Added a2nc fixes.

R/ArrayToNetCDF.R

+ArrayToNetCDF <- function(arrays, file_path) {
+  # Check parameter arrays.
+  if (is.array(arrays)) {
+    arrays <- list(arrays)
+  }
+  if (any(!sapply(arrays, function(x) is.array(x) && (is.numeric(x) || is.logical(x))))) {
+    stop("The parameter 'arrays' must be one or a list of numeric or logical arrays.")
+  }
+  # Check parameter file_path.
+  if (!is.character(file_path)) {
+    stop("Parameter 'file_path' must be a character string.")
+  }
+
+  defined_dims <- list()
+  defined_vars <- list()
+  global_attrs <- list()
+  var_dim <- NULL
+  for (i in 1:length(arrays)) {
+    array_attrs <- attributes(arrays[[i]])
+    if ('variables' %in% names(array_attrs)) {
+      vars_info <- array_attrs[['variables']]
+      array_attrs <- array_attrs[-which(names(array_attrs) == 'variables')]
+    } else {
+      vars_info <- NULL
+    }
+    global_attrs[names(array_attrs)] <- array_attrs
+    var_dim <- which(names(dim(arrays[[i]])) %in% c('var', 'variable'))
+    if (length(var_dim) > 0) {
+      var_dim <- var_dim[1]
+      num_vars <- dim(arrays[[i]])[var_dim]
+    } else {
+      var_dim <- NULL
+      num_vars <- 1
+    }
+    # Defining ncdf4 variable objects
+    for (j in 1:num_vars) {
+      var_info <- vars_info[[j]]
+      if (length(var_info) == 0) {
+        var_info <- list()
+      }
+      dim_names <- names(dim(arrays[[i]]))
+      if (!is.null(dim_names)) {
+        if (any(is.na(dim_names) | (sapply(dim_names, nchar) == 0))) {
+          stop("The provided arrays must have all named dimensions or ",
+               "all unnamed dimensions.")
+        }
+      }
+      provided_dims <- sapply(var_info$dim, '[[', 'name')
+      var_built_dims <- NULL
+      for (k in 1:length(dim(arrays[[i]]))) {
+        if (!identical(k, var_dim)) {
+          final_dim_position <- k - ifelse(!is.null(var_dim) && k > var_dim, 1, 0)
+          dim_name <- dim_names[k]
+          if (!is.null(dim_name) && (dim_name %in% provided_dims)) {
+            dim_info <- var_info$dim[[which(provided_dims == dim_name)]]
+          } else {
+            dim_info <- list()
+          }
+          if (!('name' %in% names(dim_info))) {
+            if (!is.null(dim_name)) {
+              dim_info[['name']] <- dim_name
+            } else {
+              dim_info[['name']] <- paste0('dim', final_dim_position)
+            }
+          } else {
+            if (!is.character(dim_info[['name']])) {
+              stop("The provided 'name' for the ", k, "th dimension in the ", i, "th array must be a character string.")
+            }
+            dim_info[['name']] <- dim_info[['name']][1]
+          }
+          if (!('len' %in% names(dim_info))) {
+            dim_info[['len']] <- unname(dim(arrays[[i]])[k])
+          } else {
+            if (!is.numeric(dim_info[['len']])) {
+              stop("The provided 'len' for the ", k, "th dimension in the ", i, "th array must be a numeric value.")
+            }
+            dim_info[['len']] <- as.integer(round(dim_info[['len']][1]))
+            if (dim_info[['len']] != dim(arrays[[i]])[k]) {
+              stop("The provided 'len' for the ", k, "th dimension in the ", i, "th array does not match the actual length of the provided array.")
+            }
+          }
+          if (!('unlim' %in% names(dim_info))) {
+            dim_info[['unlim']] <- ifelse(dim_info[['name']] == 'time', TRUE, FALSE)
+          } else {
+            if (!is.logical(dim_info[['unlim']])) {
+              stop("The provided 'unlim' for the ", k, "th dimension in the ", i, "th array must be a logical value.")
+            }
+            dim_info[['unlim']] <- dim_info[['unlim']][1]
+          }
+          if (!('units' %in% names(dim_info))) {
+            dim_info[['units']] <- ''
+          } else {
+            if (!is.character(dim_info[['units']])) {
+              stop("The provided 'units' for the ", k, "th dimension in the ", i, "th array must be a character string.")
+            }
+            dim_info[['units']] <- dim_info[['units']][1]
+          }
+          if (!('vals' %in% names(dim_info))) {
+            dim_info[['vals']] <- 1:dim_info[['len']]
+          } else {
+            if (!(is.numeric(dim_info[['vals']]))) {
+              stop("The provided 'vals' for the ", k, "th dimension in the ", i, "th array must be a numeric vector.")
+            }
+            if (dim_info[['units']] == '') {
+              dim_info[['vals']] <- as.integer(dim_info[['vals']])
+            }
+            if (length(dim_info[['vals']]) != dim_info[['len']]) {
+              stop("The length of the provided 'vals' for the ", k, "th dimension in the ", i, "th array does not match the length of the provided array.")
+            }
+          }
+          if (!('create_dimvar' %in% names(dim_info))) {
+            if (dim_info[['units']] == '') {
+              dim_info[['create_dimvar']] <- FALSE
+            } else {
+              dim_info[['create_dimvar']] <- TRUE
+            }
+          } else {
+            if (!is.logical(dim_info[['create_dimvar']])) {
+              stop("The provided 'create_dimvar' for the ", k, "th dimension in the ", i, "th array must be a logical value.")
+            }
+            dim_info[['create_dimvar']] <- dim_info[['create_dimvar']][1]
+            if (dim_info[['units']] != '' && !dim_info[['create_dimvar']]) {
+              stop("Provided 'units' for the ", k, "th dimension in the ", i, "th array but 'create_dimvar' set to FALSE.")
+            }
+          }
+          if (!('calendar' %in% names(dim_info))) {
+            dim_info[['calendar']] <- NA
+          } else {
+            if (!is.character(dim_info[['calendar']])) {
+              stop("The provided 'calendar' for the ", k, "th dimension in the ", i, "th array must be a character string.")
+            }
+            dim_info[['calendar']] <- dim_info[['calendar']][1]
+          }
+          if (!('longname' %in% names(dim_info))) {
+            dim_info[['longname']] <- dim_info[['name']]
+          } else {
+            if (!is.character(dim_info[['longname']])) {
+              stop("The provided 'longname' for the ", k, "th dimension in the ", i, "th array must be a character string.")
+            }
+            dim_info[['longname']] <- dim_info[['longname']][1]
+          }
+          if (dim_info[['name']] %in% names(defined_dims)) {
+            items_to_check <- c('name', 'len', 'unlim', 'units', 'vals',
+                                'create_dimvar', 'longname')
+            if (!identical(dim_info[items_to_check], 
+                           defined_dims[[dim_info[['name']]]][items_to_check]) ||
+                !(identical(dim_info[['calendar']], defined_dims[[dim_info[['name']]]][['calendar']]) || 
+                  (is.na(dim_info[['calendar']]) && is.null(defined_dims[[dim_info[['name']]]][['calendar']])))) {
+              stop("The dimension '", dim_info[['name']], "' is ",
+                   "defined or used more than once in the provided ",
+                   "data but the dimension specifications do not ",
+                   "match.")
+            }
+          } else {
+            new_dim <- list(ncdim_def(dim_info[['name']], dim_info[['units']], 
+                                      dim_info[['vals']], dim_info[['unlim']], 
+                                      dim_info[['create_dimvar']], 
+                                      dim_info[['calendar']], 
+                                      dim_info[['longname']]))
+            names(new_dim) <- dim_info[['name']]
+            defined_dims <- c(defined_dims, new_dim)
+          }
+          var_built_dims <- c(var_built_dims, dim_info[['name']])
+        }
+      }
+      if (!('name' %in% names(var_info))) {
+        var_name_from_md <- names(vars_info)[j]
+        var_name_from_ar <- names(arrays)[i]
+        if (is.character(var_name_from_md) && 
+            !is.na(var_name_from_md) &&
+            (nchar(var_name_from_md) > 0)) {
+          var_name <- var_name_from_md
+        } else if (is.character(var_name_from_ar) && 
+                   !is.na(var_name_from_ar) &&
+                   (nchar(var_name_from_ar) > 0)){
+          var_name <- var_name_from_ar
+        } else {
+          var_name <- paste0('var', i, '_', j)
+        }
+        var_info[['name']] <- var_name
+      } else {
+        if (!is.character(var_info[['name']])) {
+          stop("The provided 'name' for the ", j, "th variable in the ", i, "th array must be a character string.")
+        }
+        var_info[['name']] <- var_info[['name']][1]
+      }
+      if (!('units' %in% names(var_info))) {
+        var_info[['units']] <- ''
+      } else {
+        if (!is.character(var_info[['units']])) {
+          stop("The provided 'units' for the ", j, "th variable in the ", i, "th array must be a character string.")
+        }
+        var_info[['units']] <- var_info[['units']][1]
+      }
+      if (!('missval' %in% names(var_info))) {
+        var_info[['missval']] <- NULL
+      } else {
+        if (!is.numeric(var_info[['missval']])) {
+          stop("The provided 'missval' for the ", j, "th variable in the ", i, "th array must be a numeric value.")
+        }
+        var_info[['missval']] <- var_info[['missval']][1]
+      }
+      if (!('longname' %in% names(var_info))) {
+        var_info[['longname']] <- var_info[['name']]
+      } else {
+        if (!is.character(var_info[['longname']])) {
+          stop("The provided 'longname' for the ", j, "th variable in the ", i, "th array must be a character string.")
+        }
+        var_info[['longname']] <- var_info[['longname']][1]
+      }
+      if (!('prec' %in% names(var_info))) {
+        var_info[['prec']] <- 'float'
+      } else {
+        if (!is.character(var_info[['prec']])) {
+          stop("The provided 'prec' for the ", j, "th variable in the ", i, "th array must be a character string.")
+        }
+        var_info[['prec']] <- var_info[['prec']][1]
+      }
+      new_var <- list(ncvar_def(var_info[['name']], var_info[['units']], 
+                                defined_dims[var_built_dims], 
+                                var_info[['missval']], 
+                                var_info[['longname']], var_info[['prec']]))
+      names(new_var) <- var_info[['name']]
+      defined_vars <- c(defined_vars, new_var)
+    }
+  }
+  ncdf_object <- nc_create(file_path, defined_vars)
+  var_counter <- 1
+  # Putting the data and extra attributes.
+  for (i in 1:length(arrays)) {
+    array_attrs <- attributes(arrays[[i]])
+    if ('variables' %in% names(array_attrs)) {
+      vars_info <- array_attrs[['variables']]
+    } else {
+      vars_info <- NULL
+    }
+    var_dim <- which(names(dim(arrays[[i]])) %in% c('var', 'variable'))
+    if (length(var_dim) > 0) {
+      var_dim <- var_dim[1]
+      num_vars <- dim(arrays[[i]])[var_dim]
+    } else {
+      var_dim <- NULL
+      num_vars <- 1
+    }
+    for (j in 1:num_vars) {
+      var_info <- vars_info[[j]]
+      if (length(var_info) == 0) {
+        var_info <- list()
+      }
+      if (!('scaleFact' %in% names(var_info))) {
+        scale_factor <- 1
+      } else {
+        if (!is.numeric(var_info[['scaleFact']])) {
+          stop("The provided 'scaleFact' for the ", j, "th variable in the ", i, "th array must be a numeric value.")
+        }
+        scale_factor <- var_info[['scaleFact']][1]
+      }
+      if (!('addOffset' %in% names(var_info))) {
+        add_offset <- 0
+      } else {
+        if (!is.numeric(var_info[['addOffset']])) {
+          stop("The provided 'addOffset' for the ", j, "th variable in the ", i, "th array must be a numeric value.")
+        }
+        add_offset <- var_info[['addOffset']][1]
+      }
+      if (is.null(var_dim)) {
+        if (scale_factor != 1 || add_offset != 0) {
+          ncvar_put(ncdf_object, defined_vars[[var_counter]]$name, 
+                    (arrays[[i]] - add_offset) / scale_factor, 
+                    count = dim(arrays[[i]]))
+        } else {
+          ncvar_put(ncdf_object, defined_vars[[var_counter]]$name, 
+                    arrays[[i]], 
+                    count = dim(arrays[[i]]))
+        }
+      } else {
+        if (scale_factor != 1 || add_offset != 0) {
+          ncvar_put(ncdf_object, defined_vars[[var_counter]]$name, 
+                    (Subset(arrays[[i]], var_dim, j, drop = 'selected') - add_offset) / scale_factor, 
+                    count = dim(arrays[[i]])[-var_dim])
+        } else {
+          ncvar_put(ncdf_object, defined_vars[[var_counter]]$name, 
+                    Subset(arrays[[i]], var_dim, j, drop = 'selected'), 
+                    count = dim(arrays[[i]])[-var_dim])
+        }
+      }
+      if (scale_factor != 1 || add_offset != 0) {
+        ncatt_put(ncdf_object, defined_vars[[var_counter]]$name, 'scale_factor', scale_factor)
+        ncatt_put(ncdf_object, defined_vars[[var_counter]]$name, 'add_offset', add_offset)
+      }
+      if ('coordinates' %in% names(var_info)) {
+        if (!is.character(var_info[['coordinates']])) {
+          stop("The attribute 'coordinates' must be a character string.")
+        }
+        coords <- strsplit(var_info[['coordinates']], ' ')[[1]]
+        if (!(all(coords %in% sapply(defined_vars, '[[', 'name') | 
+                  coords %in% sapply(defined_dims[which(sapply(defined_dims, '[[', 'create_dimvar'))], '[[', 'name')))) {
+          coords <- coords[which(coords %in% sapply(defined_vars, '[[', 'name') |
+                                 coords %in% sapply(defined_dims[which(sapply(defined_dims, '[[', 'create_dimvar'))], '[[', 'name'))]
+          .warning("Some of the dimensions appearing in 'coordinates' have been removed because they point to undefined variables.")
+        }
+        ncatt_put(ncdf_object, defined_vars[[var_counter]]$name, 'coordinates', paste(coords, collapse = ' '))
+      }
+      attrs_to_skip <- which(names(var_info) %in% c('addOffset', 'scaleFact', 'coordinates', 'dim'))
+      attrs_to_add <- names(var_info)
+      if (length(attrs_to_skip) > 0) {
+        attrs_to_add <- attrs_to_add[-attrs_to_skip]
+      }
+      for (attribute_name in attrs_to_add) {
+        if (is.numeric(var_info[[attribute_name]]) ||
+            is.character(var_info[[attribute_name]])) {
+          ncatt_put(ncdf_object, defined_vars[[var_counter]]$name, attribute_name, var_info[[attribute_name]])
+        }
+      }
+      var_counter <- var_counter + 1
+    }
+  }
+  nc_close(ncdf_object)
+  invisible(NULL)
+}