Revision 91fc5062
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: 04/22/2016
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#MODIFIED ON: 04/24/2016
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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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} |
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valid_range <- values_range #if NULL don't screen values!! |
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#valid_range <- c(-100,100) #pass this as parameter!! (in the next update) |
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if(data_type=="Int16"){
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data_type_str <- "INT2S" |
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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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"--overwrite",sep=" ") #division by zero is problematic... |
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system(cmd_str3) |
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if(!is.null(r_mask_raster_name)){
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#different extent between mask and output if match extent is false!! |
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#match resolution and extent first |
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#lf_files <- c(r_m_weighted_mean_raster_name) #file(s) to be matched |
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lf_files <- c(r_m_weighted_mean_raster_name) #match to mask |
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rast_ref <- r_mask_raster_name |
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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_m_weighted_mean_raster_name_matched <- raster_match(1,list_param_raster_match) |
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} |
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#writeRaster(r_m_weighted_mean, NAflag=NA_flag_val,filename=raster_name,overwrite=TRUE) |
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###Starting rescaling, switched by masking first then screening to avoid potential problems |
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##Can merge one and 2 with parentheses operations!!, make this a function? |
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##Reclassify with valid range: -100,100 |
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raster_name <- r_m_weighted_mean_raster_name |
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#raster_name <- r_m_weighted_mean_raster_name |
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raster_name <- r_m_weighted_mean_raster_name_matched |
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max_val <- valid_range[2]*scaling #set min_valid |
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raster_name_rec1 <- file.path(out_dir_str,paste("r_m_",mosaic_method,"_weighted_mean_rec1_",out_suffix,"_tmp",".tif",sep=""))
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#rec_tmp1 <- file.path(out_dir_str,paste("r_m_",mosaic_method,"_weighted_mean_rec_",out_suffix,".tif",sep=""))
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#browser() #22minutes for one mosaic |
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#cmd_mosaic_logfile <- file.path(out_dir,paste("cmd_mosaic_",out_suffix,".txt",sep=""))
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cmd_mosaic_logfile <- file.path(out_dir,paste("cmd_mosaic_",out_suffix,".txt",sep=""))
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writeLines(cmd_str1,con=cmd_mosaic_logfile) #weights files to mosaic |
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#writeLines(cmd_str2,con=file.path(out_dir,paste("cmd_mosaic_",out_suffix,".txt",sep=""))) #weights files to mosaic
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#match resolution and extent first |
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#lf_files <- c(r_m_weighted_mean_raster_name) #file(s) to be matched |
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lf_files <- c(r_m_weighted_mean_raster_name_rec) #match to mask |
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#lf_files <- c(r_m_weighted_mean_raster_name_rec) #match to mask
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rast_ref <- r_mask_raster_name |
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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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#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_m_weighted_mean_raster_name_matched <- raster_match(1,list_param_raster_match) |
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#r_m_weighted_mean_raster_name_matched <- raster_match(1,list_param_raster_match)
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#output |
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r_m_weighted_mean_mask_raster_name <- file.path(out_dir_str,paste("r_m_",mosaic_method,"_weighted_mean_mask_",out_suffix,".tif",sep=""))
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#mask(raster(r_m_weighted_mean_raster_name_matched),mask=raster(r_mask_raster_name), |
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# filename=r_m_weighted_mean_mask_raster_name,overwrite=TRUE) |
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in_raster_name <- r_m_weighted_mean_raster_name_rec |
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mask(raster(in_raster_name), |
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mask=raster(r_mask_raster_name), |
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filename=r_m_weighted_mean_mask_raster_name, |
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datatype=data_type_str, |
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options=c("COMPRESS=LZW"),
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overwrite=TRUE, |
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NAflag=NA_flag_val) |
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##Now combine A and B and multiply by mask?? This must be faster than the mask option in R |
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#The mask must be in 1,NA format with 1 being valid values being considered in roi. |
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#r_m_weighted_mean_raster_name_rec <- file.path(out_dir_str,paste("r_m_",mosaic_method,"_weighted_mean_rec_",out_suffix,"_tmp",".tif",sep=""))
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#browser() |
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cmd_mosaic_logfile <- file.path(out_dir,paste("cmd_mosaic_",out_suffix,".txt",sep=""))
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#cmd_mosaic_logfile <- file.path(out_dir,paste("cmd_mosaic_",out_suffix,".txt",sep=""))
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#in_raster_name <- r_m_weighted_mean_raster_name_matched |
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cmd_str7 <- paste(python_cmd, |
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paste("-A ", r_m_weighted_mean_raster_name_matched,sep=""),
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paste("-B ", r_mask_raster_name,sep=""),
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paste("--outfile=",r_m_weighted_mean_mask_raster_name,sep=""),
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paste("--type=",data_type,sep=""),
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"--co='COMPRESS=LZW'", |
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paste("--NoDataValue=",NA_flag_val,sep=""),
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paste("--calc='(A*B)'",sep=""),
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"--overwrite",sep=" ") #division by zero is problematic... |
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system(cmd_str7) |
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cat(cmd_str7, file=cmd_mosaic_logfile, append=TRUE, sep = "\n") |
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#cmd_str7 <- paste(python_cmd, |
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# paste("-A ", in_raster_name,sep=""),
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# paste("-B ", r_mask_raster_name,sep=""),
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# paste("--outfile=",r_m_weighted_mean_mask_raster_name,sep=""),
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# paste("--type=",data_type,sep=""),
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# "--co='COMPRESS=LZW'", |
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# paste("--NoDataValue=",NA_flag_val,sep=""),
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# paste("--calc='(A*B)'",sep=""),
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# "--overwrite",sep=" ") #division by zero is problematic... |
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#system(cmd_str7) |
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#cat(cmd_str7, file=cmd_mosaic_logfile, append=TRUE, sep = "\n") |
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##Set min max and NA value |
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r_mosaiced <- raster(r_m_weighted_mean_mask_raster_name) |
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r_mosaiced <- setMinMax(r_mosaiced) |
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NAvalue(r_mosaiced) <- NA_flag_val |
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raster_name <- r_m_weighted_mean_mask_raster_name |
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browser() |
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#browser()
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#-32,768 is NA |
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}else{
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raster_name <- r_m_weighted_mean_raster_name |
Also available in: Unified diff
fixing problem with masking and no data values