Revision 0c4658af
Added by Benoit Parmentier over 8 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: 04/06/2016
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#MODIFIED ON: 04/08/2016
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#Version: 2 |
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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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#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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#Inputs: |
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#lf: list of raster files |
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#df_points: reference points from which to compute distance |
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#r_feature: reference features as raster image from which to compute distance from |
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#methods: options available: use_sine_weights,use_edge,use_linear_weights |
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#1)lf: list of raster files |
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#2)df_points: reference points from which to compute distance |
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#3)r_feature: reference features as raster image from which to compute distance from |
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#4)methods: options available: use_sine_weights,use_edge,use_linear_weights |
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#5)NA_flag : raster flag values, e.g. -9999 |
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#6)file_format: raster format used, default is ".tif" |
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#7)out_suffix_str: output suffix, default is NULL, it is recommended to add the variable name etc. |
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# here e.g. dailyTmax and date!! |
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#8)out_dir_str: output directory, default is NULL |
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#Outputs: |
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#raster list of weights and product of wegihts and inuts |
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#TODO: |
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# |
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############ |
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##### START SCRIPT ##### |
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##### Parse out the input parameters |
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lf <- list_param$lf |
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df_points <- list_param$df_points |
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r_feature <- list_param$r_feature #this should be change to a list |
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padding <- TRUE #if padding true then make buffer around edges?? |
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method <- list_param$method #differnt methods available to create weights |
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#NAflag,file_format,out_suffix etc... |
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NA_flag_val <- list_param$NA_flag |
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file_format <- list_param$file_format |
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out_suffix_str <- list_param$out_suffix_str |
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out_dir_str <- list_param$out_dir_str |
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####### START SCRIPT #####
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##### Prepare weight layers
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r_in <- raster(lf[i]) #input image |
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tile_no <- i |
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tile_no <- i #file being processed, assuming tiles by tiles
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set1f <- function(x){rep(NA, x)}
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r_init <- init(r_in, fun=set1f) |
| ... | ... | |
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r_init[1:n_row,1] <- 1 |
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r_init[1:n_row,n_col] <- 1 |
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#r_dist <- distance(r_init) |
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srcfile <- file.path(out_dir,paste("feature_target_",tile_no,"_",Sys.getpid(),".tif",sep=""))
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#out_suffix_str |
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srcfile <- file.path(out_dir_str,paste("feature_target_",tile_no,"_",Sys.getpid(),out_suffix_str,file_format,sep=""))
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writeRaster(r_init,filename=srcfile,overwrite=T) |
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#Sys.getpid |
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dstfile <- file.path(out_dir,paste("feature_target_edge_distance",tile_no,"_",Sys.getpid(),".tif",sep=""))
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dstfile <- file.path(out_dir_str,paste("feature_target_edge_distance",tile_no,"_",Sys.getpid(),out_suffix_str,file_format,sep=""))
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n_values <- "1" |
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cmd_str <- paste("gdal_proximity.py", srcfile, dstfile,"-values",n_values,sep=" ")
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extension_str <- extension(lf[i]) |
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raster_name_tmp <- gsub(extension_str,"",basename(lf[i])) |
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raster_name <- file.path(out_dir_str,paste(raster_name_tmp,"_",method,"_weights.tif",sep=""))
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raster_name <- file.path(out_dir_str,paste(raster_name_tmp,"_",method,"_weights_",out_suffix_str,file_format,sep=""))
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writeRaster(r, NAflag=NA_flag_val,filename=raster_name,overwrite=TRUE) |
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r_var_prod <- r_in*r |
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raster_name_prod <- file.path(out_dir_str, paste(raster_name_tmp,"_",method,"_prod_weights.tif",sep=""))
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raster_name_prod <- file.path(out_dir_str, paste(raster_name_tmp,"_",method,"_prod_weights_",out_suffix_str,file_format,sep=""))
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writeRaster(r_var_prod, NAflag=NA_flag_val,filename=raster_name_prod,overwrite=TRUE) |
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weights_obj <- list(raster_name,raster_name_prod) |
| ... | ... | |
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return(raster_name) |
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} |
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mosaicFiles <- function(lf_mosaic,mosaic_method="unweighted",num_cores=1,r_mask_raster_name=NULL,python_bin=NULL,mosaic_python="/nobackupp6/aguzman4/climateLayers/sharedCode/gdal_merge_sum_noDataTest.py",algorithm="R",match_extent=TRUE,df_points=NULL,NA_flag_val=-9999,file_format=".tif",out_suffix=NULL,out_dir=NULL){
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mosaicFiles <- function(lf_mosaic,mosaic_method="unweighted",num_cores=1,r_mask_raster_name=NULL,python_bin=NULL,mosaic_python="/nobackupp6/aguzman4/climateLayers/sharedCode/gdal_merge_sum_noDataTest.py",algorithm="R",match_extent=TRUE,df_points=NULL,NA_flag_val=-9999,file_format=".tif",out_suffix=NULL,out_dir=NULL,tmp_files=FALSE){
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#This functions mosaics tiles/files give a list of files. |
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#There are four options to mosaic: use_sine_weights,use_edge,use_linear_weights, unweighted |
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#Sine weights fits sine fuctions across rows and column producing elliptical/spherical patterns from center |
| ... | ... | |
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#11)out_dir: output directory, default is NULL |
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#12)algorithm: use R or python function |
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#13)match extent: if TRUE match extent before mosaicing |
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#14)tmp_files: if TRUE then keep temporary files |
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# |
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#OUTPUT: |
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# Object is produced with 3 components: |
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out_dir_str <- out_dir |
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if(tmp_file==T){
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out_suffix_str_tmp <- paste0(out_suffix,"_tmp") |
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} |
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lf_r_weights <- vector("list",length=length(lf_mosaic))
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############### |
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#df_points <- NULL |
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r_feature <- NULL |
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list_param_create_weights <- list(lf_mosaic,df_points,r_feature,method,out_dir_str) |
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names(list_param_create_weights) <- c("lf","df_points","r_feature","method","out_dir_str")
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#lf <- list_param$lf |
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#df_points <- list_param$df_points |
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#r_feature <- list_param$r_feature #this should be change to a list |
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#padding <- TRUE #if padding true then make buffer around edges?? |
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#method <- list_param$method #differnt methods available to create weights |
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#NAflag,file_format,out_suffix etc... |
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#NA_flag_val <- list_param$NA_flag |
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#file_format <- list_param$file_format |
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#out_suffix_str <- list_param$out_suffix_str |
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#out_dir_str <- list_param$out_dir_str |
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list_param_create_weights <- list(lf_mosaic,df_points,r_feature,method,NA_flag_val,file_format,out_suffix_str_tmp,out_dir_str) |
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names(list_param_create_weights) <- c("lf","df_points","r_feature","method","NA_flag","file_format","out_suffix_str","out_dir_str")
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#num_cores <- 11 |
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#debug(create_weights_fun) |
| ... | ... | |
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df_points <- NULL |
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r_feature <- NULL |
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list_param_create_weights <- list(lf_mosaic,df_points,r_feature,method,out_dir_str) |
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names(list_param_create_weights) <- c("lf","df_points","r_feature","method","out_dir_str")
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#list_param_create_weights <- list(lf_mosaic,df_points,r_feature,method,out_dir_str) |
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#names(list_param_create_weights) <- c("lf","df_points","r_feature","method","out_dir_str")
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list_param_create_weights <- list(lf_mosaic,df_points,r_feature,method,NA_flag_val,file_format,out_suffix_str_tmp,out_dir_str) |
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names(list_param_create_weights) <- c("lf","df_points","r_feature","method","NA_flag","file_format","out_suffix_str","out_dir_str")
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#num_cores <- 11 |
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#debug(create_weights_fun) |
| ... | ... | |
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method <- "use_edge" |
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df_points <- NULL |
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r_feature <- NULL |
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list_param_create_weights <- list(lf_mosaic,df_points,r_feature,method,out_dir_str) |
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names(list_param_create_weights) <- c("lf","df_points","r_feature","method","out_dir_str")
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list_param_create_weights <- list(lf_mosaic,df_points,r_feature,method,NA_flag_val,file_format,out_suffix_str_tmp,out_dir_str) |
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names(list_param_create_weights) <- c("lf","df_points","r_feature","method","NA_flag","file_format","out_suffix_str","out_dir_str")
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#list_param_create_weights <- list(lf_mosaic,df_points,r_feature,method,out_dir_str) |
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#names(list_param_create_weights) <- c("lf","df_points","r_feature","method","out_dir_str")
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#num_cores <- 11 |
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#debug(create_weights_fun) |
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#weights_obj <- create_weights_fun(3,list_param=list_param_create_weights) |
Also available in: Unified diff
mosaicing functions, fixing outputs names and directories