Revision ac6ed65d
Added by Benoit Parmentier over 9 years ago
| climate/research/oregon/interpolation/global_run_scalingup_mosaicing.R | ||
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#Analyses, figures, tables and data are also produced in the script. |
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#AUTHOR: Benoit Parmentier |
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#CREATED ON: 04/14/2015 |
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#MODIFIED ON: 10/05/2015
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#MODIFIED ON: 10/09/2015
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#Version: 5 |
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#PROJECT: Environmental Layers project |
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#COMMENTS: analyses run for reg4 1992 for test of mosaicing using 1500x4500km and other tiles |
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### Start new function here |
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## Add numcores |
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## use mclapply |
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create_accuracy_metric_raster <- 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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df_centroids <- merge(df_centroids,tb_date,by="tile_coord") |
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#r1 <- raster(lf[i]) |
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r1 <- raster(df_centroids$files[i]) |
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r1[] <- df_centroids[[metric_name]][i] #improve this |
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#set1f <- function(x){rep(NA, x)}
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#r_init <- init(r_in, fun=set1f) |
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raster_name_tmp <- paste("r_",metric_name,"_",interpolation_method,"_",date_processed,"_",out_suffix_str,sep="")
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raster_name <- file.path(out_dir_str,raster_name_tmp) |
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writeRaster(r1, NAflag=NA_flag_val,filename=raster_name,overwrite=TRUE) |
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#function(j,df_centroids,metric_name,date_processed,interpolation,) |
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#loop over files, make this a function later, works for now |
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#use mclapply |
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list_raster_name <- vector("list",length=length(lf))
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for(j in 1:length(lf)){
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inFilename <- df_centroids$files[j] |
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r1 <- raster(inFilename) |
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r1[] <- df_centroids[[metric_name]][j] #improve this |
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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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lf_tmp <- gsub(file_format,"",lf) |
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extension_str <- extension(inFilename) |
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raster_name_tmp <- gsub(extension_str,"",basename(inFilename)) |
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outFilename <- file.path(out_dir,paste(raster_name_tmp,"_",metric_name,"_",out_suffix,file_format,sep="")) #for use in function later... |
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#raster_name <- file.path(out_dir_str,paste(raster_name_tmp,"_",out_suffix,file_format,sep=""))#output file |
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#raster_name_tmp <- paste("r_",metric_name,"_",interpolation_method,"_",date_processed,"_",out_suffix_str,sep="")
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#raster_name <- file.path(out_dir_str,raster_name_tmp) |
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writeRaster(r1, NAflag=NA_flag_val,filename=outFilename,overwrite=TRUE) |
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list_raster_name[[j]] <- outFilename |
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} |
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raster_created_obj <- list(raster_name,df_centroids) |
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names(raster_created_obj) <- c("raster_name","df_centroids")
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raster_created_obj <- list(list_raster_name,df_centroids)
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names(raster_created_obj) <- c("list_raster_name","df_centroids")
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return(raster_created_obj) |
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} |
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#### end of function |
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lf_mosaic1 <-list.files(path=file.path(in_dir_tiles), |
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pattern=paste(".*.",day_to_mosaic[1],".*.tif$",sep=""),full.names=T) #choosing date 2...20100901
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names(list_param_accuracy_metric_raster) <- c("lf","tb","metric_name","pred_mod_name","y_var_name","interpolation_method",
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"days_to_process","NA_flag_val","file_format","out_dir_str","out_suffix_str") |
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debug(create_accuracy_metric_raster) |
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test <- create_accuracy_metric_raster(1, list_param_accuracy_metric_raster) |
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raster_created_obj <- create_accuracy_metric_raster(1, list_param_accuracy_metric_raster) |
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lf_accuracy_raster <- unlist(raster_created_obj$list_raster_name) |
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lf_r_rmse <- mclapply(1:length(days_to_process),FUN=create_accuracy_metric_raster,list_param=list_param_accuracy_metric_raster,mc.preschedule=FALSE,mc.cores = 3) |
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#lf_mosaic <- lf_mosaic[1:20] |
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r1 <- raster(lf_mosaic1[1]) |
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out_suffix_str <- paste(day_to_mosaic[i],out_suffix,sep="_") |
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#undebug(mosaicFiles) |
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#can also loop through methods!!! |
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mosaic_edge_obj <- mosaicFiles(lf_mosaic1,mosaic_method="use_edge_weights", |
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mosaic_edge_obj_prediction <- mosaicFiles(lf_mosaic1,mosaic_method="use_edge_weights",
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num_cores=num_cores, |
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python_bin=NULL, |
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df_points=NULL,NA_flag=NA_flag_val, |
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file_format=file_format,out_suffix=out_suffix_str, |
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out_dir=out_dir) |
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mosaic_method <- "use_edge_weights" #this is distance from edge |
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out_suffix_str <- paste(day_to_mosaic[i],out_suffix,sep="_") |
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#undebug(mosaicFiles) |
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#can also loop through methods!!! |
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mosaic_edge_obj_accuracy <- mosaicFiles(lf_accuracy_raster,mosaic_method="use_edge_weights", |
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num_cores=num_cores, |
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python_bin=NULL, |
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df_points=NULL,NA_flag=NA_flag_val, |
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file_format=file_format,out_suffix=out_suffix_str, |
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out_dir=out_dir) |
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#mosaic_unweighted_obj <- mosaicFiles(lf_mosaic1,mosaic_method="unweighted", |
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# num_cores=num_cores, |
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# out_dir=out_dir) |
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#list_mosaic_obj[[i]] <- list(unweighted=mosaic_unweighted_obj,edge=mosaic_edge_obj) |
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list_mosaic_obj[[i]] <- list(unweighted=mosaic_unweighted_obj,edge=mosaic_edge_obj) |
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#list_mosaic_obj[[i]] <- list(prediction=mosaic_edge_obj_accuracy,accuracy=mosaic_edge_obj_accuracy) |
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list_mosaic_obj[[i]] <- list(prediction=mosaic_edge_obj_prediction,accuracy=mosaic_edge_obj_accuracy) |
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} |
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##################### |
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list_param= list_param_plot_mosaic, |
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mc.preschedule=FALSE,mc.cores = num_cores) |
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#################### |
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#### Now difference figures... |
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lf_obj1 <- list.files(path=out_dir,pattern="*unweighted.*.RData") |
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lf_obj2 <- list.files(path=out_dir,pattern="*edge_.*.RData") |
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lf1 <- unlist(lapply(lf_obj1,function(x){load_obj(x)[["mean_mosaic"]]}))
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lf2 <- unlist(lapply(lf_obj2,function(x){load_obj(x)[["mean_mosaic"]]}))
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out_suffix_str <- paste(paste(mosaicing_method,collapse="_"),day_to_mosaic,out_suffix,sep="_") |
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list_param_plot_diff <- list(lf1=lf1,lf2=lf2,out_suffix=out_suffix_str) |
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#debug(plot_diff_raster) |
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#plot_diff_raster(1,list_param=list_param_plot_diff) |
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num_cores <- 2 |
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l_diff_png_files <- mclapply(1:length(lf1),FUN=plot_diff_raster,list_param= list_param_plot_diff, |
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mc.preschedule=FALSE,mc.cores = num_cores) |
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############### |
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##### Get all the tiles togheter merged |
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#ls -ltr ./reg*/*/*mean*.tif | wc |
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in_dir1 <- "/data/project/layers/commons/NEX_data/mosaicing_data_test" |
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lf_unweighted_20100831 <- list.files(path=in_dir1,pattern="r_m_mean_20100831.*.tif",recursive=T,full.names=T) |
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lf_edge_weighted_20100831 <- list.files(path=in_dir1,pattern="r_.*.edge.*._mean_20100831.*.tif",recursive=T,full.names=T) |
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lf_unweighted_20100901 <- list.files(path=in_dir1,pattern="r_m_mean_20100901.*.tif",recursive=T,full.names=T) |
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lf_edge_weighted_20100901 <- list.files(path=in_dir1,pattern="r_.*.edge.*.mean_20100901.*.tif",recursive=T,full.names=T) |
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output_fnames <- c("mean_unweighted_world_20100831_global_analyses_07012015.tif",
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"mean_edge_weighted_world_20100831_global_analyses_07012015.tif", |
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"mean_unweighted_world_20100901_global_analyses_07012015.tif", |
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"mean_edge_weighted_world_20100901_global_analyses_07012015.tif" |
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) |
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list_lf <- list(lf_unweighted_20100831,lf_edge_weighted_20100831,lf_unweighted_20100901,lf_edge_weighted_20100901) |
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out_dir_str <- "/data/project/layers/commons/NEX_data/mosaicing_data_test/mosaic_world_07012015" |
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list_output_fnames <- vector("list",length=length(output_fnames))
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for(i in 1:length(output_fnames)){
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rast_ref <- file.path(out_dir_str,output_fnames[i]) #this is a the ref ouput file |
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lf_to_mosaic <- list_lf[[i]] |
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cmd_str <- paste("python","/usr/bin/gdal_merge.py","-o ",rast_ref,paste(lf_to_mosaic,collapse=" "))
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system(cmd_str) |
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list_output_fnames[[i]] <- rast_ref |
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} |
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#list_lf_m <- mixedsort(list.files(path=out_dir_str,pattern="mean.*.world.*.global_analyses_07012015.tif",full.names=T)) |
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list_lf_m <- unlist(list_output_fnames) |
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reg_name <- "world" |
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out_suffix_str <- "mosaic_07092015" |
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l_dates <- c("unweighted_20100831","edge_weighted_20100831","unweighted_20100901","edge_weighted_20100901")
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list_param_plot_daily_mosaics <- list(list_lf_m,reg_name,out_dir_str,out_suffix_str,l_dates) |
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names(list_param_plot_daily_mosaics) <- c("lf_m","reg_name","out_dir_str","out_suffix","l_dates")
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#undebug(plot_daily_mosaics) |
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#test<- plot_daily_mosaics(1,list_param_plot_daily_mosaics) |
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num_cores <- 4 |
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lf_plot <- mclapply(1:length(l_dates),FUN=plot_daily_mosaics,list_param=list_param_plot_daily_mosaics, |
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mc.preschedule=FALSE,mc.cores = num_cores) |
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r_test <- raster("r_m_use_edge_weighted_mean_19920101_reg4_mosaic_run10_1500x4500_global_analyses_10052015.tif")
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plot(r_test) |
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##################### END OF SCRIPT ###################### |
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Also available in: Unified diff
testing accuracy metric function and mosaic