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tolerance = if (aiat) {
tolerance_params[[inner_dim]]
} else {
NULL
})
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if (goes_across_prime_meridian) {
sub_array_of_sri <- c(1:sub_array_of_sri[[2]], sub_array_of_sri[[1]]:length(transformed_subset_var))
#sub_array_of_sri <- c(sub_array_of_sri[[1]]:length(transformed_subset_var), 1:sub_array_of_sri[[2]])
} else if (is.list(sub_array_of_sri)) {
sub_array_of_sri <- sub_array_of_sri[[1]]:sub_array_of_sri[[2]]
}
ordered_sri <- sub_array_of_sri
sub_array_of_sri <- transformed_subset_var_unorder[sub_array_of_sri]
# In this case, the tvi are not defined and the 'transformed_subset_var'
# will be taken instead of the var transformed before in the code.
if (debug) {
if (inner_dim %in% dims_to_check) {
print("-> FIRST INDEX:")
print(first_index)
print("-> LAST INDEX:")
print(last_index)
print("-> STRUCTURE OF FIRST ROUND INDICES:")
print(str(sub_array_of_fri))
print("-> STRUCTURE OF SECOND ROUND INDICES:")
print(str(sub_array_of_sri))
print("-> STRUCTURE OF TRANSFORMED VARIABLE INDICES:")
print(str(tvi))
}
}
### # If the selectors are expressed after transformation
### } else {
###if (debug) {
###if (inner_dim %in% dims_to_check) {
###print("-> SELECTORS REQUESTED AFTER TRANSFORM.")
###}
###}
### if (goes_across_prime_meridian) {
### sub_array_of_indices <- c(sub_array_of_indices[[1]]:m,
### 1:sub_array_of_indices[[2]])
### }
### first_index <- min(unlist(sub_array_of_indices))
### last_index <- max(unlist(sub_array_of_indices))
### first_index_before_transform <- max(transform_indices(first_index, m, n) - beta, 1)
### last_index_before_transform <- min(transform_indices(last_index, m, n) + beta, n)
### sub_array_of_fri <- first_index_before_transform:last_index_before_transform
### n_of_extra_cells <- round(beta / n * m)
### if (is.list(sub_array_of_indices) && (length(sub_array_of_indices) > 1)) {
### sub_array_of_sri <- 1:(last_index - first_index + 1)
### if (is.null(tvi)) {
### tvi <- sub_array_of_sri + first_index - 1
### }
### } else {
### sub_array_of_sri <- sub_array_of_indices - first_index + 1
### if (is.null(tvi)) {
### tvi <- sub_array_of_indices
### }
### }
### sub_array_of_sri <- sub_array_of_sri + n_of_extra_cells
sri <- do.call('[[<-', c(list(x = sri), as.list(selector_store_position),
list(value = sub_array_of_sri)))
} else {
if (goes_across_prime_meridian) {
#sub_array_of_fri <- 1:n
sub_array_of_fri <- c(1:sub_array_of_indices[[2]], sub_array_of_indices[[1]]:n)
} else if (is.list(sub_array_of_indices)) {
sub_array_of_fri <- sub_array_of_indices[[1]]:sub_array_of_indices[[2]]
} else {
sub_array_of_fri <- sub_array_of_indices
}
}
if (!is.null(var_unorder_indices)) {
if (is.null(ordered_fri)) {
ordered_fri <- sub_array_of_fri
}
sub_array_of_fri <- var_unorder_indices[sub_array_of_fri]
}
fri <- do.call('[[<-', c(list(x = fri), as.list(selector_store_position),
list(value = sub_array_of_fri)))
if (!is.null(file_dim)) {
taken_chunks[selector_store_position[[file_dim]]] <- TRUE
} else {
taken_chunks <- TRUE
}
}
} else {
if (debug) {
if (inner_dim %in% dims_to_check) {
print("-> THE INNER DIMENSION GOES ACROSS A FILE DIMENSION.")
}
}
if (inner_dim %in% names(dim(sub_array_of_selectors))) {
if (is.null(var_with_selectors_name)) {
if (any(na.omit(unlist(sub_array_of_selectors)) < 1) ||
any(na.omit(unlist(sub_array_of_selectors)) > data_dims[inner_dim] * chunk_amount)) {
stop("Provided indices out of range for dimension '", inner_dim, "' ",
"for dataset '", dat[[i]][['name']], "' (accepted range: 1 to ",
data_dims[inner_dim] * chunk_amount, ").")
}
} else {
if (inner_dim %in% names(dim(sub_array_of_values))) {
inner_dim_pos_in_sub_array <- which(names(dim(sub_array_of_values)) == inner_dim)
if (inner_dim_pos_in_sub_array != 1) {
new_sub_array_order <- (1:length(dim(sub_array_of_values)))[-inner_dim_pos_in_sub_array]
new_sub_array_order <- c(inner_dim_pos_in_sub_array, new_sub_array_order)
sub_array_of_values <- .aperm2(sub_array_of_values, new_sub_array_order)
}
}
}
inner_dim_pos_in_sub_array <- which(names(dim(sub_array_of_selectors)) == inner_dim)
if (inner_dim_pos_in_sub_array != 1) {
new_sub_array_order <- (1:length(dim(sub_array_of_selectors)))[-inner_dim_pos_in_sub_array]
new_sub_array_order <- c(inner_dim_pos_in_sub_array, new_sub_array_order)
sub_array_of_selectors <- .aperm2(sub_array_of_selectors, new_sub_array_order)
}
sub_array_of_indices <- selector_checker(sub_array_of_selectors, sub_array_of_values,
tolerance = tolerance_params[[inner_dim]])
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)]
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sub_array_is_list <- FALSE
if (is.list(sub_array_of_indices)) {
sub_array_is_list <- TRUE
sub_array_of_indices <- unlist(sub_array_of_indices)
}
if (is.null(var_with_selectors_name)) {
indices_chunk <- floor((sub_array_of_indices - 1) / data_dims[inner_dim]) + 1
transformed_indices <- ((sub_array_of_indices - 1) %% data_dims[inner_dim]) + 1
} else {
indices_chunk <- floor((sub_array_of_indices - 1) / var_full_dims[inner_dim]) + 1
transformed_indices <- ((sub_array_of_indices - 1) %% var_full_dims[inner_dim]) + 1
}
if (sub_array_is_list) {
sub_array_of_indices <- as.list(sub_array_of_indices)
}
if (debug) {
if (inner_dim %in% dims_to_check) {
print("-> GOING TO ITERATE ALONG CHUNKS.")
}
}
for (chunk in 1:chunk_amount) {
if (!is.null(names(selector_store_position))) {
selector_store_position[file_dim] <- chunk
} else {
selector_store_position <- chunk
}
chunk_selectors <- transformed_indices[which(indices_chunk == chunk)]
sub_array_of_indices <- chunk_selectors
if (with_transform) {
# If the provided selectors are expressed in the world
# before transformation
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first_index <- min(unlist(sub_array_of_indices))
last_index <- max(unlist(sub_array_of_indices))
sub_array_of_fri <- max(c(first_index - beta, 1)):min(c(last_index + beta, n))
sub_array_of_sri <- transform_indices(unlist(sub_array_of_indices) - first_index + 1, n, m)
if (is.list(sub_array_of_indices)) {
if (length(sub_array_of_sri) > 1) {
sub_array_of_sri <- sub_array_of_sri[[1]]:sub_array_of_sri[[2]]
}
}
##TODO: TRANSFORM SUBSET VARIABLE AS ABOVE, TO COMPUTE SRI
# If the selectors are expressed after transformation
} else {
first_index <- min(unlist(sub_array_of_indices))
last_index <- max(unlist(sub_array_of_indices))
first_index_before_transform <- max(transform_indices(first_index, m, n) - beta, 1)
last_index_before_transform <- min(transform_indices(last_index, m, n) + beta, n)
sub_array_of_fri <- first_index_before_transform:last_index_before_transform
if (is.list(sub_array_of_indices) && (length(sub_array_of_indices) > 1)) {
sub_array_of_sri <- 1:(last_index - first_index + 1) +
round(beta / n * m)
} else {
sub_array_of_sri <- sub_array_of_indices - first_index + 1 +
round(beta / n * m)
}
##TODO: FILL IN TVI
}
sri <- do.call('[[<-', c(list(x = sri), as.list(selector_store_position),
list(value = sub_array_of_sri)))
if (length(sub_array_of_sri) > 0) {
taken_chunks[chunk] <- TRUE
}
} else {
sub_array_of_fri <- sub_array_of_indices
if (length(sub_array_of_fri) > 0) {
taken_chunks[chunk] <- TRUE
}
}
if (!is.null(var_unorder_indices)) {
ordered_fri <- sub_array_of_fri
sub_array_of_fri <- var_unorder_indices[sub_array_of_fri]
}
fri <- do.call('[[<-', c(list(x = fri), as.list(selector_store_position),
list(value = sub_array_of_fri)))
}
if (debug) {
if (inner_dim %in% dims_to_check) {
print("-> FINISHED ITERATING ALONG CHUNKS")
}
}
} else {
stop("Provided array of indices for dimension '", inner_dim, "', ",
"which goes across the file dimension '", file_dim, "', but ",
"the provided array does not have the dimension '", inner_dim,
"', which is mandatory.")
}
}
}
}
if (debug) {
if (inner_dim %in% dims_to_check) {
print("-> PROCEEDING TO CROP VARIABLES")
}
}
#if ((length(selector_array) == 1) && (selector_array %in% c('all', 'first', 'last'))) {
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#if (!is.null(var_with_selectors_name) || (is.null(var_with_selectors_name) && is.character(selector_array) &&
# (length(selector_array) == 1) && (selector_array %in% c('all', 'first', 'last')))) {
empty_chunks <- which(!taken_chunks)
if (length(empty_chunks) >= length(taken_chunks)) {
stop("Selectors do not match any of the possible values for the dimension '", inner_dim, "'.")
}
if (length(empty_chunks) > 0) {
# # Get the first group of chunks to remove, and remove them.
# # E.g., from c(1, 2, 4, 5, 6, 8, 9) remove only 1 and 2
# dist <- abs(rev(empty_chunks) - c(rev(empty_chunks)[1] - 1, head(rev(empty_chunks), length(rev(empty_chunks)) - 1)))
# if (all(dist == 1)) {
# start_chunks_to_remove <- NULL
# } else {
# first_chunk_to_remove <- tail(which(dist > 1), 1)
# start_chunks_to_remove <- rev(rev(empty_chunks)[first_chunk_to_remove:length(empty_chunks)])
# }
# # Get the last group of chunks to remove, and remove them.
# # E.g., from c(1, 2, 4, 5, 6, 8, 9) remove only 8 and 9
# dist <- abs(empty_chunks - c(empty_chunks[1] - 1, head(empty_chunks, length(empty_chunks) - 1)))
# if (all(dist == 1)) {
# first_chunk_to_remove <- 1
# } else {
# first_chunk_to_remove <- tail(which(dist > 1), 1)
# }
# end_chunks_to_remove <- empty_chunks[first_chunk_to_remove:length(empty_chunks)]
# chunks_to_keep <- which(!((1:length(taken_chunks)) %in% c(start_chunks_to_remove, end_chunks_to_remove)))
chunks_to_keep <- which(taken_chunks)
dims_to_crop[[file_dim]] <- c(dims_to_crop[[file_dim]], list(chunks_to_keep))
# found_indices <- Subset(found_indices, file_dim, chunks_to_keep)
# # Crop dataset variables file dims.
# for (picked_var in names(picked_vars[[i]])) {
# if (file_dim %in% names(dim(picked_vars[[i]][[picked_var]]))) {
# picked_vars[[i]][[picked_var]] <- Subset(picked_vars[[i]][[picked_var]], file_dim, chunks_to_keep)
# }
# }
}
#}
dat[[i]][['selectors']][[inner_dim]] <- list(fri = fri, sri = sri)
# Crop dataset variables inner dims.
# Crop common variables inner dims.
types_of_var_to_crop <- 'picked'
if (with_transform) {
types_of_var_to_crop <- c(types_of_var_to_crop, 'transformed')
}
if (!is.null(dim_reorder_params[[inner_dim]])) {
types_of_var_to_crop <- c(types_of_var_to_crop, 'reordered')
}
for (type_of_var_to_crop in types_of_var_to_crop) {
if (type_of_var_to_crop == 'transformed') {
if (is.null(tvi)) {
if (!is.null(dim_reorder_params[[inner_dim]])) {
crop_indices <- unique(unlist(ordered_sri))
} else {
crop_indices <- unique(unlist(sri))
}
} else {
crop_indices <- unique(unlist(tvi))
}
vars_to_crop <- transformed_vars[[i]]
common_vars_to_crop <- transformed_common_vars
} else if (type_of_var_to_crop == 'reordered') {
crop_indices <- unique(unlist(ordered_fri))
vars_to_crop <- picked_vars_ordered[[i]]
common_vars_to_crop <- picked_common_vars_ordered
} else {
crop_indices <- unique(unlist(fri))
vars_to_crop <- picked_vars[[i]]
common_vars_to_crop <- picked_common_vars
}
for (var_to_crop in names(vars_to_crop)) {
if (inner_dim %in% names(dim(vars_to_crop[[var_to_crop]]))) {
if (!is.null(crop_indices)) {
if (type_of_var_to_crop == 'transformed') {
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vars_to_crop[[var_to_crop]] <- Subset(transformed_subset_var, inner_dim, crop_indices)
} else {
vars_to_crop[[var_to_crop]] <- Subset(vars_to_crop[[var_to_crop]], inner_dim, crop_indices)
}
} else {
vars_to_crop[[var_to_crop]] <- Subset(vars_to_crop[[var_to_crop]], inner_dim, crop_indices)
}
}
}
}
if (i == length(dat)) {
for (common_var_to_crop in names(common_vars_to_crop)) {
if (inner_dim %in% names(dim(common_vars_to_crop[[common_var_to_crop]]))) {
common_vars_to_crop[[common_var_to_crop]] <- Subset(common_vars_to_crop[[common_var_to_crop]], inner_dim, crop_indices)
}
}
}
if (type_of_var_to_crop == 'transformed') {
if (!is.null(vars_to_crop)) {
transformed_vars[[i]] <- vars_to_crop
}
if (i == length(dat)) {
transformed_common_vars <- common_vars_to_crop
}
} else if (type_of_var_to_crop == 'reordered') {
if (!is.null(vars_to_crop)) {
picked_vars_ordered[[i]] <- vars_to_crop
}
if (i == length(dat)) {
picked_common_vars_ordered <- common_vars_to_crop
}
} else {
if (!is.null(vars_to_crop)) {
picked_vars[[i]] <- vars_to_crop
}
if (i == length(dat)) {
picked_common_vars <- common_vars_to_crop
}
}
}
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}
# After the selectors have been picked (using the original variables),
# the variables are transformed. At that point, the original selectors
# for the transformed variables are also kept in the variable original_selectors.
#print("L")
}
}
}
# if (!is.null(transformed_common_vars)) {
# picked_common_vars[names(transformed_common_vars)] <- transformed_common_vars
# }
# Remove the trailing chunks, if any.
for (file_dim in names(dims_to_crop)) {
# indices_to_keep <- min(sapply(dims_to_crop[[file_dim]], min)):max(sapply(dims_to_crop[[file_dim]], max))
## TODO: Merge indices in dims_to_crop with some advanced mechanism?
indices_to_keep <- unique(unlist(dims_to_crop[[file_dim]]))
array_of_files_to_load <- Subset(array_of_files_to_load, file_dim, indices_to_keep)
array_of_not_found_files <- Subset(array_of_not_found_files, file_dim, indices_to_keep)
for (i in 1:length(dat)) {
# Crop selectors
for (selector_dim in names(dat[[i]][['selectors']])) {
if (selector_dim == file_dim) {
for (j in 1:length(dat[[i]][['selectors']][[selector_dim]][['fri']])) {
dat[[i]][['selectors']][[selector_dim]][['fri']][[j]] <- dat[[i]][['selectors']][[selector_dim]][['fri']][[j]][indices_to_keep]
}
for (j in 1:length(dat[[i]][['selectors']][[selector_dim]][['sri']])) {
dat[[i]][['selectors']][[selector_dim]][['sri']][[j]] <- dat[[i]][['selectors']][[selector_dim]][['sri']][[j]][indices_to_keep]
}
}
if (file_dim %in% names(dim(dat[[i]][['selectors']][[selector_dim]][['fri']]))) {
dat[[i]][['selectors']][[selector_dim]][['fri']] <- Subset(dat[[i]][['selectors']][[selector_dim]][['fri']], file_dim, indices_to_keep)
dat[[i]][['selectors']][[selector_dim]][['sri']] <- Subset(dat[[i]][['selectors']][[selector_dim]][['sri']], file_dim, indices_to_keep)
}
}
# Crop dataset variables file dims.
for (picked_var in names(picked_vars[[i]])) {
if (file_dim %in% names(dim(picked_vars[[i]][[picked_var]]))) {
picked_vars[[i]][[picked_var]] <- Subset(picked_vars[[i]][[picked_var]], file_dim, indices_to_keep)
}
}
for (transformed_var in names(transformed_vars[[i]])) {
if (file_dim %in% names(dim(transformed_vars[[i]][[transformed_var]]))) {
transformed_vars[[i]][[transformed_var]] <- Subset(transformed_vars[[i]][[transformed_var]], file_dim, indices_to_keep)
}
}
}
# Crop common variables file dims.
for (picked_common_var in names(picked_common_vars)) {
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if (file_dim %in% names(dim(picked_common_vars[[picked_common_var]]))) {
picked_common_vars[[picked_common_var]] <- Subset(picked_common_vars[[picked_common_var]], file_dim, indices_to_keep)
}
}
for (transformed_common_var in names(transformed_common_vars)) {
if (file_dim %in% names(dim(transformed_common_vars[[transformed_common_var]]))) {
transformed_common_vars[[transformed_common_var]] <- Subset(transformed_common_vars[[transformed_common_var]], file_dim, indices_to_keep)
}
}
}
# Calculate the size of the final array.
total_inner_dims <- NULL
for (i in 1:length(dat)) {
if (dataset_has_files[i]) {
inner_dims <- expected_inner_dims[[i]]
inner_dims <- sapply(inner_dims,
function(x) {
if (!all(sapply(dat[[i]][['selectors']][[x]][['sri']], is.null))) {
max(sapply(dat[[i]][['selectors']][[x]][['sri']], length))
} else {
if (length(var_params[[x]]) > 0) {
if (var_params[[x]] %in% names(transformed_vars[[i]])) {
length(transformed_vars[[i]][[var_params[[x]]]])
} else if (var_params[[x]] %in% names(transformed_common_vars)) {
length(transformed_common_vars[[var_params[[x]]]])
} else {
max(sapply(dat[[i]][['selectors']][[x]][['fri']], length))
}
} else {
max(sapply(dat[[i]][['selectors']][[x]][['fri']], length))
}
}
})
names(inner_dims) <- expected_inner_dims[[i]]
if (is.null(total_inner_dims)) {
total_inner_dims <- inner_dims
} else {
new_dims <- .MergeArrayDims(total_inner_dims, inner_dims)
total_inner_dims <- pmax(new_dims[[1]], new_dims[[2]])
}
}
}
new_dims <- .MergeArrayDims(dim(array_of_files_to_load), total_inner_dims)
final_dims <- pmax(new_dims[[1]], new_dims[[2]])[dim_names]
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# final_dims_fake is the vector of final dimensions after having merged the
# 'across' file dimensions with the respective 'across' inner dimensions, and
# after having broken into multiple dimensions those dimensions for which
# multidimensional selectors have been provided.
# final_dims will be used for collocation of data, whereas final_dims_fake
# will be used for shaping the final array to be returned to the user.
final_dims_fake <- final_dims
if (merge_across_dims) {
if (!is.null(inner_dims_across_files)) {
for (file_dim_across in names(inner_dims_across_files)) {
inner_dim_pos <- which(names(final_dims_fake) == inner_dims_across_files[[file_dim_across]])
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new_dims <- c()
if (inner_dim_pos > 1) {
new_dims <- c(new_dims, final_dims_fake[1:(inner_dim_pos - 1)])
}
new_dims <- c(new_dims, setNames(prod(final_dims_fake[c(inner_dim_pos, inner_dim_pos + 1)]),
inner_dims_across_files[[file_dim_across]]))
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if (inner_dim_pos + 1 < length(final_dims_fake)) {
new_dims <- c(new_dims, final_dims_fake[(inner_dim_pos + 2):length(final_dims_fake)])
}
final_dims_fake <- new_dims
}
}
}
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if (split_multiselected_dims) {
for (dim_param in 1:length(dim_params)) {
if (!is.null(dim(dim_params[[dim_param]]))) {
if (length(dim(dim_params[[dim_param]])) > 1) {
split_dims <- dim(dim_params[[dim_param]])
all_split_dims <- c(all_split_dims, setNames(list(split_dims),
names(dim_params)[dim_param]))
if (is.null(names(split_dims))) {
names(split_dims) <- paste0(names(dim_params)[dim_param],
1:length(split_dims))
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}
old_dim_pos <- which(names(final_dims_fake) == names(dim_params)[dim_param])
new_dims <- c()
if (old_dim_pos > 1) {
new_dims <- c(new_dims, final_dims_fake[1:(old_dim_pos - 1)])
}
new_dims <- c(new_dims, split_dims)
if (old_dim_pos < length(final_dims_fake)) {
new_dims <- c(new_dims, final_dims_fake[(old_dim_pos + 1):length(final_dims_fake)])
}
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}
}
}
}
if (!silent) {
.message("Detected dimension sizes:")
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longest_dim_len <- max(sapply(names(final_dims_fake), nchar))
longest_size_len <- max(sapply(paste0(final_dims_fake, ''), nchar))
sapply(names(final_dims_fake),
function(x) {
message(paste0("* ", paste(rep(' ', longest_dim_len - nchar(x)), collapse = ''),
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x, ": ", paste(rep(' ', longest_size_len - nchar(paste0(final_dims_fake[x], ''))), collapse = ''),
final_dims_fake[x]))
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bytes <- prod(c(final_dims_fake, 8))
dim_sizes <- paste(final_dims_fake, collapse = ' x ')
if (retrieve) {
.message(paste("Total size of requested data:"))
} else {
.message(paste("Total size of involved data:"))
}
.message(paste(dim_sizes, " x 8 bytes =",
format(structure(bytes, class = "object_size"), units = "auto")),
indent = 2)
}
# The following several lines will only be run if retrieve = TRUE
if (retrieve) {
########## CREATING THE SHARED MATRIX AND DISPATCHING WORK PIECES ###########
# TODO: try performance of storing all in cols instead of rows
# Create the shared memory array, and a pointer to it, to be sent
# to the work pieces.
data_array <- big.matrix(nrow = prod(final_dims), ncol = 1)
shared_matrix_pointer <- describe(data_array)
if (is.null(num_procs)) {
# Creating a shared tmp folder to store metadata from each chunk
array_of_metadata_flags <- array(FALSE, dim = dim(array_of_files_to_load))
if (!is.null(metadata_dims)) {
metadata_indices_to_load <- as.list(rep(1, length(dim(array_of_files_to_load))))
names(metadata_indices_to_load) <- names(dim(array_of_files_to_load))
metadata_indices_to_load[metadata_dims] <- as.list(rep(TRUE, length(metadata_dims)))
array_of_metadata_flags <- do.call('[<-', c(list(array_of_metadata_flags), metadata_indices_to_load,
list(value = rep(TRUE, prod(dim(array_of_files_to_load)[metadata_dims])))))
}
metadata_file_counter <- 0
metadata_folder <- tempfile('metadata')
dir.create(metadata_folder)
# Build the work pieces, each with:
# - file path
# - total size (dims) of store array
# - start position in store array
# - file selectors (to provide extra info. useful e.g. to select variable)
# - indices to take from file
work_pieces <- list()
for (i in 1:length(dat)) {
if (dataset_has_files[i]) {
selectors <- dat[[i]][['selectors']]
file_dims <- found_file_dims[[i]]
inner_dims <- expected_inner_dims[[i]]
sub_array_dims <- final_dims[file_dims]
sub_array_dims[found_pattern_dim] <- 1
sub_array_of_files_to_load <- array(1:prod(sub_array_dims),
dim = sub_array_dims)
names(dim(sub_array_of_files_to_load)) <- names(sub_array_dims)
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# Detect which of the dimensions of the dataset go across files.
file_dim_across_files <- lapply(inner_dims,
function(x) {
dim_across <- sapply(inner_dims_across_files, function(y) x %in% y)
if (any(dim_across)) {
names(inner_dims_across_files)[which(dim_across)[1]]
} else {
NULL
}
})
names(file_dim_across_files) <- inner_dims
j <- 1
while (j <= prod(sub_array_dims)) {
# Work out file path.
file_to_load_sub_indices <- which(sub_array_of_files_to_load == j, arr.ind = TRUE)[1, ]
names(file_to_load_sub_indices) <- names(sub_array_dims)
file_to_load_sub_indices[found_pattern_dim] <- i
big_dims <- rep(1, length(dim(array_of_files_to_load)))
names(big_dims) <- names(dim(array_of_files_to_load))
file_to_load_indices <- .MergeArrayDims(file_to_load_sub_indices, big_dims)[[1]]
file_to_load <- do.call('[[', c(list(array_of_files_to_load),
as.list(file_to_load_indices)))
not_found_file <- do.call('[[', c(list(array_of_not_found_files),
as.list(file_to_load_indices)))
load_file_metadata <- do.call('[', c(list(array_of_metadata_flags),
as.list(file_to_load_indices)))
if (load_file_metadata) {
metadata_file_counter <- metadata_file_counter + 1
}
if (!is.na(file_to_load) && !not_found_file) {
# Work out indices to take
first_round_indices <- lapply(inner_dims,
function (x) {
if (is.null(file_dim_across_files[[x]])) {
selectors[[x]][['fri']][[1]]
} else {
which_chunk <- file_to_load_sub_indices[file_dim_across_files[[x]]]
selectors[[x]][['fri']][[which_chunk]]
}
})
names(first_round_indices) <- inner_dims
second_round_indices <- lapply(inner_dims,
function (x) {
if (is.null(file_dim_across_files[[x]])) {
selectors[[x]][['sri']][[1]]
} else {
which_chunk <- file_to_load_sub_indices[file_dim_across_files[[x]]]
selectors[[x]][['sri']][[which_chunk]]
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}
})
if (debug) {
print("-> BUILDING A WORK PIECE")
#print(str(selectors))
}
names(second_round_indices) <- inner_dims
if (!any(sapply(first_round_indices, length) == 0)) {
work_piece <- list()
work_piece[['first_round_indices']] <- first_round_indices
work_piece[['second_round_indices']] <- second_round_indices
work_piece[['file_indices_in_array_of_files']] <- file_to_load_indices
work_piece[['file_path']] <- file_to_load
work_piece[['store_dims']] <- final_dims
# Work out store position
store_position <- final_dims
store_position[names(file_to_load_indices)] <- file_to_load_indices
store_position[inner_dims] <- rep(1, length(inner_dims))
work_piece[['store_position']] <- store_position
# Work out file selectors
file_selectors <- sapply(file_dims,
function (x) {
vector_to_pick <- 1
if (x %in% names(depending_file_dims)) {
vector_to_pick <- file_to_load_indices[depending_file_dims[[x]]]
}
selectors[file_dims][[x]][[vector_to_pick]][file_to_load_indices[x]]
})
names(file_selectors) <- file_dims
work_piece[['file_selectors']] <- file_selectors
# Send variables for transformation
if (!is.null(transform) && (length(transform_vars) > 0)) {
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]
vars_to_transform <- c(vars_to_transform, picked_vars[[i]][picked_vars_to_transform])
if (any(picked_vars_to_transform %in% names(picked_vars_ordered[[i]]))) {
picked_vars_ordered_to_transform <- picked_vars_to_transform[which(picked_vars_to_transform %in% names(picked_vars_ordered[[i]]))]
vars_to_transform[picked_vars_ordered_to_transform] <- picked_vars_ordered[[i]][picked_vars_ordered_to_transform]
}
}
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]
vars_to_transform <- c(vars_to_transform, picked_common_vars[picked_common_vars_to_transform])
if (any(picked_common_vars_to_transform %in% names(picked_common_vars_ordered))) {
picked_common_vars_ordered_to_transform <- picked_common_vars_to_transform[which(picked_common_vars_to_transform %in% names(picked_common_vars_ordered))]
vars_to_transform[picked_common_vars_ordered_to_transform] <- picked_common_vars_ordered[picked_common_vars_ordered_to_transform]
}
}
work_piece[['vars_to_transform']] <- vars_to_transform
}
# Send flag to load metadata
if (load_file_metadata) {
work_piece[['save_metadata_in']] <- paste0(metadata_folder, '/', metadata_file_counter)
}
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work_pieces <- c(work_pieces, list(work_piece))
}
}
j <- j + 1
}
}
}
#print("N")
if (debug) {
print("-> WORK PIECES BUILT")
}
# Calculate the progress %s that will be displayed and assign them to
# the appropriate work pieces.
if (length(work_pieces) / num_procs >= 2 && !silent) {
if (length(work_pieces) / num_procs < 10) {
amount <- 100 / ceiling(length(work_pieces) / num_procs)
reps <- ceiling(length(work_pieces) / num_procs)
} else {
amount <- 10
reps <- 10
}
progress_steps <- rep(amount, reps)
if (length(work_pieces) < (reps + 1)) {
selected_pieces <- length(work_pieces)
progress_steps <- c(sum(head(progress_steps, reps)),
tail(progress_steps, reps))
} else {
selected_pieces <- round(seq(1, length(work_pieces),
length.out = reps + 1))[-1]
}
progress_steps <- paste0(' + ', round(progress_steps, 2), '%')
progress_message <- 'Progress: 0%'
} else {
progress_message <- ''
selected_pieces <- NULL
}
piece_counter <- 1
step_counter <- 1
work_pieces <- lapply(work_pieces,
function (x) {
if (piece_counter %in% selected_pieces) {
wp <- c(x, list(progress_amount = progress_steps[step_counter]))
step_counter <<- step_counter + 1
} else {
wp <- x
}
piece_counter <<- piece_counter + 1
wp
})
if (!silent) {
.message("If the size of the requested data is close to or above the free shared RAM memory, R may crash.")
.message("If the size of the requested data is close to or above the half of the free RAM memory, R may crash.")
.message(paste0("Will now proceed to read and process ", length(work_pieces), " data files:"))
if (length(work_pieces) < 30) {
lapply(work_pieces, function (x) .message(x[['file_path']], indent = 2))
} else {
.message("The list of files is long. You can check it after Start() finishes in the output '$Files'.", indent = 2, exdent = 5)
}
}
# Build the cluster of processes that will do the work and dispatch work pieces.
# The function .LoadDataFile is applied to each work piece. This function will
# open the data file, regrid if needed, subset, apply the mask,
# compute and apply the weights if needed,
# disable extreme values and store in the shared memory matrix.
#print("O")
if (!silent) {
.message("Loading... This may take several minutes...")
if (progress_message != '') {
.message(progress_message, appendLF = FALSE)
}
}
if (num_procs == 1) {
found_files <- lapply(work_pieces, .LoadDataFile,
shared_matrix_pointer = shared_matrix_pointer,
file_data_reader = file_data_reader,
transform = transform,
transform_params = transform_params,
silent = silent, debug = debug)
} else {
cluster <- makeCluster(num_procs, outfile = "")
# Send the heavy work to the workers
work_errors <- try({
found_files <- clusterApplyLB(cluster, work_pieces, .LoadDataFile,
shared_matrix_pointer = shared_matrix_pointer,
file_data_reader = file_data_reader,
transform = transform,
transform_params = transform_params,
silent = silent, debug = debug)
})
stopCluster(cluster)
}
if (!silent) {
if (progress_message != '') {
.message("\n", tag = '')
}
}
#print("P")
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data_array <- array(bigmemory::as.matrix(data_array), dim = final_dims_fake)
# Load metadata and remove the metadata folder
if (!is.null(metadata_dims)) {
loaded_metadata_files <- list.files(metadata_folder)
loaded_metadata <- lapply(paste0(metadata_folder, '/', loaded_metadata_files), readRDS)
unlink(metadata_folder, recursive = TRUE)
return_metadata <- vector('list', length = prod(dim(array_of_metadata_flags)[metadata_dims]))
return_metadata[as.numeric(loaded_metadata_files)] <- loaded_metadata
dim(return_metadata) <- dim(array_of_metadata_flags[metadata_dims])
attr(data_array, 'Variables') <- return_metadata
# TODO: Try to infer data type from loaded_metadata
# as.integer(data_array)
}
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failed_pieces <- work_pieces[which(unlist(found_files))]
for (failed_piece in failed_pieces) {
array_of_not_found_files <- do.call('[<-',
c(list(array_of_not_found_files),
as.list(failed_piece[['file_indices_in_array_of_files']]),
list(value = TRUE)))
}
if (any(array_of_not_found_files)) {
for (i in 1:prod(dim(array_of_files_to_load))) {
if (is.na(array_of_not_found_files[i])) {
array_of_files_to_load[i] <- NA
} else {
if (array_of_not_found_files[i]) {
array_of_not_found_files[i] <- array_of_files_to_load[i]
array_of_files_to_load[i] <- NA
} else {
array_of_not_found_files[i] <- NA
}
}
}
} else {
array_of_not_found_files <- NULL
}
# Replace the vars and common vars by the transformed vars and common vars
for (i in 1:length(dat)) {
if (length(names(transformed_vars[[i]])) > 0) {
picked_vars[[i]][names(transformed_vars[[i]])] <- transformed_vars[[i]]
} else if (length(names(picked_vars_ordered[[i]])) > 0) {
picked_vars[[i]][names(picked_vars_ordered[[i]])] <- picked_vars_ordered[[i]]
}
}
if (length(names(transformed_common_vars)) > 0) {
picked_common_vars[names(transformed_common_vars)] <- transformed_common_vars
} else if (length(names(picked_common_vars_ordered)) > 0) {
picked_common_vars[names(picked_common_vars_ordered)] <- picked_common_vars_ordered
}
if (debug) {
print("-> THE TRANSFORMED VARS:")
print(str(transformed_vars))
print("-> THE PICKED VARS:")
print(str(picked_vars))
}
file_selectors <- NULL
for (i in 1:length(dat)) {
file_selectors[[dat[[i]][['name']]]] <- dat[[i]][['selectors']][which(names(dat[[i]][['selectors']]) %in% found_file_dims[[i]])]
}
if (retrieve) {
if (!silent) {
.message("Successfully retrieved data.")
}
var_backup <- attr(data_array, 'Variables')[[1]]
attr(data_array, 'Variables') <- NULL
attributes(data_array) <- c(attributes(data_array),
list(Variables = c(list(common = c(picked_common_vars, var_backup)),
picked_vars),
Files = array_of_files_to_load,
NotFoundFiles = array_of_not_found_files,
FileSelectors = file_selectors,
PatternDim = found_pattern_dim)
)
attr(data_array, 'class') <- c('startR_cube', attr(data_array, 'class'))
data_array
} else {
if (!silent) {
.message("Successfully discovered data dimensions.")
}
start_call <- match.call()
start_call[[i]] <- eval.parent(start_call[[i]])
start_call[['retrieve']] <- TRUE
attributes(start_call) <- c(attributes(start_call),
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list(Dimensions = final_dims_fake,
Variables = c(list(common = picked_common_vars), picked_vars),
ExpectedFiles = array_of_files_to_load,
PatternDim = found_pattern_dim,
MergedDims = if (merge_across_dims) {
inner_dims_across_files
} else {
NULL
},
SplitDims = if (split_multiselected_dims) {
all_split_dims
} else {
NULL
})
)
attr(start_call, 'class') <- c('startR_header', attr(start_call, 'class'))
start_call
}
# This function is the responsible for loading the data of each work
# piece.
.LoadDataFile <- function(work_piece, shared_matrix_pointer,
file_data_reader, synonims,
transform, transform_params,
silent = FALSE, debug = FALSE) {
# suppressPackageStartupMessages({library(bigmemory)})
### TODO: Specify dependencies as parameter
# suppressPackageStartupMessages({library(ncdf4)})
#print("1")
store_indices <- as.list(work_piece[['store_position']])
first_round_indices <- work_piece[['first_round_indices']]
second_round_indices <- work_piece[['second_round_indices']]
#print("2")
file_to_open <- work_piece[['file_path']]
sub_array <- file_data_reader(file_to_open, NULL,
work_piece[['file_selectors']],
first_round_indices, synonims)
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if (debug) {
if (all(unlist(store_indices[1:6]) == 1)) {
print("-> LOADING A WORK PIECE")
print("-> STRUCTURE OF READ UNTRANSFORMED DATA:")
print(str(sub_array))
print("-> STRUCTURE OF VARIABLES TO TRANSFORM:")
print(str(work_piece[['vars_to_transform']]))
print("-> COMMON ARRAY DIMENSIONS:")
print(str(work_piece[['store_dims']]))
}
}
if (!is.null(sub_array)) {
# Apply data transformation once we have the data arrays.
if (!is.null(transform)) {
if (debug) {
if (all(unlist(store_indices[1:6]) == 1)) {
print("-> PROCEEDING TO TRANSFORM ARRAY")
print("-> DIMENSIONS OF ARRAY RIGHT BEFORE TRANSFORMING:")
print(dim(sub_array))
}
}
sub_array <- do.call(transform, c(list(data_array = sub_array,
variables = work_piece[['vars_to_transform']],
file_selectors = work_piece[['file_selectors']]),
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transform_params))
if (debug) {
if (all(unlist(store_indices[1:6]) == 1)) {
print("-> STRUCTURE OF ARRAY AND VARIABLES RIGHT AFTER TRANSFORMING:")
print(str(sub_array))
print("-> DIMENSIONS OF ARRAY RIGHT AFTER TRANSFORMING:")
print(dim(sub_array$data_array))
}
}
sub_array <- sub_array$data_array
# Subset with second round of indices
dims_to_crop <- which(!sapply(second_round_indices, is.null))
if (length(dims_to_crop) > 0) {
dimnames_to_crop <- names(second_round_indices)[dims_to_crop]
sub_array <- Subset(sub_array, dimnames_to_crop,
second_round_indices[dimnames_to_crop])
}
if (debug) {
if (all(unlist(store_indices[1:6]) == 1)) {
print("-> STRUCTURE OF ARRAY AND VARIABLES RIGHT AFTER SUBSETTING WITH 2nd ROUND INDICES:")
print(str(sub_array))
}
}
}
metadata <- attr(sub_array, 'variables')
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store_indices <- lapply(names(store_indices),
function (x) {
if (!(x %in% names(first_round_indices))) {
store_indices[[x]]
} else if (is.null(second_round_indices[[x]])) {
1:dim(sub_array)[x]
} else {
if (is.numeric(second_round_indices[[x]])) {
## TODO: Review carefully this line. Inner indices are all
## aligned to the left-most positions. If dataset A has longitudes
## 1, 2, 3, 4 but dataset B has only longitudes 3 and 4, then
## they will be stored as follows:
## 1, 2, 3, 4
## 3, 4, NA, NA
##x - min(x) + 1
1:length(second_round_indices[[x]])
} else {
1:length(second_round_indices[[x]])
}
}
})
if (debug) {
print("-> STRUCTURE OF FIRST ROUND INDICES FOR THIS WORK PIECE:")
print(str(first_round_indices))
print("-> STRUCTURE OF SECOND ROUND INDICES FOR THIS WORK PIECE:")
print(str(second_round_indices))
print("-> STRUCTURE OF STORE INDICES FOR THIS WORK PIECE:")
print(str(store_indices))
}
}
# Converting array indices to vector indices
store_dims <- work_piece[['store_dims']]
store_indices <- do.call('expand.grid', store_indices)
### Given a matrix where each row is a set of array indices of an element
### the vector indices are computed
weights <- sapply(1:length(store_dims),
function(i) prod(c(1, store_dims)[1:i]))
matrix_indices <- 1 + colSums(t(store_indices - 1) * weights)
###
data_array <- bigmemory::attach.big.matrix(shared_matrix_pointer)
rm(data_array)
gc()
if (!is.null(work_piece[['save_metadata_in']])) {
saveRDS(metadata, file = work_piece[['save_metadata_in']])
}
}
if (!is.null(work_piece[['progress_amount']]) && !silent) {
message(work_piece[['progress_amount']], appendLF = FALSE)
}
is.null(sub_array)
}