Newer
Older
NetCDFToArray <- function(file_to_read, vars_to_read, inner_indices,
drop_var_dim = FALSE, unlist = TRUE) {
file_opener <- NcOpen
file_closer <- NcClose
file_dim_reader <- NetCDFReadDims
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$filename
} else {
stop("Either the path to a NetCDF file or a ncdf object must be provided as 'file_to_read'.")
}
# Check var_names
if (is.character(vars_to_read) || is.numeric(vars_to_read)) {
vars_to_read <- list(vars_to_read)
}
print_error <- FALSE
if (is.list(vars_to_read)) {
if (!all(sapply(vars_to_read, function(x) is.character(x) || is.numeric(x)))) {
print_error <- TRUE
}
} else {
print_error <- TRUE
}
if (print_error) {
stop("Parameter 'vars_to_read' must be one or a list of numeric vectors or vectors of character strings or NULL.")
# if (!is.character(var_names) && !is.numeric(var_names)) {
# stop("Parameter 'var_names' must be a numeric vector or vector of character strings.")
# }
result_list <- NULL
for (vars_to_read_vector in vars_to_read) {
result <- NULL
if (!is.null(file_object)) {
# Create all variables that are 'dimvars'
extra_dimvars <- NULL
extra_dimvars_list <- NULL
for (dim_name in names(file_object$dim)) {
if (file_object$dim[[dim_name]]$create_dimvar) {
new_var <- list(name = dim_name, ndims = 1,
size = file_object$dim[[dim_name]]$len,
units = file_object$dim[[dim_name]]$units,
dim = list(file_object$dim[[dim_name]]))
new_var_extra_atts <- ncatt_get(file_object, dim_name)
new_var[names(new_var_extra_atts)] <- new_var_extra_atts
extra_dimvars_list <- c(extra_dimvars_list, setNames(list(new_var), dim_name))
extra_dimvars <- c(extra_dimvars, dim_name)
}
}
#file_object$var[extra_dimvars] <- extra_dimvars_list
#file_object$nvars <- file_object$nvars + length(extra_dimvars)
nmv <- numeric_var_indices <- which(is.numeric(vars_to_read_vector))
if (length(nmv) > 0) {
if (any(vars_to_read_vector[nmv] > (length(file_object$var) + length(extra_dimvars)))) {
stop("Provided numerical variable indices out of bounds in 'vars_to_read'.")
}
vars_to_read_vector[nmv] <- c(sapply(file_object$var, '[[', 'name'), extra_dimvars)[vars_to_read_vector[nmv]]
}
for (var_name in vars_to_read_vector) {
66
67
68
69
70
71
72
73
74
75
76
77
78
79
80
81
82
83
84
85
86
87
88
89
90
91
92
93
94
95
96
97
98
99
100
101
102
103
104
105
106
107
108
109
110
111
112
113
if (var_name %in% extra_dimvars) {
var_result <- file_object$dim[[var_name]]$vals
#atts <- file_object$dim[[var_name]]
atts <- extra_dimvars_list[[var_name]]
atts_to_remove <- c('vals', 'name', 'len', 'group_index',
'group_id', 'id', 'dimvarid', 'create_dimvar')
if (any(names(atts) %in% atts_to_remove)) {
atts <- atts[-which(names(atts) %in% atts_to_remove)]
}
units <- file_object$dim[[var_name]]$units
names(dim(var_result)) <- sapply(extra_dimvars_list[[var_name]]$dim, '[[', 'name')
} else {
if (!(var_name %in% names(file_object$var))) {
stop("Could not find the variable '", var_name, "' in the file.")
}
try({
var_result <- ncvar_get(file_object, var_name)
}, silent = TRUE)
atts <- file_object$var[[var_name]]
atts_to_remove <- c('id', 'name', 'ndims', 'natts', 'size',
'dimids', 'group_index', 'chunksizes',
'storage', 'shuffle', 'compression', 'dims',
'varsize', 'longname')
if (any(names(atts) %in% atts_to_remove)) {
atts <- atts[-which(names(atts) %in% atts_to_remove)]
}
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')
}
if (units %in% c('seconds', 'minutes', 'hours', 'days', 'weeks', 'months', 'years')) {
if (units == 'seconds') {
units <- 'secs'
} else if (units == 'minutes') {
units <- 'mins'
}
var_result[] <- paste(var_result, units)
} else if (grepl(' since ', units)) {
parts <- strsplit(units, ' since ')[[1]]
units <- parts[1]
if (units == 'seconds') {
units <- 'secs'
} else if (units == 'minutes') {
units <- 'mins'
}
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))
}
attr(var_result, 'variables') <- structure(list(atts), .Names = var_name)
## TODO: Take the general attributes out of atts and put them as
## global attributes.
if (is.null(result)) {
result <- var_result
} else {
new_attrs <- c(attr(result, 'variables'),
attr(var_result, 'variables'))
result <- .MergeArrays(result, var_result, 'var')
attr(result, 'variables') <- new_attrs
}
}
}
if (is.null(result_list)) {
if (length(vars_to_read) == 1 && unlist) {
result_list <- result
} else {
if (length(vars_to_read_vector) == 1) {
result_list <- structure(list(result), .Names = vars_to_read_vector)
} else {
result_list <- list(result)
}
}
} else {
if (length(vars_to_read_vector) == 1) {
result_list <- do.call('[[<-', list(x = result_list,
i = vars_to_read_vector,
value = result))
} else {
result_list <- do.call('[[<-', list(x = result_list,
i = length(result_list) + 1,
value = result))
}
}
}
if (close) {
file_closer(file_object)
}
result_list
156
157
158
159
160
161
162
163
164
165
166
167
168
169
170
171
172
173
174
175
176
177
178
179
180
181
182
183
184
185
186
187
188
189
190
191
192
193
194
195
196
197
198
199
200
201
202
203
204
205
206
207
208
209
210
211
212
213
214
215
216
217
218
219
220
221
222
223
224
225
226
227
228
229
230
231
232
233
234
235
236
237
238
239
240
241
242
243
244
245
246
247
248
249
250
251
252
253
254
255
256
257
258
259
260
261
262
263
264
265
266
267
268
269
270
271
272
273
274
275
276
277
278
279
280
281
282
283
284
285
286
287
288
289
290
291
292
293
294
295
296
297
298
299
300
301
302
303
304
305
306
307
308
309
310
311
312
313
314
315
316
317
318
319
320
321
322
323
324
325
326
327
328
329
330
331
332
333
334
335
336
337
338
}
# Parameter 'file_selectos' expects a named character vector of single
# file dimension selectors.
# Parameter 'inner_selectors' expects a named list of numeric vectors.
.NcDataReader <- function(file_path = NULL, file_object = NULL,
file_selectors = NULL, inner_indices,
file_opener = NULL, file_closer = NULL) {
file_dim_reader <- .NcDimReader
#print("aa")
close <- FALSE
if (is.null(file_object)) {
if (is.null(file_path)) {
stop("Either 'file_path' or 'file_object' must be provided.")
}
if (is.null(file_opener) || is.null(file_closer)) {
stop("Both 'file_opener' and 'file_closer' must be provided if ",
"no 'file_object' is directly provided.")
} else if (!is.function(file_opener) || !is.function(file_closer)) {
stop("Parameters 'file_opener' and 'file_closer' must be functions.")
}
file_object <- file_opener(file_path)
close <- !is.null(file_object)
} else {
file_path <- file_object$filename
}
result <- NULL
if (!is.null(file_object)) {
var_names <- NULL
var_dim_name <- NULL
if (any(c('var', 'variable') %in% c(names(file_selectors), names(inner_indices)))) {
var_dim_name <- c('var', 'variable')[which(c('var', 'variable') %in% c(names(file_selectors), names(inner_indices)))]
if (var_dim_name %in% names(file_selectors)) {
if (is.character(file_selectors[[var_dim_name]])) {
var_names <- file_selectors[[var_dim_name]]
}
} else if (var_dim_name %in% names(inner_indices)) {
var_names <- names(file_object$var)
if (is.character(inner_indices[[var_dim_name]])) {
var_names <- inner_indices[[var_dim_name]][which(inner_indices[[var_dim_name]] %in% var_names)]
} else if (is.numeric(inner_indices[[var_dim_name]])) {
if (any(inner_indices[[var_dim_name]] > length(var_names)) ||
any(inner_indices[[var_dim_name]] < 0)) {
stop("Selectors out of range for '", var_dim_name, "'.")
}
var_names <- var_names[inner_indices[[var_dim_name]]]
} else {
stop("Selectors for '", var_dim_name, "' must be numeric or ",
"character strings.")
}
}
}
if (is.null(var_names)) {
if (length(file_object$var) == 1) {
var_names <- names(file_object$var)[1]
} else {
stop(paste0("Could not disambiguate which variable in the file ",
"is being requested. Either provide the parameter ",
"'var'/'variable' or force the file to contain only ",
"one variable.\n", file_path))
}
}
result <- try({
res <- NULL
metadata <- NULL
dims <- file_dim_reader(file_path, file_object, file_selectors,
inner_indices)
#print("bb")
if (!all(names(inner_indices) %in% names(dims))) {
stop("Missing dimensions in the file.\nExpected: ",
paste(names(inner_indices), collapse = ', '), "\n",
"Found: ", paste(names(dims), collapse = ', '), "\n",
file_path)
}
extra_dims <- NULL
if (length(dims) > length(inner_indices)) {
common_dims <- which(names(dims) %in% names(inner_indices))
if (length(common_dims) > 0) {
extra_dims <- dims[-common_dims]
} else {
extra_dims <- dims
}
if (any(extra_dims != 1)) {
stop("Unexpected extra dimensions (of length > 1) in the file.\nExpected: ",
paste(names(inner_indices), collapse = ', '), "\n",
"Found: ", paste(names(dims), collapse = ', '), "\n",
file_path)
} else {
inner_indices[names(extra_dims)] <- rep(1, length(extra_dims))
}
extra_dims <- names(extra_dims)
}
any_empty_selectors <- FALSE
# Here we are allowing for indices out of range (simply discarding them).
for (inner_dim in names(inner_indices)) {
inds_out_of_range <- which(inner_indices[[inner_dim]] > dims[inner_dim])
if (length(inds_out_of_range) > 0) {
inner_indices[[inner_dim]] <- inner_indices[[inner_dim]][-which(inner_indices[[inner_dim]] > dims[inner_dim])]
}
if (length(inner_indices[[inner_dim]]) == 0) {
any_empty_selectors <- TRUE
}
if (any(inner_indices[[inner_dim]] < 0)) {
stop("Invalid indices provided for '", inner_dim, "'.")
}
}
if (!any_empty_selectors) {
missing_dims <- NULL
if (length(dims) < length(inner_indices)) {
missing_dim_names <- names(inner_indices)[-which(names(inner_indices) %in% names(dims))]
missing_dim_indices <- lapply(missing_dim_names, function(x) inner_indices[[x]])
if (any(!sapply(missing_dim_indices, identical, 1))) {
stop("Could not find all expected dimensions in the file.\nExpected: ",
paste(names(inner_indices), collapse = ', '), "\n",
"Found: ", paste(names(dims), collapse = ', '), "\n",
file_path)
} else {
original_dims <- sapply(inner_indices, length)
names(original_dims) <- names(inner_indices)
inner_indices <- inner_indices[-which(names(inner_indices) %in% missing_dim_names)]
}
missing_dims <- missing_dim_names
}
#print("cc")
inner_dims <- names(inner_indices)
reorder <- NULL
if (any(names(dims) != inner_dims)) {
reorder <- sapply(names(dims), function(x) which(inner_dims == x))
reorder_back <- sapply(inner_dims, function(x) which(names(dims) == x))
inner_indices <- inner_indices[reorder]
}
if (!is.null(var_dim_name) && (var_dim_name %in% names(inner_indices))) {
inner_indices <- inner_indices[-which(names(inner_indices) == var_dim_name)]
}
for (var_name in var_names) {
tmp <- do.call('[', c(list(ncvar_get(file_object, var_name, sapply(inner_indices, min),
sapply(inner_indices, max) - sapply(inner_indices, min) + 1,
collapse_degen = FALSE)),
lapply(inner_indices, function(x) x - min(x) + 1), list(drop = FALSE)))
if (!is.null(var_dim_name) && (var_dim_name %in% inner_dims)) {
dim(tmp) <- c(dim(tmp)[which(1:length(dim(tmp)) < which(inner_dims == var_dim_name))], 1,
dim(tmp)[which(1:length(dim(tmp)) >= which(inner_dims == var_dim_name))])
if (is.null(res)) {
res <- tmp
} else {
res <- abind(res, tmp, along = which(inner_dims == var_dim_name))
}
} else {
res <- tmp
}
metadata <- c(metadata, structure(list(file_object$var[[var_name]]), .Names = var_name))
}
if (!is.null(reorder)) {
res <- aperm(res, reorder_back)
}
if (!is.null(missing_dims)) {
dim(res) <- original_dims
}
if (!is.null(extra_dims)) {
dim(res) <- dim(res)[-which(inner_dims %in% extra_dims)]
}
attr(res, 'variables') <- metadata
names(dim(res)) <- inner_dims
## TODO: Take the common parts in metadata and put them as
## global attributes.
}
#print("dd")
res
})
if ('try-error' %in% class(result)) {
result <- NULL
}
}
if (close) {
file_closer(file_object)
}
result
}
nc2a <- NetCDFToArray