod_m),con=filename_list_mosaics_prod_weights_m) #prod weights files to mosaic
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writeLines(unlist(list_weights),con=filename_list_mosaics_weights_m) #weights files to mosaic |
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writeLines(unlist(list_weights_prod),con=filename_list_mosaics_prod_weights_m) #prod weights files to mosaic |
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#out_mosaic_name_weights_m <- r_weights_sum_raster_name <- file.path(out_dir,paste("r_weights_sum_m_",mosaic_method,"_weighted_mean_",out_suffix,".tif",sep=""))
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#out_mosaic_name_prod_weights_m <- r_weights_sum_raster_name <- file.path(out_dir,paste("r_prod_weights_sum_m_",mosaic_method,"_weighted_mean_",out_suffix,".tif",sep=""))
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input_file <- filename_list_mosaics_weights_m |
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module_path <- mosaic_python #this should be a parameter for the function... |
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mosaic_python_merge <- function(module_path,module_name,input_file,out_mosaic_name){
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#d |
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#out_mosaic_name <- r_weights_sum_raster_name <- file.path(out_dir,paste("r_weights_sum_m_",method_str,"_weighted_mean_",out_suffix,".tif",sep=""))
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cmd_str <- paste("python", file.path(module_path,module_name),
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"--config GDAL_CACHEMAX=1500", |
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"--overwrite=TRUE", |
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paste("-o",out_mosaic_name,sep=" "),
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paste("--optfile", input_file,sep=" "))
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system(cmd_str) |
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#list(out_mosaic_name,cmd_str) |
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return(out_mosaic_name) |
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} |
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#python /nobackupp6/aguzman4/climateLayers/sharedCode/gdal_merge_sum.py |
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#--config GDAL_CACHEMAX=1500 --overwrite=TRUE -o outputname.tif --optfile input.txt |
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r_weights_sum_raster_name <- mosaic_python_merge(module_path=mosaic_python, |
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if(algorithm=="R"){
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#If using R, it is necessary to match extent firt |
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lf_files <- unlist(list_weights) |
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##Maching resolution is probably only necessary for the r mosaic function |
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#MOdify later to take into account option R or python... |
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list_param_raster_match <- list(lf_files,rast_ref,file_format,python_bin,out_suffix,out_dir) |
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names(list_param_raster_match) <- c("lf_files","rast_ref","file_format","python_bin","out_suffix","out_dir_str")
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#undebug(raster_match) |
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#r_test <- raster_match(1,list_param_raster_match) |
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#r_test <- raster(raster_match(1,list_param_raster_match)) |
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list_weights_m <- mclapply(1:length(lf_files),FUN=raster_match,list_param=list_param_raster_match,mc.preschedule=FALSE,mc.cores = num_cores) |
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lf_files <- unlist(list_weights_prod) |
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list_param_raster_match <- list(lf_files,rast_ref,file_format,python_bin,out_suffix,out_dir) |
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names(list_param_raster_match) <- c("lf_files","rast_ref","file_format","python_bin","out_suffix","out_dir_str")
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#num_cores <-11 |
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list_weights_prod_m <- mclapply(1:length(lf_files),FUN=raster_match,list_param=list_param_raster_match,mc.preschedule=FALSE,mc.cores = num_cores) |
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#The file to do the merge is /nobackupp6/aguzman4/climateLayers/sharedCode/gdal_merge_sum.py. Sample call below. |
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#python /nobackupp6/aguzman4/climateLayers/sharedCode/gdal_merge_sum.py --config GDAL_CACHEMAX=1500 --overwrite=TRUE -o outputname.tif --optfile input.txt |
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##Make this a function later |
Also available in: Unified diff
mosaicing function adding python and R options to mosaicFile