Move internal dataInventory.NetCDF to separate file

SantanderMetGroup · Jun 15, 2020 · 87ff16a · 87ff16a
1 parent 245c635
commit 87ff16a
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diff --git a/R/dataInventory.NetCDF.R b/R/dataInventory.NetCDF.R
@@ -0,0 +1,52 @@
+#' @title Inventory of a gridded dataset
+#' @description Returns a list with summary information about the variables stored in a gridded dataset.
+#' Sub-routine of \code{dataInventory}
+#' @param dataset A full path to the file describing the dataset (NcML)
+#' @return A (named) list whose length is determined by the number of variables stored in the dataset,
+#' its names corresponding to the short names of the variables.
+#' For each variable, information on the variable long name, data type, units, data size (in Mb) and
+#' characteristics of its dimensions is provided.
+#' @author J. Bedia 
+#' @keywords internal
+#' @importFrom rJava J
+
+
+dataInventory.NetCDF <- function(dataset) {
+    gds <- J("ucar.nc2.dt.grid.GridDataset")$open(dataset)
+    varNames <- unlist(strsplit(gsub("\\[|]|\\s", "", gds$getGrids()$toString()), ","))
+    rm.ind <- grep("^lon|^lat", varNames)  
+    if (length(rm.ind) > 0) {
+        varNames <- varNames[-rm.ind]
+    }
+    if (length(varNames) == 0) {
+        stop("No variables found", call. = FALSE)
+    } else {
+        var.list <- vector(mode = "list", length = length(varNames))   
+        for (i in 1:length(varNames)) {
+            message("[", Sys.time(), "] Retrieving info for \'", varNames[i], "\' (", length(varNames) - i, " vars remaining)")
+            datavar <- gds$getDataVariable(varNames[i])
+            description <- datavar$getDescription()
+            varName <- datavar$getShortName()
+            version <- tryCatch({trimws(datavar$findAttribute("version")$getValues()$toString())}, error = function(e){NA})
+            dataType <- datavar$getDataType()$toString()
+            element.size <- datavar$getDataType()$getSize()
+            data.number <- datavar$getSize()
+            dataSize <- element.size * data.number * 1e-06
+            units <- datavar$getUnitsString()
+            shape <- datavar$getShape()
+            grid <- gds$findGridByShortName(varName)
+            dim.list <- scanVarDimensions(grid)
+            var.list[[i]] <- list("Description" = description,
+                                  "DataType" = dataType,
+                                  "Shape" = shape,
+                                  "Units" = units,
+                                  "DataSizeMb" = dataSize,
+                                  "Version" = version,
+                                  "Dimensions" = dim.list)
+        }
+        names(var.list) <- varNames
+    }
+    gds$close()
+    return(var.list)
+}
+# End
diff --git a/R/dataInventory.R b/R/dataInventory.R
@@ -183,59 +183,6 @@ dataInventory.ASCII <- function(dataset, rs) {
 # End
 
 
-#' @title Inventory of a gridded dataset
-#' @description Returns a list with summary information about the variables stored in a gridded dataset.
-#' Sub-routine of \code{dataInventory}
-#' @param dataset A full path to the file describing the dataset (NcML)
-#' @return A (named) list whose length is determined by the number of variables stored in the dataset,
-#' its names corresponding to the short names of the variables.
-#' For each variable, information on the variable long name, data type, units, data size (in Mb) and
-#' characteristics of its dimensions is provided.
-#' @author J. Bedia 
-#' @keywords internal
-#' @importFrom rJava J
-
-
-dataInventory.NetCDF <- function(dataset) {
-   gds <- J("ucar.nc2.dt.grid.GridDataset")$open(dataset)
-   varNames <- unlist(strsplit(gsub("\\[|]|\\s", "", gds$getGrids()$toString()), ","))
-   rm.ind <- grep("^lon|^lat", varNames)  
-   if (length(rm.ind) > 0) {
-      varNames <- varNames[-rm.ind]
-   }
-   if (length(varNames) == 0) {
-      stop("No variables found", call. = FALSE)
-   } else {
-      var.list <- vector(mode = "list", length = length(varNames))   
-      for (i in 1:length(varNames)) {
-         message("[", Sys.time(), "] Retrieving info for \'", varNames[i], "\' (", length(varNames) - i, " vars remaining)")
-         datavar <- gds$getDataVariable(varNames[i])
-         description <- datavar$getDescription()
-         varName <- datavar$getShortName()
-         version <- tryCatch({trimws(datavar$findAttribute("version")$getValues()$toString())}, error = function(e){NA})
-         dataType <- datavar$getDataType()$toString()
-         element.size <- datavar$getDataType()$getSize()
-         data.number <- datavar$getSize()
-         dataSize <- element.size * data.number * 1e-06
-         units <- datavar$getUnitsString()
-         shape <- datavar$getShape()
-         grid <- gds$findGridByShortName(varName)
-         dim.list <- scanVarDimensions(grid)
-         var.list[[i]] <- list("Description" = description,
-                               "DataType" = dataType,
-                               "Shape" = shape,
-                               "Units" = units,
-                               "DataSizeMb" = dataSize,
-                               "Version" = version,
-                               "Dimensions" = dim.list)
-      }
-      names(var.list) <- varNames
-   }
-   gds$close()
-   return(var.list)
-}
-# End
-
 #' @title Inventory of a Time Series dataset
 #' @description Returns a list with summary information about the variables stored in a time series dataset.
 #' Sub-routine of \code{dataInventory}