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picked_common_vars[[var_to_read]] <- new_array
pick_ordered <- FALSE
if (var_to_read %in% unlist(var_params)) {
if (associated_dim_name %in% names(dim_reorder_params) && !aiat) {
picked_common_vars_ordered[[var_to_read]] <- new_array
pick_ordered <- TRUE
}
}
if (!pick_ordered) {
picked_common_vars_ordered[[var_to_read]] <- NULL
}
} else {
picked_vars[[i]][[var_to_read]] <- new_array
pick_ordered <- FALSE
if (var_to_read %in% unlist(var_params)) {
if (associated_dim_name %in% names(dim_reorder_params) && !aiat) {
picked_vars_ordered[[i]][[var_to_read]] <- new_array
pick_ordered <- TRUE
}
}
if (!pick_ordered) {
picked_vars_ordered[[i]][[var_to_read]] <- NULL
}
}
} else {
if (var_to_read %in% names(common_return_vars)) {
array_var_dims <- dim(picked_common_vars[[var_to_read]])
} else {
array_var_dims <- dim(picked_vars[[i]][[var_to_read]])
}
full_array_var_dims <- array_var_dims
if (any(names(array_var_dims) %in% names(var_file_dims))) {
array_var_dims <- array_var_dims[-which(names(array_var_dims) %in% names(var_file_dims))]
}
if (names(array_var_dims) != names(var_dims)) {
stop("Error while reading the variable '", var_to_read, "' from ",
"the file. Dimensions do not match.\nExpected ",
paste(paste0("'", names(array_var_dims), "'"),
collapse = ', '), " but found ",
paste(paste0("'", names(var_dims), "'"),
collapse = ', '), ".\n", array_of_var_files[j])
}
if (any(var_dims > array_var_dims)) {
longer_dims <- which(var_dims > array_var_dims)
if (length(longer_dims) == 1) {
longer_dims_in_full_array <- longer_dims
if (any(names(full_array_var_dims) %in% names(var_file_dims))) {
candidates <- (1:length(full_array_var_dims))[-which(names(full_array_var_dims) %in% names(var_file_dims))]
longer_dims_in_full_array <- candidates[longer_dims]
}
padding_dims <- full_array_var_dims
padding_dims[longer_dims_in_full_array] <- var_dims[longer_dims] -
array_var_dims[longer_dims]
special_types <- list('POSIXct' = as.POSIXct, 'POSIXlt' = as.POSIXlt,
'Date' = as.Date)
if (var_to_read %in% names(common_return_vars)) {
var_class <- class(picked_common_vars[[var_to_read]])
} else {
var_class <- class(picked_vars[[i]][[var_to_read]])
}
if (any(var_class %in% names(special_types))) {
padding_size <- prod(padding_dims)
padding <- rep(special_types[[var_class[1]]](NA), padding_size)
dim(padding) <- padding_dims
} else {
padding <- array(dim = padding_dims)
}
if (var_to_read %in% names(common_return_vars)) {
picked_common_vars[[var_to_read]] <- .abind2(
picked_common_vars[[var_to_read]],
padding,
names(full_array_var_dims)[longer_dims_in_full_array]
)
} else {
picked_vars[[i]][[var_to_read]] <- .abind2(
picked_vars[[i]][[var_to_read]],
padding,
names(full_array_var_dims)[longer_dims_in_full_array]
)
}
} else {
stop("Error while reading the variable '", var_to_read, "' from ",
"the file. Found size (", paste(var_dims, collapse = ' x '),
") is greater than expected maximum size (",
array_var_dims, ").")
}
}
}
var_store_indices <- c(as.list(current_indices[names(var_file_dims)]), lapply(var_dims, function(x) 1:x))
var_values <- file_var_reader(NULL, file_object, NULL, var_to_read, synonims)
if (var_to_read %in% unlist(var_params)) {
if ((associated_dim_name %in% names(dim_reorder_params)) && !aiat) {
## Is this check really needed?
if (length(dim(var_values)) > 1) {
stop("Requested a '", associated_dim_name, "_reorder' for a dimension ",
"whose coordinate variable that has more than 1 dimension. This is ",
"not supported.")
}
ordered_var_values <- dim_reorder_params[[associated_dim_name]](var_values)
attr(ordered_var_values$x, 'variables') <- attr(var_values, 'variables')
if (!all(c('x', 'ix') %in% names(ordered_var_values))) {
stop("All the dimension reorder functions must return a list with the components 'x' and 'ix'.")
}
# Save the indices to reorder back the ordered variable values.
# This will be used to define the first round indices.
unorder <- sort(ordered_var_values$ix, index.return = TRUE)$ix
if (var_to_read %in% names(common_return_vars)) {
picked_common_vars_ordered[[var_to_read]] <- do.call('[<-',
c(list(x = picked_common_vars_ordered[[var_to_read]]),
var_store_indices,
list(value = ordered_var_values$x)))
picked_common_vars_unorder_indices[[var_to_read]] <- do.call('[<-',
c(list(x = picked_common_vars_unorder_indices[[var_to_read]]),
var_store_indices,
list(value = unorder)))
} else {
picked_vars_ordered[[i]][[var_to_read]] <- do.call('[<-',
c(list(x = picked_vars_ordered[[i]][[var_to_read]]),
var_store_indices,
list(value = ordered_var_values$x)))
picked_vars_unorder_indices[[i]][[var_to_read]] <- do.call('[<-',
c(list(x = picked_vars_unorder_indices[[i]][[var_to_read]]),
var_store_indices,
list(value = unorder)))
}
}
}
if (var_to_read %in% names(common_return_vars)) {
picked_common_vars[[var_to_read]] <- do.call('[<-',
c(list(x = picked_common_vars[[var_to_read]]),
var_store_indices,
list(value = var_values)))
# Turn time zone back to UTC if this var_to_read is 'time'
if (all(class(picked_common_vars[[var_to_read]]) == c('POSIXct', 'POSIXt'))) {
attr(picked_common_vars[[var_to_read]], "tzone") <- 'UTC'
}
} else {
picked_vars[[i]][[var_to_read]] <- do.call('[<-',
c(list(x = picked_vars[[i]][[var_to_read]]),
var_store_indices,
list(value = var_values)))
# Turn time zone back to UTC if this var_to_read is 'time'
if (all(class(picked_vars[[i]][[var_to_read]]) == c('POSIXct', 'POSIXt'))) {
attr(picked_vars[[i]][[var_to_read]], "tzone") <- 'UTC'
}
}
if (var_to_read %in% names(first_found_file)) {
first_found_file[var_to_read] <- TRUE
}
if (var_to_read %in% names(common_first_found_file)) {
common_first_found_file[var_to_read] <- TRUE
}
} else {
stop("Could not find variable '", var_to_read,
"' in the file ", array_of_var_files[j])
}
}
file_closer(file_object)
}
}
previous_indices <- current_indices
}
}
}
# Once we have the variable values, we can work out the indices
# for the implicitly defined selectors.
#
# Trnasforms a vector of indices v expressed in a world of
# length N from 1 to N, into a world of length M, from
# 1 to M. Repeated adjacent indices are collapsed.
transform_indices <- function(v, n, m) {
#unique2 turns e.g. 1 1 2 2 2 3 3 1 1 1 into 1 2 3 1
unique2 <- function(v) {
if (length(v) < 2) {
v
} else {
v[c(1, v[2:length(v)] - v[1:(length(v) - 1)]) != 0]
}
}
unique2(round(((v - 1) / (n - 1)) * (m - 1))) + 1 # this rounding may generate 0s. what then?
}
beta <- transform_extra_cells
dims_to_crop <- vector('list')
transformed_vars <- vector('list', length = length(dat))
names(transformed_vars) <- dat_names
transformed_vars_ordered <- transformed_vars
transformed_vars_unorder_indices <- transformed_vars
transformed_common_vars <- NULL
transformed_common_vars_ordered <- NULL
transformed_common_vars_unorder_indices <- NULL
for (i in 1:length(dat)) {
if (dataset_has_files[i]) {
indices <- indices_of_first_files_with_data[[i]]
if (!is.null(indices)) {
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if (largest_dims_length == FALSE | is.numeric(largest_dims_length)) { #old code. use the 1st valid file to determine the dims
file_path <- do.call("[", c(list(array_of_files_to_load), as.list(indices_of_first_files_with_data[[i]])))
# The following 5 lines should go several lines below, but were moved
# here for better performance.
# If any of the dimensions comes without defining variable, then we read
# the data dimensions.
data_dims <- NULL
if (length(unlist(var_params[expected_inner_dims[[i]]])) < length(expected_inner_dims[[i]])) {
file_to_open <- file_path
data_dims <- file_dim_reader(file_to_open, NULL, selectors_of_first_files_with_data[[i]],
lapply(dat[[i]][['selectors']][expected_inner_dims[[i]]], '[[', 1),
synonims)
# file_dim_reader returns dimension names as found in the file.
# Need to translate accoridng to synonims:
names(data_dims) <- sapply(names(data_dims),
function(x) {
which_entry <- which(sapply(synonims, function(y) x %in% y))
if (length(which_entry) > 0) {
names(synonims)[which_entry]
} else {
x
}
})
}
if (is.numeric(largest_dims_length)) { # largest_dims_length is a named vector
# Check if the names fit the inner dimension names
if (!all(names(largest_dims_length) %in% names(data_dims))) {
#NOTE: stop or warning?
stop("Parameter 'largest_dims_length' has inconsistent names with inner dimensions.")
} else {
match_ind <- match(names(largest_dims_length), names(data_dims))
data_dims[match_ind] <- largest_dims_length
}
}
} else { # largest_dims_length == TRUE
# Open and get all the dim from all the files
data_dims_all_files <- vector('list', length = length(selectors_total_list[[i]]))
for (selectors_kk in 1:length(data_dims_all_files)) {
file_path <- do.call("[", c(list(array_of_files_to_load), as.list(selector_indices_save[[i]][[selectors_kk]])))
file_to_open <- file_path
data_dims_all_files[[selectors_kk]] <- try(file_dim_reader(file_to_open, NULL, selectors_total_list[[i]][[selectors_kk]],
lapply(dat[[i]][['selectors']][expected_inner_dims[[i]]], '[[', 1),
synonims), silent = TRUE)
# Remove the missing files (i.e., fail try above)
if (!identical(which(substr(data_dims_all_files, 1, 5) == 'Error'), integer(0))) {
tmp <- which(substr(data_dims_all_files, 1, 5) == 'Error')
data_dims_all_files <- data_dims_all_files[-tmp]
}
# Find the longest dimensions from all the files
largest_data_dims <- rep(0, length(data_dims_all_files[[1]]))
# The inner dim order may differ among files. Need to align them before
# find out the largest dim length.
dim_names_first_file <- names(data_dims_all_files[[1]])
same_dim_order <-lapply(lapply(data_dims_all_files, names),
identical, dim_names_first_file)
for (to_fix in which(!unlist(same_dim_order))) {
data_dims_all_files[[to_fix]] <- data_dims_all_files[[to_fix]][match(dim_names_first_file,
names(data_dims_all_files[[to_fix]]))]
}
for (kk in 1:length(data_dims_all_files[[1]])) {
largest_data_dims[kk] <- max(sapply(data_dims_all_files, '[', kk))
}
names(largest_data_dims) <- names(data_dims_all_files[[1]])
# file_dim_reader returns dimension names as found in the file.
# Need to translate accoridng to synonims:
names(largest_data_dims) <- sapply(names(largest_data_dims),
function(x) {
which_entry <- which(sapply(synonims, function(y) x %in% y))
if (length(which_entry) > 0) {
names(synonims)[which_entry]
} else {
x
}
})
# replace data_dims with largest_data_dims
data_dims <- largest_data_dims
} # end of if (largest_dims_length == TRUE)
# Transform the variables if needed and keep them apart.
if (!is.null(transform) && (length(transform_vars) > 0)) {
if (!all(transform_vars %in% c(names(picked_vars[[i]]), names(picked_common_vars)))) {
stop("Could not find all the required variables in 'transform_vars' ",
"for the dataset '", dat[[i]][['name']], "'.")
}
vars_to_transform <- NULL
picked_vars_to_transform <- which(names(picked_vars[[i]]) %in% transform_vars)
if (length(picked_vars_to_transform) > 0) {
picked_vars_to_transform <- names(picked_vars[[i]])[picked_vars_to_transform]
new_vars_to_transform <- picked_vars[[i]][picked_vars_to_transform]
which_are_ordered <- which(!sapply(picked_vars_ordered[[i]][picked_vars_to_transform], is.null))
##NOTE: The following 'if' replaces the original with reordering vector
if (length(which_are_ordered) > 0) {
tmp <- which(!is.na(match(names(picked_vars_ordered[[i]]), names(which_are_ordered))))
new_vars_to_transform[which_are_ordered] <- picked_vars_ordered[[i]][tmp]
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}
vars_to_transform <- c(vars_to_transform, new_vars_to_transform)
}
##NOTE: Above is non-common vars, here is common vars (ie, return_vars = NULL).
picked_common_vars_to_transform <- which(names(picked_common_vars) %in% transform_vars)
if (length(picked_common_vars_to_transform) > 0) {
picked_common_vars_to_transform <- names(picked_common_vars)[picked_common_vars_to_transform]
new_vars_to_transform <- picked_common_vars[picked_common_vars_to_transform]
which_are_ordered <- which(!sapply(picked_common_vars_ordered[picked_common_vars_to_transform], is.null))
if (length(which_are_ordered) > 0) {
tmp <- which(!is.na(match(names(picked_common_vars_ordered), names(which_are_ordered))))
new_vars_to_transform[which_are_ordered] <- picked_common_vars_ordered[tmp]
}
vars_to_transform <- c(vars_to_transform, new_vars_to_transform)
}
# Transform the variables
transformed_data <- do.call(transform, c(list(data_array = NULL,
variables = vars_to_transform,
file_selectors = selectors_of_first_files_with_data[[i]]),
transform_params))
# Discard the common transformed variables if already transformed before
if (!is.null(transformed_common_vars)) {
common_ones <- which(names(picked_common_vars) %in% names(transformed_data$variables))
if (length(common_ones) > 0) {
transformed_data$variables <- transformed_data$variables[-common_ones]
}
}
transformed_vars[[i]] <- list()
transformed_vars_ordered[[i]] <- list()
transformed_vars_unorder_indices[[i]] <- list()
# Order the transformed variables if needed
# 'var_to_read' should be 'transformed_var', but is kept to reuse the same code as above.
for (var_to_read in names(transformed_data$variables)) {
if (var_to_read %in% unlist(var_params)) {
associated_dim_name <- names(var_params)[which(unlist(var_params) == var_to_read)]
if ((associated_dim_name %in% names(dim_reorder_params)) && aiat) {
## Is this check really needed?
if (length(dim(transformed_data$variables[[associated_dim_name]])) > 1) {
stop("Requested a '", associated_dim_name, "_reorder' for a dimension ",
"whose coordinate variable that has more than 1 dimension (after ",
"transform). This is not supported.")
}
ordered_var_values <- dim_reorder_params[[associated_dim_name]](transformed_data$variables[[associated_dim_name]])
attr(ordered_var_values, 'variables') <- attr(transformed_data$variables[[associated_dim_name]], 'variables')
if (!all(c('x', 'ix') %in% names(ordered_var_values))) {
stop("All the dimension reorder functions must return a list with the components 'x' and 'ix'.")
}
# Save the indices to reorder back the ordered variable values.
# This will be used to define the first round indices.
unorder <- sort(ordered_var_values$ix, index.return = TRUE)$ix
if (var_to_read %in% names(picked_common_vars)) {
transformed_common_vars_ordered[[var_to_read]] <- ordered_var_values$x
transformed_common_vars_unorder_indices[[var_to_read]] <- unorder
} else {
transformed_vars_ordered[[i]][[var_to_read]] <- ordered_var_values$x
transformed_vars_unorder_indices[[i]][[var_to_read]] <- unorder
}
}
}
}
transformed_picked_vars <- which(names(picked_vars[[i]]) %in% names(transformed_data$variables))
if (length(transformed_picked_vars) > 0) {
transformed_picked_vars <- names(picked_vars[[i]])[transformed_picked_vars]
transformed_vars[[i]][transformed_picked_vars] <- transformed_data$variables[transformed_picked_vars]
}
if (is.null(transformed_common_vars)) {
transformed_picked_common_vars <- which(names(picked_common_vars) %in% names(transformed_data$variables))
if (length(transformed_picked_common_vars) > 0) {
transformed_picked_common_vars <- names(picked_common_vars)[transformed_picked_common_vars]
transformed_common_vars <- transformed_data$variables[transformed_picked_common_vars]
}
}
}
# Once the variables are transformed, we compute the indices to be
# taken for each inner dimension.
# In all cases, indices will have to be computed to know which data
# values to take from the original data for each dimension (if a
# variable is specified for that dimension, it will be used to
# convert the provided selectors into indices). These indices are
# referred to as 'first round of indices'.
# The taken data will then be transformed if needed, together with
# the dimension variable if specified, and, in that case, indices
# will have to be computed again to know which values to take from the
# transformed data. These are the 'second round of indices'. In the
# case there is no transformation, the second round of indices will
# be all the available indices, i.e. from 1 to the number of taken
# values with the first round of indices.
for (inner_dim in expected_inner_dims[[i]]) {
if (debug) {
print("-> DEFINING INDICES FOR INNER DIMENSION:")
print(inner_dim)
}
file_dim <- NULL
if (inner_dim %in% unlist(inner_dims_across_files)) {
file_dim <- names(inner_dims_across_files)[which(sapply(inner_dims_across_files, function(x) inner_dim %in% x))[1]]
chunk_amount <- length(dat[[i]][['selectors']][[file_dim]][[1]])
names(chunk_amount) <- file_dim
} else {
chunk_amount <- 1
}
# In the special case that the selectors for a dimension are 'all', 'first', ...
# and chunking (dividing in more than 1 chunk) is requested, the selectors are
# replaced for equivalent indices.
if ((any(dat[[i]][['selectors']][[inner_dim]][[1]] %in% c('all', 'first', 'last'))) &&
(chunks[[inner_dim]]['n_chunks'] != 1)) {
selectors <- dat[[i]][['selectors']][[inner_dim]][[1]]
if (selectors == 'all') {
selectors <- indices(1:(data_dims[[inner_dim]] * chunk_amount))
} else if (selectors == 'first') {
selectors <- indices(1)
} else {
selectors <- indices(data_dims[[inner_dim]] * chunk_amount)
}
dat[[i]][['selectors']][[inner_dim]][[1]] <- selectors
}
# The selectors for the inner dimension are taken.
selector_array <- dat[[i]][['selectors']][[inner_dim]][[1]]
if (debug) {
if (inner_dim %in% dims_to_check) {
print(paste0("-> DEBUG MESSAGES FOR THE DATASET", i, " AND INNER DIMENSION '", inner_dim, "':"))
print("-> STRUCTURE OF SELECTOR ARRAY:")
print(str(selector_array))
print("-> PICKED VARS:")
print(picked_vars)
print("-> TRANSFORMED VARS:")
print(transformed_vars)
}
}
if (is.null(dim(selector_array))) {
dim(selector_array) <- length(selector_array)
}
if (is.null(names(dim(selector_array)))) {
if (length(dim(selector_array)) == 1) {
names(dim(selector_array)) <- inner_dim
} else {
stop("Provided selector arrays must be provided with dimension ",
"names. Found an array of selectors without dimension names ",
"for the dimension '", inner_dim, "'.")
}
}
selectors_are_indices <- FALSE
if (!is.null(attr(selector_array, 'indices'))) {
if (!is.logical(attr(selector_array, 'indices'))) {
stop("The atribute 'indices' for the selectors for the dimension '",
inner_dim, "' must be TRUE or FALSE.")
}
selectors_are_indices <- attr(selector_array, 'indices')
}
taken_chunks <- rep(FALSE, chunk_amount)
selector_file_dims <- 1
#NOTE: Change 'selector_file_dims' (from 1) if selector is an array with a file_dim dimname.
# I.e., If time = [sdate = 2, time = 4], selector_file_dims <- array(sdate = 2)
if (any(found_file_dims[[i]] %in% names(dim(selector_array)))) {
selector_file_dims <- dim(selector_array)[which(names(dim(selector_array)) %in% found_file_dims[[i]])]
}
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selector_inner_dims <- dim(selector_array)[which(!(names(dim(selector_array)) %in% found_file_dims[[i]]))]
var_with_selectors <- NULL
var_with_selectors_name <- var_params[[inner_dim]]
var_ordered <- NULL
var_unorder_indices <- NULL
with_transform <- FALSE
# If the selectors come with an associated variable
if (!is.null(var_with_selectors_name)) {
if ((var_with_selectors_name %in% transform_vars) && (!is.null(transform))) {
with_transform <- TRUE
if (!is.null(file_dim)) {
stop("Requested a transformation over the dimension '",
inner_dim, "', wich goes across files. This feature ",
"is not supported. Either do the request without the ",
"transformation or request it over dimensions that do ",
"not go across files.")
}
}
if (debug) {
if (inner_dim %in% dims_to_check) {
print("-> NAME OF THE VARIABLE WITH THE SELECTOR VALUES FOR THE CURRENT INNER DIMENSION:")
print(var_with_selectors_name)
print("-> NAMES OF THE VARIABLES TO BE TRANSFORMED:")
print(transform_vars)
print("-> STRUCTURE OF THE TRANSFORMATION FUNCTION:")
print(str(transform))
}
}
if (var_with_selectors_name %in% names(picked_vars[[i]])) {
var_with_selectors <- picked_vars[[i]][[var_with_selectors_name]]
var_ordered <- picked_vars_ordered[[i]][[var_with_selectors_name]]
var_unorder_indices <- picked_vars_unorder_indices[[i]][[var_with_selectors_name]]
} else if (var_with_selectors_name %in% names(picked_common_vars)) {
var_with_selectors <- picked_common_vars[[var_with_selectors_name]]
var_ordered <- picked_common_vars_ordered[[var_with_selectors_name]]
var_unorder_indices <- picked_common_vars_unorder_indices[[var_with_selectors_name]]
}
n <- prod(dim(var_with_selectors))
if (is.null(var_unorder_indices)) {
var_unorder_indices <- 1:n
}
if (with_transform) {
if (var_with_selectors_name %in% names(transformed_vars[[i]])) {
m <- prod(dim(transformed_vars[[i]][[var_with_selectors_name]]))
if (aiat) {
var_with_selectors <- transformed_vars[[i]][[var_with_selectors_name]]
var_ordered <- transformed_vars_ordered[[i]][[var_with_selectors_name]]
var_unorder_indices <- transformed_vars_unorder_indices[[i]][[var_with_selectors_name]]
}
} else if (var_with_selectors_name %in% names(transformed_common_vars)) {
m <- prod(dim(transformed_common_vars[[var_with_selectors_name]]))
if (aiat) {
var_with_selectors <- transformed_common_vars[[var_with_selectors_name]]
var_ordered <- transformed_common_vars_ordered[[var_with_selectors_name]]
var_unorder_indices <- transformed_common_vars_unorder_indices[[var_with_selectors_name]]
}
}
if (is.null(var_unorder_indices)) {
var_unorder_indices <- 1:m
}
}
if (debug) {
if (inner_dim %in% dims_to_check) {
print("-> SIZE OF ORIGINAL VARIABLE:")
print(n)
print("-> SIZE OF TRANSFORMED VARIABLE:")
if (with_transform) print(m)
print("-> STRUCTURE OF ORDERED VAR:")
print(str(var_ordered))
print("-> UNORDER INDICES:")
print(var_unorder_indices)
}
}
var_dims <- dim(var_with_selectors)
var_file_dims <- 1
if (any(names(var_dims) %in% found_file_dims[[i]])) {
if (with_transform) {
stop("Requested transformation for inner dimension '",
inner_dim, "' but provided selectors for such dimension ",
"over one or more file dimensions. This is not ",
"supported. Either request no transformation for the ",
"dimension '", inner_dim, "' or specify the ",
"selectors for this dimension without the file dimensions.")
}
var_file_dims <- var_dims[which(names(var_dims) %in% found_file_dims[[i]])]
var_dims <- var_dims[-which(names(var_dims) %in% found_file_dims[[i]])]
}
## # Keep the selectors if they correspond to a variable that will be transformed.
## if (with_transform) {
## if (var_with_selectors_name %in% names(picked_vars[[i]])) {
## transformed_var_with_selectors <- transformed_vars[[i]][[var_with_selectors_name]]
## } else if (var_with_selectors_name %in% names(picked_common_vars)) {
## transformed_var_with_selectors <- transformed_common_vars[[var_with_selectors_name]]
## }
## transformed_var_dims <- dim(transformed_var_with_selectors)
## transformed_var_file_dims <- 1
## if (any(names(transformed_var_dims) %in% found_file_dims[[i]])) {
## transformed_var_file_dims <- transformed_var_dims[which(names(transformed_var_dims) %in% found_file_dims[[i]])]
## transformed_var_dims <- tranasformed_var_dims[-which(names(transformed_var_dims) %in% found_file_dims[[i]])]
## }
##if (inner_dim %in% dims_to_check) {
##print("111m")
##print(str(transformed_var_dims))
##}
##
## m <- prod(transformed_var_dims)
## }
# Work out var file dims and inner dims.
if (inner_dim %in% unlist(inner_dims_across_files)) {
#TODO: if (chunk_amount != number of chunks in selector_file_dims), crash
if (length(var_dims) > 1) {
stop("Specified a '", inner_dim, "_var' for the dimension '",
inner_dim, "', which goes across files (across '", file_dim,
"'). The specified variable, '", var_with_selectors_name, "', has more ",
"than one dimension and can not be used as selector variable. ",
"Select another variable or fix it in the files.")
}
}
## TODO HERE::
#- indices_of_first_files_with_data may change, because array is now extended
var_full_dims <- dim(var_with_selectors)
if (!(inner_dim %in% names(var_full_dims))) {
stop("Could not find the dimension '", inner_dim, "' in ",
"the file. Either change the dimension name in ",
"your request, adjust the parameter ",
"'dim_names_in_files' or fix the dimension name in ",
"the file.\n", file_path)
}
} else if (((is.numeric(selector_array) || is.list(selector_array)) && selectors_are_indices) ||
(is.character(selector_array) && (length(selector_array) == 1) &&
(selector_array %in% c('all', 'first', 'last')) &&
!is.null(file_dim_reader))) {
#### TODO HERE::
###- indices_of_first_files_with_data may change, because array is now extended
# Lines moved above for better performance.
##data_dims <- file_dim_reader(file_path, NULL, selectors_of_first_files_with_data[[i]],
## lapply(dat[[i]][['selectors']][expected_inner_dims[[i]]], '[[', 1))
if (!(inner_dim %in% names(data_dims))) {
stop("Could not find the dimension '", inner_dim, "' in ",
"the file. Either change the dimension name in ",
"your request, adjust the parameter ",
"'dim_names_in_files' or fix the dimension name in ",
"the file.\n", file_path)
}
} else {
stop(paste0("Can not translate the provided selectors for '", inner_dim,
"' to numeric indices. Provide numeric indices and a ",
"'file_dim_reader' function, or a '", inner_dim,
"_var' in order to calculate the indices."))
}
# At this point, if no selector variable was provided, the variable
# data_dims has been populated. If a selector variable was provided,
# the variables var_dims, var_file_dims and var_full_dims have been
# populated instead.
fri <- first_round_indices <- NULL
sri <- second_round_indices <- NULL
# This variable will keep the indices needed to crop the transformed
# variable (the one that has been transformed without being subset
# with the first round indices).
tvi <- tranaformed_variable_indices <- NULL
ordered_fri <- NULL
ordered_sri <- NULL
if ((length(selector_array) == 1) && is.character(selector_array) &&
(selector_array %in% c('all', 'first', 'last')) &&
(chunks[[inner_dim]]['n_chunks'] == 1)) {
if (is.null(var_with_selectors_name)) {
fri <- vector('list', length = chunk_amount)
dim(fri) <- c(chunk_amount)
sri <- vector('list', length = chunk_amount)
dim(sri) <- c(chunk_amount)
if (selector_array == 'all') {
fri[] <- replicate(chunk_amount, list(1:(data_dims[inner_dim])))
taken_chunks <- rep(TRUE, chunk_amount)
#sri <- NULL
} else if (selector_array == 'first') {
fri[[1]] <- 1
taken_chunks[1] <- TRUE
#sri <- NULL
} else if (selector_array == 'last') {
fri[[chunk_amount]] <- data_dims[inner_dim]
taken_chunks[length(taken_chunks)] <- TRUE
#sri <- NULL
}
} else {
if ((!is.null(file_dim)) && !(file_dim %in% names(var_file_dims))) {
stop("The variable '", var_with_selectors_name, "' must also be ",
"requested for the file dimension '", file_dim, "' in ",
"this configuration.")
}
fri <- vector('list', length = prod(var_file_dims))
dim(fri) <- var_file_dims
ordered_fri <- fri
sri <- vector('list', length = prod(var_file_dims))
dim(sri) <- var_file_dims
ordered_sri <- sri
if (selector_array == 'all') {
# TODO: Populate ordered_fri
ordered_fri[] <- replicate(prod(var_file_dims), list(1:n))
fri[] <- replicate(prod(var_file_dims), list(var_unorder_indices[1:n]))
taken_chunks <- rep(TRUE, chunk_amount)
if (!with_transform) {
#fri[] <- replicate(prod(var_file_dims), list(1:n))
#taken_chunks <- rep(TRUE, chunk_amount)
#sri <- NULL
} else {
ordered_sri[] <- replicate(prod(var_file_dims), list(1:m))
sri[] <- replicate(prod(var_file_dims), list(1:m))
## var_file_dims instead??
#if (!aiat) {
#fri[] <- replicate(prod(var_file_dims), list(1:n))
#taken_chunks <- rep(TRUE, chunk_amount)
#sri[] <- replicate(prod(transformed_var_file_dims), list(1:m))
#} else {
#fri[] <- replicate(prod(var_file_dims), list(1:n))
#taken_chunks <- rep(TRUE, chunk_amount)
#sri[] <- replicate(prod(transformed_var_file_dims), list(1:m))
#}
tvi <- 1:m
}
} else if (selector_array == 'first') {
taken_chunks[1] <- TRUE
if (!with_transform) {
ordered_fri[[1]] <- 1
fri[[1]] <- var_unorder_indices[1]
#taken_chunks[1] <- TRUE
#sri <- NULL
} else {
if (!aiat) {
ordered_fri[[1]] <- 1
fri[[1]] <- var_unorder_indices[1]
# TODO: TO BE IMPROVED
#taken_chunks[1] <- TRUE
ordered_sri[[1]] <- 1:ceiling(m / n)
sri[[1]] <- 1:ceiling(m / n)
tvi <- 1:ceiling(m / n)
} else {
ordered_fri[[1]] <- 1:ceiling(m / n)
fri[[1]] <- var_unorder_indices[1:ceiling(m / n)]
#taken_chunks[1] <- TRUE
ordered_sri[[1]] <- 1
sri[[1]] <- 1
tvi <- 1
}
}
} else if (selector_array == 'last') {
taken_chunks[length(taken_chunks)] <- TRUE
if (!with_transform) {
ordered_fri[[prod(var_file_dims)]] <- n
fri[[prod(var_file_dims)]] <- var_unorder_indices[n]
#taken_chunks[length(taken_chunks)] <- TRUE
#sri <- NULL
} else {
if (!aiat) {
ordered_fri[[prod(var_file_dims)]] <- prod(var_dims)
fri[[prod(var_file_dims)]] <- var_unorder_indices[prod(var_dims)]
#taken_chunks[length(taken_chunks)] <- TRUE
ordered_sri[[prod(var_file_dims)]] <- 1:ceiling(m / n)
sri[[prod(var_file_dims)]] <- 1:ceiling(m / n)
# TODO: TO BE IMPROVED. THE TVI MAY BE WRONG IF THERE'S BEEN A REORDERING.
tvi <- 1:ceiling(m / n)
} else {
ordered_fri[[prod(var_file_dims)]] <- (n - ceiling(m / n) + 1):n
fri[[prod(var_file_dims)]] <- var_unorder_indices[(n - ceiling(m / n) + 1):n]
#taken_chunks[length(taken_chunks)] <- TRUE
ordered_sri[[prod(var_file_dims)]] <- 1
sri[[prod(var_file_dims)]] <- 1
tvi <- 1
}
}
}
}
# If the selectors are not 'all', 'first', 'last', ...
} else {
if (!is.null(var_with_selectors_name)) {
unmatching_file_dims <- which(!(names(var_file_dims) %in% names(selector_file_dims)))
if ((length(unmatching_file_dims) > 0)) {
raise_error <- FALSE
if (is.null(file_dim)) {
raise_error <- TRUE
} else {
if (!((length(unmatching_file_dims) == 1) &&
(names(var_file_dims)[unmatching_file_dims] == file_dim) &&
(inner_dim %in% names(selector_inner_dims)))) {
raise_error <- TRUE
}
}
if (raise_error) {
stop("Provided selectors for the dimension '", inner_dim, "' must have as many ",
"file dimensions as the variable the dimension is defined along, '",
var_with_selectors_name, "', with the exceptions of the file pattern dimension ('",
found_pattern_dim, "') and any depended file dimension (if specified as ",
"depended dimension in parameter 'inner_dims_across_files' and the ",
"depending file dimension is present in the provided selector array).")
}
}
if (any(names(selector_file_dims) %in% names(dim(var_with_selectors)))) {
if (any(dim(var_with_selectors)[names(selector_file_dims)] != selector_file_dims)) {
stop("Size of selector file dimensions must mach size of requested ",
"variable dimensions.")
}
}
}
## TODO: If var dimensions are not in the same order as selector dimensions, reorder
if (is.null(names(selector_file_dims))) {
if (is.null(file_dim)) {
fri_dims <- 1
} else {
fri_dims <- chunk_amount
names(fri_dims) <- file_dim
}
} else {
fri_dim_names <- names(selector_file_dims)
if (!is.null(file_dim)) {
fri_dim_names <- c(fri_dim_names, file_dim)
}
fri_dim_names <- found_file_dims[[i]][which(found_file_dims[[i]] %in% fri_dim_names)]
fri_dims <- rep(NA, length(fri_dim_names))
names(fri_dims) <- fri_dim_names
fri_dims[names(selector_file_dims)] <- selector_file_dims
if (!is.null(file_dim)) {
fri_dims[file_dim] <- chunk_amount
}
}
fri <- vector('list', length = prod(fri_dims))
dim(fri) <- fri_dims
sri <- vector('list', length = prod(fri_dims))
dim(sri) <- fri_dims
selector_file_dim_array <- array(1:prod(selector_file_dims), dim = selector_file_dims)
selector_store_position <- fri_dims
for (j in 1:prod(dim(selector_file_dim_array))) {
selector_indices_to_take <- which(selector_file_dim_array == j, arr.ind = TRUE)[1, ]
names(selector_indices_to_take) <- names(selector_file_dims)
selector_store_position[names(selector_indices_to_take)] <- selector_indices_to_take
sub_array_of_selectors <- Subset(selector_array, names(selector_indices_to_take),
as.list(selector_indices_to_take), drop = 'selected')
if (debug) {
if (inner_dim %in% dims_to_check) {
print("-> ITERATING OVER FILE DIMENSIONS OF THE SELECTORS.")
print("-> STRUCTURE OF A SUB ARRAY:")
print(str(sub_array_of_selectors))
print("-> STRUCTURE OF THE VARIABLE WITH SELECTORS:")
print(str(var_with_selectors))
print(dim(var_with_selectors))
}
}
if (selectors_are_indices) {
sub_array_of_values <- NULL
#} else if (!is.null(var_ordered)) {
# sub_array_of_values <- var_ordered
} else {
if (length(var_file_dims) > 0) {
var_indices_to_take <- selector_indices_to_take[which(names(selector_indices_to_take) %in% names(var_file_dims))]
sub_array_of_values <- Subset(var_with_selectors, names(var_indices_to_take),
as.list(var_indices_to_take), drop = 'selected')
} else {
sub_array_of_values <- var_with_selectors
}
}
if (debug) {
if (inner_dim %in% dims_to_check) {
print("-> STRUCTURE OF THE SUB ARRAY FROM THE VARIABLE CORRESPONDING TO THE SUB ARRAY OF SELECTORS")
print(str(sub_array_of_values))
print(dim(sub_array_of_values))
print("-> NAME OF THE FILE DIMENSION THE CURRENT INNER DIMENSION EXTENDS ALONG:")
print(file_dim)
}
}
if ((!is.null(file_dim) && (file_dim %in% names(selector_file_dims))) || is.null(file_dim)) {
if (length(sub_array_of_selectors) > 0) {
if (debug) {
if (inner_dim %in% dims_to_check) {
print("-> THE INNER DIMENSION DOES NOT GO ACROSS ANY FILE DIMENSION OR IT DOES BUT IS IN THE PROVIDED SELECTOR ARRAY.")
}
}
if (selectors_are_indices) {
if (!is.null(var_with_selectors_name)) {
max_allowed <- ifelse(aiat, m, n)
} else {
max_allowed <- data_dims[inner_dim]
}
if (any(na.omit(unlist(sub_array_of_selectors)) > max_allowed) ||
any(na.omit(unlist(sub_array_of_selectors)) < 1)) {
stop("Provided indices out of range for dimension '", inner_dim, "' ",
"for dataset '", dat[[i]][['name']], "' (accepted range: 1 to ",
max_allowed, ").")
}
}
# The selector_checker will return either a vector of indices or a list
# with the first and last desired indices.
goes_across_prime_meridian <- FALSE
if (!is.null(var_ordered) && !selectors_are_indices) {
if (!is.null(dim_reorder_params[[inner_dim]])) {
if (is.list(sub_array_of_selectors)) {
## NOTE: The check of 'goes_across_prime_meridian' is moved forward to here.
is_circular_dim <- attr(dim_reorder_params[[inner_dim]], "circular")
if (!is.null(is_circular_dim)) {
if (is_circular_dim) {
# NOTE: Use CircularSort() to put the values in the assigned range, and get the order.
# For example, [-10, 20] in CircularSort(0, 360) is [350, 20]. The $ix list is [2, 1].
# 'goes_across_prime_meridian' means the selector range across the border. For example,
# CircularSort(-180, 180) with selector [170, 190] -> goes_across_prime_meridian = TRUE.
tmp <- dim_reorder_params[[inner_dim]](unlist(sub_array_of_selectors))$ix
goes_across_prime_meridian <- tmp[1] > tmp[2]
}
}
# HERE change to the same code as below (under 'else'). Not sure why originally
#it uses additional lines, which make reorder not work.
sub_array_of_selectors <- as.list(dim_reorder_params[[inner_dim]](unlist(sub_array_of_selectors))$x)
#sub_array_reordered <- dim_reorder_params[[inner_dim]](unlist(sub_array_of_selectors))
#sub_array_unorder <- sort(sub_array_reordered$ix, index.return = TRUE)$ix
#sub_array_of_selectors <- as.list(sub_array_reordered$x[sub_array_unorder])
# Add warning if the boundary is out of range
if (sub_array_of_selectors[1] < range(var_ordered)[1] | sub_array_of_selectors[1] > range(var_ordered)[2]) {
.warning(paste0("The lower boundary of selector of ",
inner_dim,
" is out of range [",
min(var_ordered), ", ", max(var_ordered), "]. ",
"Check if the desired range is all included."))
}
if (sub_array_of_selectors[2] < range(var_ordered)[1] | sub_array_of_selectors[2] > range(var_ordered)[2]) {
.warning(paste0("The upper boundary of selector of ",
inner_dim,
" is out of range [",
min(var_ordered), ", ", max(var_ordered), "]. ",
"Check if the desired range is all included."))
}
} else {
sub_array_of_selectors <- dim_reorder_params[[inner_dim]](sub_array_of_selectors)$x
}
}
# NOTE: The ideal solution for selecting indices in goes_across_prime_meridian case
# is modified SelectorCheckor.R. But now SelectorCheckor doesn't know the info of
#goes_across_prime_meridian, so I do the adjustion after calling SelectorCheckor().
sub_array_of_indices <- selector_checker(sub_array_of_selectors, var_ordered,
tolerance = if (aiat) {
NULL
} else {
tolerance_params[[inner_dim]]
})
if (goes_across_prime_meridian & sub_array_of_indices[[1]] < sub_array_of_indices[[2]]) {
if (!(sub_array_of_selectors[[1]] %in% var_ordered)){
sub_array_of_indices[[1]] <- sub_array_of_indices[[1]] - 1
}
if (!(sub_array_of_selectors[[2]] %in% var_ordered)){
sub_array_of_indices[[2]] <- sub_array_of_indices[[2]] + 1
}
}
#NOTE: the possible case?
if (goes_across_prime_meridian & sub_array_of_indices[[1]] > sub_array_of_indices[[2]]) {
stop("The case is goes_across_prime_meridian but no adjustion for the indices!")
}
if (any(is.na(sub_array_of_indices))) {
stop(paste0("The selectors of ", inner_dim,
" are out of range [", min(var_ordered),
", ", max(var_ordered), "]."))
}
} else {
# Add warning if the boundary is out of range
if (is.list(sub_array_of_selectors)) {
if (sub_array_of_selectors[1] <
min(sub_array_of_values) | sub_array_of_selectors[1] >
max(sub_array_of_values)) {
.warning(paste0("The lower boundary of selector of ",
inner_dim, " is out of range [",
min(sub_array_of_values), ", ",
max(sub_array_of_values), "]. ",
"Check if the desired range is all included."))
}
if (sub_array_of_selectors[2] <
min(sub_array_of_values) | sub_array_of_selectors[2] >
max(sub_array_of_values)) {
.warning(paste0("The upper boundary of selector of ",
inner_dim, " is out of range [",
min(sub_array_of_values), ", ",
max(sub_array_of_values), "]. ",
"Check if the desired range is all included."))
}
}
sub_array_of_indices <- selector_checker(sub_array_of_selectors, sub_array_of_values,
tolerance = if (aiat) {
NULL
} else {
tolerance_params[[inner_dim]]
})
if (any(is.na(sub_array_of_indices))) {
stop(paste0("The selectors of ", inner_dim,
" are out of range [", min(sub_array_of_values),
", ", max(sub_array_of_values), "]."))
}
}
## This 'if' runs in both Start() and Compute(). In Start(), it doesn't have any effect (no chunk).
## In Compute(), it creates the indices for each chunk. For example, if 'sub_array_of_indices'
## is c(5:10) and chunked into 2, 'sub_array_of_indices' becomes c(5:7) for chunk = 1, c(8:10)
## for chunk = 2. If 'sub_array_of_indices' is list(55, 62) and chunked into 2, it becomes
## list(55, 58) for chunk = 1 and list(59, 62) for chunk = 2.
## TODO: The list can be turned into vector here? So afterward no need to judge if it is list
## or vector.
if (!is.list(sub_array_of_indices)) {
sub_array_of_indices <- sub_array_of_indices[chunk_indices(length(sub_array_of_indices),
chunks[[inner_dim]]["chunk"],
chunks[[inner_dim]]["n_chunks"],
inner_dim)]
} else {
tmp <- chunk_indices(length(sub_array_of_indices[[1]]:sub_array_of_indices[[2]]),
chunks[[inner_dim]]["chunk"], chunks[[inner_dim]]["n_chunks"],
inner_dim)
vect <- sub_array_of_indices[[1]]:sub_array_of_indices[[2]]
sub_array_of_indices[[1]] <- vect[tmp[1]]
sub_array_of_indices[[2]] <- vect[tmp[length(tmp)]]
}
# The sub_array_of_indices now contains numeric indices of the values to be taken by each chunk.
if (debug) {
if (inner_dim %in% dims_to_check) {
print("-> TRANSFORMATION REQUESTED?")
print(with_transform)