updated some functions

SCRIPTS/functionR2Netcdf.R

@@ -4,10 +4,25 @@ R2Netcdf <- function(outFile, rData) {
   ## CREATE NETCDF
   FillValue <- 1e20
   
+  ## Check dimensions
+  dimensions<-attributes(rData$Data)$dimensions
+  
+  ## Check if 'member', or 4th dimension exist
+  nDims <- length(dim(rData$Data))
+  if (nDims > 3) {
+    if (!'member' %in% dimensions){
+      stop("dimension 'member' not defined!")
+    }
+  }
+  
+  
   ## Define dimensions
   dimX <- ncdim_def("lon", "degrees_east", rData$xyCoords$x)
   dimY <- ncdim_def("lat", "degrees_north",rData$xyCoords$y)
-  
+  if (nDims > 3) {
+    dimZ <- ncdim_def("member", "layer",1:dim(rData$Data)[which(dimensions == "member")])
+    #dimZ <- ncdim_def(name = "layer",units = '',vals = 1:dim(rData$Data)[which(dimensions == "member")], create_dimvar = FALSE)
+  }
   timeString<-format(strptime(rData$Dates$start[1], format = "%Y-%m-%d", tz = "GMT"),format="%Y-%m-%d %T")
   timeArray<-as.double(difftime(rData$Dates$start,rData$Dates$start[1], units = c("days")))
   dimT <- ncdim_def("time", paste0("days since ",timeString), timeArray, unlim = FALSE)
@@ -18,17 +33,27 @@ R2Netcdf <- function(outFile, rData) {
     units<-""
   }
   
-  data <- ncvar_def(name=rData$Variable$varName, units=units, dim=list(dimX,dimY,dimT), missval=FillValue, prec="float",chunksizes = c(length(rData$xyCoords$x),length(rData$xyCoords$y),1), compression=4)
+  if (nDims > 3) {
+    data <- ncvar_def(name=rData$Variable$varName, units=units, dim=list(dimX,dimY,dimZ,dimT), missval=FillValue, prec="float",chunksizes = c(length(rData$xyCoords$x),length(rData$xyCoords$y),1,1), compression=4)
+  } else {
+    data <- ncvar_def(name=rData$Variable$varName, units=units, dim=list(dimX,dimY,dimT), missval=FillValue, prec="float",chunksizes = c(length(rData$xyCoords$x),length(rData$xyCoords$y),1), compression=4)
+  }
   
   ## SAVE AS NC-DATA
   print(paste0("Writing: ", outFile))
   
   ncid <- nc_create(outFile, list(data))
   
-  dimensions<-attributes(rData$Data)$dimensions
-  ncvar_put(ncid, data, aperm(rData$Data, c(which(dimensions == "lon"),
-                                            which(dimensions == "lat"),
-                                            which(dimensions == "time"))))
+  if (nDims > 3) {
+    ncvar_put(ncid, data, aperm(rData$Data, c(which(dimensions == "lon"),
+                                              which(dimensions == "lat"),
+                                              which(dimensions == "time"),
+                                              which(dimensions == "member"))))
+  } else {
+    ncvar_put(ncid, data, aperm(rData$Data, c(which(dimensions == "lon"),
+                                              which(dimensions == "lat"),
+                                              which(dimensions == "time"))))
+  }
   
   ncatt_put( ncid, "lon", "standard_name", "longitude")
   ncatt_put( ncid, "lon", "long_name",     "Longitude")
@@ -45,7 +70,10 @@ R2Netcdf <- function(outFile, rData) {
   
   ## Global Attributes
   if ('InitializationDates' %in% names(rData)) ncatt_put( ncid, 0, "InitializationDates", rData$InitializationDates)
-  if ('Members' %in% names(rData)) ncatt_put( ncid, 0, "Members", rData$Members)
+  if ('Members' %in% names(rData)) {
+    membernames<-paste(rData$Members, sep = ' ', collapse = ' ')
+    ncatt_put( ncid, 0, "Members", membernames)
+  }
   
   ## Get all global attributes from rData and put them in the NetCDF file
   attributeList<-attributes(rData)
@@ -54,7 +82,7 @@ R2Netcdf <- function(outFile, rData) {
     ncatt_put( ncid, 0, names(attributeList)[iAttribute], as.character(attributeList[iAttribute[]]))
   }
   ncatt_put( ncid, 0, "NetcdfCreatationDate", as.character(Sys.Date()))
-
+  
   length(attributeList)
   ## Close Netcdf file
   nc_close(ncid)

SCRIPTS/functionReformat.R

 rm(list=ls())
 source(file = "./functionsGeneral.R")
 
-reformat2Bias<-function(members, initYears, initMonth, varName, locName, iPath = "/home/wietse/TODO/output/") {
+reformat2Bias<-function(members, initYears, initMonth, varName, locName, 
+                        iFile = "./forcing_seas15_GHA_ref__E<MEMBERS>_<YEARS>_01.Rdata") {
   sYear<-initYears[1]
   eYear<-initYears[length(initYears)]
   nYears<-length(initYears)
@@ -22,13 +23,12 @@ reformat2Bias<-function(members, initYears, initMonth, varName, locName, iPath =
     for (initYear in initYears) {
       indexesYearsLeadMonths<-indexesForYearsPerLeadMonth(sYear,eYear,initMonth)
       
-      nameFileR <- sprintf(paste0(iPath,"/%s_forcing_seas15_%s_ref__E%02d_%4d_%02d.Rdata"), 
-                           varName,
-                           locName,
-                           iMember,
-                           initYear,
-                           initMonth)
-      print(paste0("Opening: ", nameFileR))
+      nameFileR <- iFile
+      strYear <- sprintf("%4d",initYear)
+      strMember <- sprintf("%02d",iMember)
+      nameFileR <-gsub("<MEMBERS>", strMember, nameFileR)
+      nameFileR <-gsub("<YEARS>", strYear, nameFileR)
+      print(paste0("Opening2 ", nameFileR))
       load(nameFileR)
       
       if (!allocatedOutputArray) {
@@ -50,6 +50,7 @@ reformat2Bias<-function(members, initYears, initMonth, varName, locName, iPath =
           finalList[[iLM]]$Dates$start<-character(length=totalDays)
           finalList[[iLM]]$Dates$end<-character(length=totalDays)
           attr(finalList[[iLM]]$Data,"dimensions") <- c("member","time","lat","lon")
+          attr(finalList[[iLM]],"LeadMonth") <- iLM-1
         }
         names(finalList)<-listNames
         allocatedOutputArray<-TRUE

SCRIPTS/tryReformat.R

@@ -3,19 +3,18 @@ rm(list=ls())
 source(file = "./functionReformat.R")
 source(file = "./functionR2Netcdf.R")
 
-iPath<-"/home/wietse/TODO/tttas/"
-
 initYears<-c(1981:1982)
-#initYears<-c(1981:2010)
+# initYears<-c(1981:2010)
 members<-c(1:2)
-#members<-c(1:15)
+# members<-c(1:15)
 
 varName<-"tas"
 locName<-"GHA"
 #locName<-"EU"
 initMonth<-1
 
-rData<-reformat2Bias(members, initYears, initMonth, varName, locName, iPath = iPath)
+iFile = paste0("/home/wietse/TODO/tttas/",varName,"_forcing_seas15_",locName, "_ref__E<MEMBERS>_<YEARS>_01.Rdata")
+rData <- reformat2Bias(members, initYears, initMonth, varName, locName, iFile = iFile)
 
-# outF<-("/home/wietse/TODO/SCRIPTS/fileTest2.nc4")
-# R2Netcdf(outF, rData$LeadMonth_1)
+outF<-("/home/wietse/TODO/SCRIPTS/test.nc4")
+R2Netcdf(outF, rData$LeadMonth_3)