-Improved handling of time in ncLoad and ncWrite

-added support for Yearly timestep in ncLoad
-added "z" dimension in ncLoad

NAMESPACE

 # Generated by roxygen2 (4.1.0): do not edit by hand
 
+export(makeMask)
 export(ncLoad)
 export(ncPlot)
+export(ncWrite)
 export(plotje)

R/WFRTools.R

@@ -16,7 +16,6 @@ plotje <-function(data, title = NULL) {
     }
   }
   
-  
   if (length(dim(data$Data)) > 2) {
     dataTmp<-data$Data[,,1]
     cat("Plotting first timestep\n")
@@ -33,8 +32,8 @@ plotje <-function(data, title = NULL) {
 #' @author Wietse Franssen \email{wietse.franssen@@wur.nl}
 #' @keywords internal
 #' @export
-ncPlot <-function(file, varName = NULL, lonlatbox = NULL, timesteps = NULL) {
-  data<-ncLoad(file, varName, lonlatbox, timesteps)
+ncPlot <-function(file, varName = NULL, lonlatbox = NULL, timesteps = NULL, z = NULL) {
+  data<-ncLoad(file, varName, lonlatbox, timesteps, z)
   plotje(data)
 }
 
@@ -84,6 +83,7 @@ ncCheck <-function(ncFile, variable) {
 #' @description Loads a NetCDF file as a R-data structure
 #' @param file Name of the NetCDF file
 #' @param varName Variable name of the NetCDF file
+#' @param timesteps "all", Nothing or array of Timesteps
 #' @details Loads a NetCDF file as a R-data structure.
 #' @details eg: data <- ncLoad("~/DATA/example.nc4", lonlatbox = c(-24.25,37.75,33.25,60.25), varName = "tasmin", timesteps = c(1:3))
 #' @details eg: ncPlot("~/DATA/example.nc4", lonlatbox = c(-24.25,37.75,33.25,60.25), varName = "tasmin", timesteps = c(1:3))
@@ -91,7 +91,7 @@ ncCheck <-function(ncFile, variable) {
 #' @author Wietse Franssen \email{wietse.franssen@@wur.nl}
 #' @keywords internal
 #' @export
-ncLoad <-function(file, varName = NULL, lonlatbox = NULL, timesteps = NULL) {
+ncLoad <-function(file, varName = NULL, lonlatbox = NULL, timesteps = NULL, z = NULL) {
   
   ## first build an empty data structure
   data<-rDataStructure()
@@ -124,10 +124,12 @@ ncLoad <-function(file, varName = NULL, lonlatbox = NULL, timesteps = NULL) {
                   "Given:   ", min(timesteps), " till ", max(timesteps), "\n",
                   "Allowed: NONE!"), call. = FALSE)
     }
-    if(min(timesteps) < 1 || max(timesteps) > ncFile$dim$time$len) {
-      stop(paste0("Timestep(s) out of range!\n",
-                  "Given:   ", min(timesteps), " till ", max(timesteps), "\n",
-                  "Allowed: 1 till ", ncFile$dim$time$len), call. = FALSE)
+    if(!timesteps[1] == "all") {
+      if(min(timesteps) < 1 || max(timesteps) > ncFile$dim$time$len) {
+        stop(paste0("Timestep(s) out of range!\n",
+                    "Given:   ", min(timesteps), " till ", max(timesteps), "\n",
+                    "Allowed: 1 till ", ncFile$dim$time$len), call. = FALSE)
+      }
     }
   }
   
@@ -148,8 +150,7 @@ ncLoad <-function(file, varName = NULL, lonlatbox = NULL, timesteps = NULL) {
                   "Allowed: ", minLat, " till ", maxLat), call. = FALSE)
     }
   }
-  
-  ## Fill lon, lat and time indexes
+  ## Fill lon and lat indexes
   if (is.null(lonlatbox)) { 
     LonIdx <- c(1: ncFile$dim$lon$len)
     LatIdx <- c(1: ncFile$dim$lat$len)
@@ -157,8 +158,12 @@ ncLoad <-function(file, varName = NULL, lonlatbox = NULL, timesteps = NULL) {
     LonIdx <- which( ncFile$dim$lon$vals >= lonlatbox[1] & ncFile$dim$lon$vals <= lonlatbox[2])
     LatIdx <- which( ncFile$dim$lat$vals >= lonlatbox[3] & ncFile$dim$lat$vals <= lonlatbox[4])
   }
+  
+  ## Fill time indexes
   if (is.null(timesteps)) {
     timeIdx<-c(1)
+  } else if (timesteps[1] == "all") {
+    timeIdx<-c(1:ncFile$dim$time$len)
   } else {
     timeIdx<-timesteps
   }
@@ -169,23 +174,29 @@ ncLoad <-function(file, varName = NULL, lonlatbox = NULL, timesteps = NULL) {
   
   ## Fill time
   if(!is.null(ncFile$dim$time)) {
-  NCtime          <- ncvar_get( ncFile, "time" ) [timeIdx]
-  #NCtime          <- ncvar_get( ncFile, "time" ) 
-  NCtimeAtt       <- ncatt_get( ncFile, "time", "units" )$value
-  firstTime<-unlist(strsplit(NCtimeAtt, split=' ', fixed=TRUE))[3]
-  firstTime<-strptime(firstTime, format = "%Y-%m-%d", tz = "GMT")
-  data$Dates$start <- format(firstTime + (86400 * (NCtime+0)), format="%Y-%m-%d %T %Z")
-  data$Dates$end   <- format(firstTime + (86400 * (NCtime+1)), format="%Y-%m-%d %T %Z")
+    NCtime          <- ncvar_get( ncFile, "time" ) [timeIdx]
+    NCtimeAtt       <- ncatt_get( ncFile, "time", "units" )$value
+    if (NCtimeAtt == "Years") {
+      data$Dates$start<-format(strptime(paste0(NCtime[],"-01-01"), format="%Y-%m-%d", tz = "GMT"), format="%Y-%m-%d %T %Z")
+      data$Dates$end<-format(strptime(paste0(NCtime[]+1,"-01-01"), format="%Y-%m-%d", tz = "GMT"), format="%Y-%m-%d %T %Z")
+    } else { ## if attributes is "days since..."
+      firstTime<-unlist(strsplit(NCtimeAtt, split=' ', fixed=TRUE))[3]
+      firstTime<-strptime(firstTime, format = "%Y-%m-%d", tz = "GMT")
+      data$Dates$start <- format(firstTime + (86400 * (NCtime+0)), format="%Y-%m-%d %T %Z")
+      data$Dates$end   <- format(firstTime + (86400 * (NCtime+1)), format="%Y-%m-%d %T %Z")
+    }
   }
   
   ## Fill data
-  #data <- ncvar_get( ncFile, "pr")[ LonIdx, LatIdx, 1]
-  if(!is.null(ncFile$dim$time)) {
-    data$Data <- ncvar_get( ncFile, varName ) [ LonIdx, LatIdx, timeIdx]
+  if(is.null(z)) {
+    if(!is.null(ncFile$dim$time)) {
+      data$Data <- ncvar_get( ncFile, varName, start=c(LonIdx[1],LatIdx[1],timeIdx[1]),count=c(length(LonIdx),length(LatIdx),length(timeIdx)))
+    } else {
+      data$Data <- ncvar_get( ncFile, varName, start=c(LonIdx[1],LatIdx[1]),count=c(length(LonIdx),length(LatIdx)))
+    } 
   } else {
-    data$Data <- ncvar_get( ncFile, varName ) [ LonIdx, LatIdx]
+    data$Data <- ncvar_get( ncFile, varName, start=c(LonIdx[1],LatIdx[1],z,timeIdx[1]),count=c(length(LonIdx),length(LatIdx),1,length(timeIdx)))
   }
-  #data$Data <- ncvar_get( ncFile, varName ) 
   attr(data$Data,"dimensions") <- ncCheckResult$dims
   data$Variable$varName  <- varName
   
@@ -216,15 +227,84 @@ ncLoad <-function(file, varName = NULL, lonlatbox = NULL, timesteps = NULL) {
   return(data)
 }
 
+#' ncLoad
+#' @description Loads a NetCDF file as a R-data structure
+#' @param file Name of the NetCDF file
+#' @param varName Variable name of the NetCDF file
+#' @details Loads a NetCDF file as a R-data structure.
+#' @return An object of class \code{WF}
+#' @author Wietse Franssen \email{wietse.franssen@@wur.nl}
+#' @keywords internal
+#' @export
+makeMask <-function(data) {
+  
+  ## first build an empty data structure
+  mask<-rDataStructure()
+  
+  ## lon and lats
+  mask$xyCoords$x<-data$xyCoords$x
+  mask$xyCoords$y<-data$xyCoords$y
+  ## Maskout
+  if (length(dim(data$Data)) > 2 ) {
+    mask$Data<-data$Data[,,1]
+  } else {
+    mask$Data<-data$Data    
+  }
+  mask$Data[!is.na(mask$Data)] <- 1
+  naCells<-sum(is.na( mask$Data ))
+  naValid<-sum(!is.na( mask$Data ))
+  total<-naCells+naValid
+  cat(paste0("mask succesfully made!\n") )
+  cat(paste0("valid values: ", naValid, "\n" ) )
+  cat(paste0("NA values:    ", naCells, "\n" ) )
+  cat(paste0("Total:        ", total, "\n" ) )
+  return(mask)  
+}
 
-
-
-
-
-
-
-
-
+#' ncWrite
+#' @description Write a R-data structure to a NetCDF file
+#' @param file Name of the NetCDF file
+#' @param varName Variable name of the NetCDF file
+#' @details Loads a NetCDF file as a R-data structure.
+#' @details eg: data <- ncLoad("~/DATA/example.nc4", lonlatbox = c(-24.25,37.75,33.25,60.25), varName = "tasmin", timesteps = c(1:3))
+#' @details eg: ncPlot("~/DATA/example.nc4", lonlatbox = c(-24.25,37.75,33.25,60.25), varName = "tasmin", timesteps = c(1:3))
+#' @return An object of class \code{WF}
+#' @author Wietse Franssen \email{wietse.franssen@@wur.nl}
+#' @keywords internal
+#' @export
+ncWrite <-function(outFile = "~/out.nc", rData = data) {
+  timeString<-format(strptime(rData$Dates$start, format = "%Y-%m-%d", tz = "GMT"),format="%Y-%m-%d %T")
+  #timeArray<-as.double(c(0:(length(rData$Dates$start)-1)))
+  timeArray<-as.numeric(difftime(timeString,timeString[1],units="days"))
+  dimT <- ncdim_def("time", paste0("days since ",timeString[1]), timeArray, unlim = FALSE)
+  dimX <- ncdim_def("lon", "degrees_east", round(rData$xyCoords$x,2))
+  dimY <- ncdim_def("lat", "degrees_north",round(rData$xyCoords$y,2))
+  
+  FillValue <- NA
+  FillValue <- 1e20
+  
+  datavar <- ncvar_def( rData$Variable$varName, rData$Variable$units, list(dimX,dimY,dimT), FillValue, prec="float")
+  ncid_out <- nc_create(outFile, datavar)
+  
+  ## ADD ATTRIBUTES
+  ncatt_put( ncid_out, 0, "institution", "Wageningen University and Research centre (WUR)")
+  ncatt_put( ncid_out, 0, "contact", "Wietse Franssen <wietse.franssen@wur.nl>")
+  
+  ncatt_put( ncid_out, "lon", "standard_name", "longitude")
+  ncatt_put( ncid_out, "lon", "long_name",     "Longitude")
+  ncatt_put( ncid_out, "lon", "axis",          "X")
+  ncatt_put( ncid_out, "lat", "standard_name", "latitude")
+  ncatt_put( ncid_out, "lat", "long_name",     "Latitude")
+  ncatt_put( ncid_out, "lat", "axis",          "Y")
+  ncatt_put( ncid_out, "time", "standard_name", "time")
+  ncatt_put( ncid_out, "time", "calendar",     "standard")
+  ncatt_put( ncid_out, rData$Variable$varName, "long_name", rData$Variable$longName)
+  ncatt_put( ncid_out, rData$Variable$varName, "_FillValue", FillValue)
+  
+  ncvar_put( ncid_out, datavar, rData$Data )
+  
+  nc_close(ncid_out)
+}
 
 # rm(list=ls())
 # library(ncdf4)

man/makeMask.Rd

+% Generated by roxygen2 (4.1.0): do not edit by hand
+% Please edit documentation in R/WFRTools.R
+\name{makeMask}
+\alias{makeMask}
+\title{ncLoad}
+\usage{
+makeMask(data)
+}
+\arguments{
+\item{file}{Name of the NetCDF file}
+
+\item{varName}{Variable name of the NetCDF file}
+}
+\value{
+An object of class \code{WF}
+}
+\description{
+Loads a NetCDF file as a R-data structure
+}
+\details{
+Loads a NetCDF file as a R-data structure.
+}
+\author{
+Wietse Franssen \email{wietse.franssen@wur.nl}
+}
+\keyword{internal}
+

man/ncLoad.Rd

@@ -10,6 +10,8 @@ ncLoad(file, varName = NULL, lonlatbox = NULL, timesteps = NULL)
 \item{file}{Name of the NetCDF file}
 
 \item{varName}{Variable name of the NetCDF file}
+
+\item{timesteps}{"all", Nothing or array of Timesteps}
 }
 \value{
 An object of class \code{WF}

man/ncWrite.Rd

+% Generated by roxygen2 (4.1.0): do not edit by hand
+% Please edit documentation in R/WFRTools.R
+\name{ncWrite}
+\alias{ncWrite}
+\title{ncWrite}
+\usage{
+ncWrite(outFile = "~/out.nc", rData = data)
+}
+\arguments{
+\item{file}{Name of the NetCDF file}
+
+\item{varName}{Variable name of the NetCDF file}
+}
+\value{
+An object of class \code{WF}
+}
+\description{
+Write a R-data structure to a NetCDF file
+}
+\details{
+Loads a NetCDF file as a R-data structure.
+}
+\author{
+Wietse Franssen \email{wietse.franssen@wur.nl}
+}
+\keyword{internal}
+

man/plotje.Rd

@@ -4,7 +4,7 @@
 \alias{plotje}
 \title{Plot a simple map}
 \usage{
-plotje(data, title = " ")
+plotje(data, title = NULL)
 }
 \description{
 Plot a simple map