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#' HDF5 utilities
#'
#' Basically just better versions of those in \pkg{rhdf5}, dedicated to \pkg{alabaster.base} and its dependents.
#' Intended for \pkg{alabaster.*} developers only.
#'
#' @name hdf5
#' @import rhdf5
#' @aliases
#' h5_guess_vector_chunks
#' h5_create_vector
#' h5_write_vector
#' h5_write_attribute
#' h5_read_vector
#' h5_read_attribute
#' h5_object_exists
#' h5_cast
NULL
.choose_type <- function(x) {
if (is.integer(x)) {
type <- "H5T_NATIVE_INT32"
} else if (is.double(x)) {
type <- "H5T_NATIVE_DOUBLE"
} else if (is.character(x)) {
tid <- H5Tcopy("H5T_C_S1")
H5Tset_strpad(tid, strpad = "NULLPAD")
H5Tset_size(tid, max(nchar(x, type="bytes"), 1L, na.rm=TRUE))
enc <- unique(Encoding(x))
if ("UTF-8" %in% enc) {
H5Tset_cset(tid, "UTF8")
} else {
H5Tset_cset(tid, "ASCII")
}
tid
} else {
stop("unsupported type '", typeof(x) + "'")
}
}
#' @export
h5_guess_vector_chunks <- function(len) {
# Some reasonable number between 10000 and 100000, depending on the size.
chunks <- sqrt(len)
if (chunks < 10000) {
chunks <- min(len, 10000)
} else if (chunks > 100000) {
chunks <- 100000
}
return(chunks)
}
#' @export
h5_create_vector <- function(handle, name, len, type, compress=6, chunks=NULL, scalar=FALSE, emit=FALSE) {
if (len == 1 && scalar) {
shandle <- H5Screate("H5S_SCALAR")
compress <- 0
} else {
shandle <- H5Screate_simple(len)
}
on.exit(H5Sclose(shandle), add=TRUE, after=FALSE)
phandle <- H5Pcreate("H5P_DATASET_CREATE")
on.exit(H5Pclose(phandle), add=TRUE, after=FALSE)
H5Pset_fill_time(phandle, "H5D_FILL_TIME_NEVER")
H5Pset_obj_track_times(phandle, FALSE)
if (compress > 0 && len) {
H5Pset_shuffle(phandle)
H5Pset_deflate(phandle, level=compress)
if (is.null(chunks)) {
chunks <- h5_guess_vector_chunks(len)
}
H5Pset_chunk(phandle, chunks)
}
H5Dcreate(handle, name, dtype_id=type, h5space=shandle, dcpl=phandle)
}
#' @export
h5_write_vector <- function(handle, name, x, type=NULL, compress=6, chunks=NULL, scalar=FALSE, emit=FALSE) {
if (is.null(type)) {
if (is.character(x)) {
x <- enc2utf8(x) # avoid mis-encoding multi-byte characters from Latin-1.
}
type <- .choose_type(x)
}
dhandle <- h5_create_vector(handle, name, length(x), type=type, compress=compress, chunks=chunks, scalar=scalar, emit=emit)
if (!emit) {
on.exit(H5Dclose(dhandle), add=TRUE, after=FALSE)
}
H5Dwrite(dhandle, x)
if (emit) {
return(dhandle)
} else {
return(invisible(NULL))
}
}
#' @export
h5_write_attribute <- function(handle, name, x, type=NULL, scalar=FALSE) {
if (is.null(type)) {
if (is.character(x)) {
x <- enc2utf8(x) # avoid mis-encoding multi-byte characters from Latin-1.
}
type <- .choose_type(x)
}
if (length(x) == 1 && scalar) {
shandle <- H5Screate("H5S_SCALAR")
} else {
shandle <- H5Screate_simple(length(x))
}
on.exit(H5Sclose(shandle), add=TRUE, after=FALSE)
ahandle <- H5Acreate(handle, name, dtype_id=type, h5space=shandle)
on.exit(H5Aclose(ahandle), add=TRUE, after=FALSE)
H5Awrite(ahandle, x)
invisible(NULL)
}
#' @export
h5_object_exists <- function(handle, name) {
name %in% h5ls(handle, datasetinfo=FALSE, recursive=FALSE)$name
}
#' @export
h5_read_vector <- function(handle, name, check=FALSE, default=NULL, bit64conversion) {
if (check) {
if (!h5_object_exists(handle, name)) {
return(default)
}
}
dhandle <- H5Dopen(handle, name)
on.exit(H5Dclose(dhandle), add=TRUE, after=FALSE)
output <- H5Dread(dhandle, bit64conversion=bit64conversion, drop=TRUE)
if (is.raw(output)) {
storage.mode(output) <- "integer"
} else if (is.character(output) && H5Tget_cset(H5Dget_type(dhandle)) == 1L) {
Encoding(output) <- "UTF-8"
}
output
}
#' @export
h5_read_attribute <- function(handle, name, check=FALSE, default=NULL, bit64conversion) {
if (check) {
if (!H5Aexists(handle, name)) {
return(default)
}
}
ahandle <- H5Aopen_by_name(handle, name=name)
on.exit(H5Aclose(ahandle), add=TRUE, after=FALSE)
output <- H5Aread(ahandle, bit64conversion=bit64conversion)
if (is.raw(output)) {
storage.mode(output) <- "integer"
} else if (is.character(output) && H5Tget_cset(H5Aget_type(ahandle)) == 1L) {
Encoding(output) <- "UTF-8"
}
output
}
#' @export
h5_cast <- function(current, expected.type, missing.placeholder, respect.nan.payload=FALSE) {
restore_min_integer <- function(y) {
z <- FALSE
if (is.integer(y) && anyNA(y)) { # promote integer NAs back to the actual number.
y <- as.double(y)
y[is.na(y)] <- -2^31
z <- TRUE
}
list(y=y, converted=z)
}
converted <- FALSE
if (is.null(missing.placeholder)) {
out <- restore_min_integer(current)
current <- out$y
converted <- out$converted
} else if (is.na(missing.placeholder)) {
if (!is.double(current)) {
# No-op as the placeholder is already R's NA of the relevant type.
} else {
if (respect.nan.payload && !is.nan(missing.placeholder)) {
# No-op as we're considering the NaN payload and the placeholder
# is not NaN (and thus must be an R NA).
} else {
# We set all NaN values to missing, regardless of their payloads.
# This is possible because is.na(), despite its name, calls the
# C isnan() under the hood, which just returns TRUE for all NaNs.
current[is.na(current)] <- NA
}
}
} else {
out <- restore_min_integer(current)
current <- out$y
converted <- out$converted
current[which(current == missing.placeholder)] <- NA # Using which() to avoid problems with existing NAs.
}
if (!converted && !is.null(expected.type)) {
target.type <- as.character(.atomics[expected.type])
if (target.type != typeof(current)) {
storage.mode(current) <- target.type
}
}
current
}
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