Fixes.

R/ArrayToNc.R

-ArrayToNetCDF <- function(arrays, file_path) {
+ArrayToNc <- function(arrays, file_path) {
   # Check parameter arrays.
   if (is.array(arrays)) {
     arrays <- list(arrays)

R/NcReadVarNames.R

+NcReadVarNames <- function(file_to_read) {
+  file_opener <- nc_open
+  file_closer <- nc_close
+  close <- FALSE
+  if (is.character(file_to_read)) {
+    file_object <- file_opener(file_to_read)
+    file_path <- file_to_read
+    close <- TRUE
+  } else if (grepl('^ncdf', class(file_to_read))) {
+    file_object <- file_to_read
+    file_path <- file_object$filename
+  } else {
+    stop("Either the path to a NetCDF file or a ncdf object must be provided as 'file_to_read'.")
+  }
+
+  var_names <- names(file_object$var)
+  if (!is.null(file_object)) {
+    extra_dimvars <- NULL
+    # Create all variables that are 'dimvars'
+    for (dim_name in names(file_object$dim)) {
+      if (file_object$dim[[dim_name]]$create_dimvar) {
+        extra_dimvars <- c(extra_dimvars, dim_name)
+      }
+    }
+    var_names <- c(var_names, extra_dimvars)
+  }
+
+  var_names
+}

R/NcToArray.R

@@ -17,30 +17,37 @@ NcToArray <- function(file_to_read, dim_indices = NULL, vars_to_read = NULL,
     stop("Either the path to a NetCDF file or a ncdf object must be provided as 'file_to_read'.")
   }
 
+  var_tag <- 'var'
   # Check dim_indices
+  if (length(dim_indices) == 0) {
+    dim_indices <- NULL
+  }
   if (!is.null(dim_indices)) {
     if (!is.list(dim_indices)) {
       stop("Parameter 'dim_indices' must be a list of numeric vectors.")
     }
     if (is.null(names(dim_indices))) {
-      stop("Parameter 'dim_indices' must have dimension names.")
+      stop("Parameter 'dim_indices' must have dimension names as names.")
     }
     var_indices_position <- NULL
-    for (i in 1:length(dim_indices)) {
+    i <- 1
+    while (i <= length(dim_indices)) {
       if (names(dim_indices)[i] %in% c('var', 'variable')) {
         vars_to_read <- dim_indices[[i]]
         var_indices_position <- i
+        var_tag <- names(dim_indices)[i]
       } else {
         if (!(names(dim_indices)[i] %in% names(file_object$dim))) {
           stop("Provided indices in 'dim_indices' for a non-existing dimension.")
         }
-        if (!is.numeric(dim_indices[[i]])) {
-          stop("Parameter 'dim_indices' must be a list of numeric vectors.")
+        if (!(is.numeric(dim_indices[[i]]) || is.logical(dim_indices[[i]]))) {
+          stop("Parameter 'dim_indices' must be a list of numeric vectors, TRUE or NA.")
         }
       }
       if (identical(dim_indices[[i]], TRUE)) {
         dim_indices[[i]] <- NA
       }
+      i <- i + 1
     }
     if (!is.null(var_indices_position)) {
       dim_indices <- dim_indices[-var_indices_position]
@@ -134,6 +141,9 @@ NcToArray <- function(file_to_read, dim_indices = NULL, vars_to_read = NULL,
           common_dims <- which(names(found_dims) %in% names(dim_indices))
           if (length(common_dims) > 0) {
             extra_dims <- found_dims[-common_dims]
+            if (length(extra_dims) == 0) {
+              extra_dims <- NULL
+            }
           } else {
             extra_dims <- found_dims
           }
@@ -190,12 +200,12 @@ NcToArray <- function(file_to_read, dim_indices = NULL, vars_to_read = NULL,
             #  }
             #  missing_dims <- missing_dim_names
             #}
-            inner_dims <- names(indices_to_take)
-            reorder <- NULL
-            if (any(names(found_dims) != inner_dims)) {
-              reorder <- sapply(names(found_dims), function(x) which(inner_dims == x))
-              reorder_back <- sapply(inner_dims, function(x) which(names(found_dims) == x))
-              indices_to_take <- indices_to_take[reorder]
+            indices_dims <- names(dim_indices)[which(names(dim_indices) %in% names(found_dims))]
+            reorder_back <- NULL
+            if (any(names(found_dims) != indices_dims)) {
+              #reorder <- sapply(names(found_dims), function(x) which(indices_dims == x))
+              reorder_back <- sapply(indices_dims, function(x) which(names(found_dims) == x))
+              #indices_to_take <- indices_to_take[reorder]
             }
             start <- sapply(indices_to_take, function(x) if (is_single_na(x)) 1 else min(x))
             count <- sapply(indices_to_take, function(x) if (is_single_na(x)) -1 else max(x) - min(x) + 1)
@@ -203,17 +213,17 @@ NcToArray <- function(file_to_read, dim_indices = NULL, vars_to_read = NULL,
                                          lapply(indices_to_take, function(x) if (is_single_na(x)) TRUE else x - min(x) + 1), list(drop = FALSE)))
             #metadata <- c(metadata, structure(list(file_object$var[[var_name]]), .Names = var_name))
             ## TODO: Crop dimensions in attributes
-            if (!is.null(reorder)) {
+            if (!is.null(reorder_back)) {
               var_result <- aperm(var_result, reorder_back)
             }
             #if (!is.null(missing_dims)) {
             #  dim(var_result) <- original_dims
             #}
             if (!is.null(extra_dims)) {
-              dim(var_result) <- dim(var_result)[-which(inner_dims %in% extra_dims)]
+              dim(var_result) <- dim(var_result)[-which(indices_dims %in% extra_dims)]
             }
             #attr(var_result, 'variables') <- metadata
-            names(dim(var_result)) <- inner_dims
+            names(dim(var_result)) <- indices_dims
           }
           atts <- file_object$var[[var_name]]
           atts_to_remove <- c('id', 'name', 'ndims', 'natts', 'size', 
@@ -226,7 +236,7 @@ NcToArray <- function(file_to_read, dim_indices = NULL, vars_to_read = NULL,
           extra_atts <- ncatt_get(file_object, var_name)
           atts[names(extra_atts)] <- extra_atts
           units <- file_object$var[[var_name]]$units
-          names(dim(var_result)) <- sapply(file_object$var[[var_name]]$dim, '[[', 'name')
+          #names(dim(var_result)) <- sapply(file_object$var[[var_name]]$dim, '[[', 'name')
         }
         if (!is.null(var_result)) {
 #          if (units %in% c('seconds', 'minutes', 'hours', 'days', 'weeks', 'months', 'years')) {
@@ -247,7 +257,7 @@ NcToArray <- function(file_to_read, dim_indices = NULL, vars_to_read = NULL,
 #            var_result <- seq(as.POSIXct(parts[2]), length = max(var_result, na.rm = TRUE) + 1, by = units)[var_result + 1]
 #          }
           if (!drop_var_dim && (length(vars_to_read_vector) == 1)) {
-            dim(var_result) <- c(c(var = 1), dim(var_result))
+            dim(var_result) <- c(setNames(1, var_tag), dim(var_result))
           }
           attr(var_result, 'variables') <- structure(list(atts), .Names = var_name)
           ## TODO: Take the general attributes out of atts and put them as
@@ -257,7 +267,7 @@ NcToArray <- function(file_to_read, dim_indices = NULL, vars_to_read = NULL,
           } else {
             new_attrs <- c(attr(result, 'variables'), 
                            attr(var_result, 'variables'))
-            result <- .MergeArrays(result, var_result, 'var')
+            result <- .MergeArrays(result, var_result, var_tag)
             attr(result, 'variables') <- new_attrs
           }
         }