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#############################################################################
##
## Copyright 2016 Novartis Institutes for BioMedical Research Inc.
## Licensed under the Apache License, Version 2.0 (the "License");
## you may not use this file except in compliance with the License.
## You may obtain a copy of the License at
##
## http://www.apache.org/licenses/LICENSE-2.0
##
## Unless required by applicable law or agreed to in writing, software
## distributed under the License is distributed on an "AS IS" BASIS,
## WITHOUT WARRANTIES OR CONDITIONS OF ANY KIND, either express or implied.
## See the License for the specific language governing permissions and
## limitations under the License.
##
#############################################################################
setOldClass("H5D")
##' Class for representing HDF5 datasets
##'
##' In HDF5, datasets can be located in a group (see \code{\link{H5Group}}) or at the
##' root of a file (see \code{\link{H5File}}). They can be created either with a pre-existing R-object
##' (arrays as well as data.frames are supported, but not lists or other complex objects), or by specifying
##' an explicit datatype (for available datatypes see \code{h5types$overview} as well as the dimension.
##' In addition, other features are supported such as transparent compression (for which a chunk-size can be selected).
##'
##' In order to create a dataset, the \code{create_dataset} methods of either \code{\link{H5Group}} or
##' \code{\link{H5File}} should be used. Please see the documentation there for how to create them.
##'
##' The most important parts of a dataset are the
##' \describe{
##' \item{Space}{The space of the dataset. It describes the dimension of the dataset as well as the maximum dimensions.
##' Can be obtained using the \code{get_space} of the \code{\link{H5S}} object.}
##' \item{Datatype}{The datatypes that is being used in the dataset. Can be obtained using the \code{get_type} method.
##' See \code{\link{H5T}} to get more information about using datatypes.}
##' }
##'
##' In order to read and write datasets, the \code{read} and \code{write} methods are available. In addition, the standard way of using
##' \code{[} to access arrays is supported as well (see \code{\link{H5S_H5D_subset_assign}} for more help).
##'
##' Other information/action of possible interest are
##' \describe{
##' \item{Storage size}{The size of the dataset can be extracted using \code{get_storage_size}}
##' \item{Size change}{The size of the dataset can be changed using the \code{set_extent} method}
##' }
##'
##' Please also note the active methods
##' \describe{
##' \item{dims}{Dimension of the dataset}
##' \item{maxdims}{Maximum dimensions of the dataset}
##' \item{chunk_dims}{Dimension of the chunks}
##' \item{key_info}{Returns the space, type, property-list and dimensions}
##' }
##'
##' @docType class
##' @importFrom R6 R6Class
##' @return Object of class \code{\link{H5D}}.
##' @author Holger Hoefling
##' @examples
##' # First create a file to create datasets in it
##' fname <- tempfile(fileext = ".h5")
##' file <- H5File$new(fname, mode = "a")
##'
##' # Show the 3 different ways how to create a dataset
##' file[["directly"]] <- matrix(1:10, ncol=2)
##' file$create_dataset("from_robj", matrix(1:10, ncol=2))
##' dset <- file$create_dataset("basic", dtype=h5types$H5T_NATIVE_INT,
##' space=H5S$new("simple", dims=c(5, 2), maxdims=c(10,2)), chunk_dims=c(5,2))
##'
##' # Different ways of reading the dataset
##' dset$read(args=list(1:5, 1))
##' dset$read(args=list(1:5, quote(expr=)))
##' dset$read(args=list(1:5, NULL))
##' dset[1:5, 1]
##' dset[1:5, ]
##' dset[1:5, NULL]
##'
##' # Writing to the dataset
##' dset$write(args=list(1:3, 1:2), value=11:16)
##' dset[4:5, 1:2] <- -(1:4)
##' dset[,]
##'
##' # Extract key information
##' dset$dims
##' dset$maxdims
##' dset$chunk_dims
##' dset$key_info
##' dset
##'
##' file$close_all()
##' file.remove(fname)
##' @export
H5D <- R6Class("H5D",
inherit=H5RefClass,
public=list(
initialize=function(id=NULL) {
"Initializes a new dataset-object. Only for internal use. Use the \\code{create_dataset} function for \\code{\\link{H5Group}}"
"and \\code{\\link{H5File}} objects"
"@param id For internal use only"
if(is.null(id)) {
stop("An id has to be provided for a dataset of class H5D. For creating a dataset, use 'create_dataset' for an H5File or H5Group")
}
super$initialize(id=id)
},
get_space=function() {
"This function implements the HDF5-API function H5Dget_space."
"Please see the documentation at \\url{https://portal.hdfgroup.org/display/HDF5/H5D_GET_SPACE} for details."
id <- .Call("R_H5Dget_space", self$id, PACKAGE="hdf5r")$return_val
if(id < 0) {
stop("Error retrieving dataspace")
}
return(H5S$new(id=id))
},
get_space_status=function() {
"This function implements the HDF5-API function H5Dget_space_status."
"Please see the documentation at \\url{https://portal.hdfgroup.org/display/HDF5/H5D_GET_SPACE_STATUS} for details."
res <- .Call("R_H5Dget_space_status", self$id, request_empty(1), PACKAGE="hdf5r")
if(res$return_val < 0) {
stop("Error retrieving space status")
}
return(res$allocation)
},
get_type=function(native=TRUE) {
"This function implements the HDF5-API function H5Dget_type."
"Please see the documentation at \\url{https://portal.hdfgroup.org/display/HDF5/H5D_GET_TYPE} for details."
id <- standalone_H5D_get_type(h5d_id=self$id, native=native)
return(H5T_factory(id))
},
get_create_plist=function() {
"This function implements the HDF5-API function H5Dget_create_plist."
"Please see the documentation at \\url{https://portal.hdfgroup.org/display/HDF5/H5D_GET_CREATE_PLIST} for details."
id <- .Call("R_H5Dget_create_plist", self$id, PACKAGE="hdf5r")$return_val
if(id < 0) {
stop("Error retrieving dataset creation property list")
}
return(H5P_DATASET_CREATE$new(id=id))
},
get_access_plist=function() {
"This function implements the HDF5-API function H5Dget_access_plist."
"Please see the documentation at \\url{https://portal.hdfgroup.org/display/HDF5/H5D_GET_ACCESS_PLIST} for details."
id <- .Call("R_H5Dget_access_plist", self$id, PACKAGE="hdf5r")$return_val
if(id < 0) {
stop("Error retrieving dataset access property list")
}
return(H5P_DATASET_ACCESS$new(id=id))
},
get_offset=function() {
"This function implements the HDF5-API function H5Dget_offset."
"Please see the documentation at \\url{https://portal.hdfgroup.org/display/HDF5/H5D_GET_OFFSET} for details."
haddr <- .Call("R_H5Dget_offset", self$id, PACKAGE="hdf5r")$return_val
if(haddr < 0) {
stop("Error retrieving address; is undefined")
}
return(haddr)
},
get_storage_size=function() {
"This function implements the HDF5-API function H5Dget_storage_size."
"Please see the documentation at \\url{https://portal.hdfgroup.org/display/HDF5/H5D_GET_STORAGE_SIZE} for details."
size <- .Call("R_H5Dget_storage_size", self$id, PACKAGE="hdf5r")$return_val
return(size)
},
vlen_get_buf_size=function(type, space) {
"This function implements the HDF5-API function H5Dvlen_get_buf_size."
"Please see the documentation at \\url{https://portal.hdfgroup.org/display/HDF5/H5D_VLEN_GET_BUF_SIZE} for details."
check_class(type, "H5T")
check_class(space, "H5S")
res <- .Call("R_H5Dvlen_get_buf_size", self$id, type$id, space$id, request_empty(1), PACKAGE="hdf5r")
if(res$return_val < 0) {
stop("Error trying to calculate vlen buffer size")
}
return(res$size)
},
vlen_reclaim=function(buffer, type, space, dataset_xfer_pl=h5const$H5P_DEFAULT) {
"This function implements the HDF5-API function H5Dvlen_reclaim."
"Please see the documentation at \\url{https://portal.hdfgroup.org/display/HDF5/H5D_VLEN_RECLAIM} for details."
check_class(type, "H5T")
check_class(space, "H5S")
check_pl(dataset_xfer_pl, "H5P_DATASET_XFER")
herr <- .Call("R_H5Dvlen_reclaim", type$id, space$id, dataset_xfer_pl$id, buffer, FALSE, PACKAGE="hdf5r")$return_val
if(herr < 0 ) {
stop("Error trying to reclaim buffer vlen data")
}
return(invisible(self))
},
read_low_level=function(file_space=h5const$H5S_ALL, mem_space=NULL, mem_type=NULL,
dataset_xfer_pl=h5const$H5P_DEFAULT, flags=getOption("hdf5r.h5tor_default"), set_dim=FALSE, dim_to_set=NULL, drop=TRUE) {
"This function is for advanced users. It is recommended to use \\code{read} instead or the \\code{[} interface."
"This function implements the HDF5-API function H5Dread, with minor changes to the API to accommodate R."
"Please see the documentation at \\url{https://portal.hdfgroup.org/display/HDF5/H5D_READ} for details."
"It reads the data in the dataset as specified by \\code{mem_space} and return it as an R-obj"
"@param file_space An HDF5-space, represented as class \\code{\\link{H5S}} that determines which part"
"of the dataset is being read. Can also be given as an id"
"@param mem_space The space as it is represented in memory; advanced feature; may be removed in the future."
"Can also be given as an id."
"@param mem_type Memory type; extracted from the dataset if null (can be passed in for efficiency reasons"
"Can also be given as an id."
"@param dataset_xfer_pl Dataset transfer property list. See \\code{\\link{H5P_DATASET_XFER}}"
"@param flags Conversion rules for integer values. See also \\code{\\link{h5const}}"
"@param set_dim If \\code{TRUE}, the dimension attribute is set in the return value. How it is set "
"is determined by \\code{dim_to_set}."
"@param dim_to_set The dimension to set; Has to be numeric and needs to be specified if \\code{set_dim} is \\code{TRUE}."
"If the result is a data.frame, i.e. the data-type is a compound, then the dimension is ignored as the"
"correct dimension is already set."
"@param drop Logical. Should dimensions of length 1 be dropped (R-default for arrays)"
## first ensure that file_space of the correct types and extract the id
if(!inherits(file_space, "H5S") && !(is.integer64(file_space) && length(file_space) == 1)) {
stop("file_space has to be an id or of type H5T")
}
file_space_id <- get_id(file_space)
if(file_space_id==h5const$H5S_ALL$id) {
## get the actual file-space and ascertain its size
file_space_id <- .Call("R_H5Dget_space", self$id, PACKAGE="hdf5r")$return_val
on.exit(.Call("R_H5Sclose", file_space_id, PACKAGE = "hdf5r"), add=TRUE)
.Call("R_H5Sselect_all", file_space_id, PACKAGE = "hdf5r")
nelem <- .Call("R_H5Sget_select_npoints", file_space_id, PACKAGE = "hdf5r")$return_val
## in this case, we ignore what mem_space is set to
mem_space_id <- h5const$H5S_ALL$id
}
else {
## else, just get a linear space
nelem <- .Call("R_H5Sget_select_npoints", file_space_id, PACKAGE = "hdf5r")$return_val
if(is.null(mem_space)) {
## use this simple space; this may come with some speed penalties
## arguements are rank, dims, maxdims
mem_space_id <- as.integer64(.Call("R_H5Screate_simple", 1, nelem, nelem, PACKAGE="hdf5r")$return_val)
if(mem_space_id < 0) {
stop("Error creating simple dataspace")
}
on.exit(.Call("R_H5Sclose", mem_space_id, PACKAGE = "hdf5r"), add=TRUE)
}
else {
if(!inherits(mem_space, "H5S") && !(is.integer64(mem_space) && length(mem_space) == 1)) {
stop("mem_space has to be an id or of type H5T")
}
## extract the id that was given
mem_space_id <- get_id(mem_space)
}
}
## ok, now the file_space_id and the mem_space_id are set
if(is.null(mem_type)) {
mem_type_id <- standalone_H5D_get_type(h5d_id=self$id, native=TRUE)
on.exit(.Call("R_H5Tclose", mem_type_id, PACKAGE = "hdf5r"), add=TRUE)
}
else {
if(!inherits(mem_type, "H5T") && !(is.integer64(mem_type) && length(mem_type) == 1)) {
stop("mem_type has to be an id or of type H5T")
}
## now extract the ids
mem_type_id <- get_id(mem_type)
}
check_pl(dataset_xfer_pl, "H5P_DATASET_XFER")
## need to create the buffer to write this into
buffer <- .Call("R_H5ToR_Pre", mem_type_id, nelem, PACKAGE="hdf5r")
res <- .Call("R_H5Dread", self$id, mem_type_id, mem_space_id, file_space_id, dataset_xfer_pl$id,
buffer, FALSE, PACKAGE="hdf5r")
if(res$return_val < 0) {
stop("Error reading dataset")
}
buffer_post <- .Call("R_H5ToR_Post", res$buf, mem_type_id, nelem, flags, self$id, PACKAGE="hdf5r")
if(set_dim && !inherits(buffer_post, "data.frame")) {
if(is.null(dim_to_set)) {
stop("dim_to_set needs to be specified if set_dim is true")
}
if(length(buffer_post) != prod(dim_to_set)) {
stop("Length of read object unequal to product of dim_to_set")
}
if(drop) {
dim_to_set <- dim_to_set[dim_to_set != 1]
}
if(length(dim_to_set) > 1) {
.Call("set_dim_attribute", buffer_post, as.numeric(dim_to_set), PACKAGE = "hdf5r")
}
}
## reclaim vlen data if the mem_type is vlen
## first need to know if it is vlen; may in future integrate with R_H5ToR_Post
mem_type_is_vlen <- as.logical(.Call("R_H5Tdetect_vlen", mem_type_id, PACKAGE = "hdf5r")$return_val)
if(mem_type_is_vlen) {
mem_space_explicit_id <- as.integer64(.Call("R_H5Screate_simple", 1, nelem, nelem, PACKAGE="hdf5r")$return_val)
if(mem_space_explicit_id < 0) {
stop("Error creating simple dataspace")
}
on.exit(.Call("R_H5Sclose", mem_space_explicit_id, PACKAGE = "hdf5r"), add=TRUE)
herr <- .Call("R_H5Dvlen_reclaim", mem_type_id, mem_space_explicit_id,
dataset_xfer_pl$id, buffer, FALSE, PACKAGE="hdf5r")$return_val
if(herr < 0 ) {
stop("Error trying to reclaim buffer vlen data")
}
}
return(buffer_post)
},
read=function(args=NULL, dataset_xfer_pl=h5const$H5P_DEFAULT, flags=getOption("hdf5r.h5tor_default"), drop=TRUE, envir=parent.frame()) {
"Main interface for reading data from the dataset. It is the function that is used by \\code{[}, where"
"all indices are being passed in the parameter \\code{args}."
"@param args The indices for each dimension to subset given as a list. This makes this easier to use as a programmatic API."
"For interactive use we recommend the use of the \\code{[} operator. If set to \\code{NULL}, the entire dataset will be read."
"@param envir The environment in which to evaluate \\code{args}"
"@param dataset_xfer_pl An object of class \\code{\\link{H5P_DATASET_XFER}}."
"@param flags Some flags governing edge cases of conversion from HDF5 to R. This is related to how integers are being treated and"
"the issue of R not being able to natively represent 64bit integers and not at all being able to represent unsigned 64bit integers"
"(even using add-on packages). The constants governing this are part of \\code{\\link{h5const}}. The relevant ones start with the term"
"\\code{H5TOR} and are documented there. The default set here returns a regular 32bit integer if it doesn't lead to an overflow"
"and returns a 64bit integer from the \\code{bit64} package otherwise. For 64bit unsigned int that are larger than 64bit signed int,"
"it return a \\code{double}. This looses precision, however."
"@param drop Logical. When reading data, should dimensions of size 1 be dropped."
"@return The data that was read as an R object"
self_space_id <- as.integer64(.Call("R_H5Dget_space", self$id, PACKAGE="hdf5r")$return_val)
on.exit(.Call("R_H5Sclose", self_space_id, PACKAGE = "hdf5r"), add=TRUE)
self_space_is_simple <- as.logical(.Call("R_H5Sis_simple", self_space_id, PACKAGE = "hdf5r")$return_val)
if(!self_space_is_simple) {
stop("Dataspace has to be simple for a selection to occur")
}
simple_extent <- standalone_H5S_get_simple_extent_dims(self_space_id)
## distinguish between scalar and non-scalar
if(simple_extent$rank == 0) {
if(is.null(args)) {
args <- list(quote(expr=))
}
## is a scalar
if(are_args_scalar(args)) {
res <- self$read_low_level(file_space=self_space_id, mem_space=self_space_id, dataset_xfer_pl=dataset_xfer_pl)
}
else {
stop("Scalar dataspace; arguments have to be of length 1 and empty or equal to 1")
}
}
else {
dset_rank <- simple_extent$rank
if(is.null(args)) {
## create arguments that are missing in every dimension, i.e. represent all
args <- rep(list(quote(expr=)), dset_rank)
}
reg_eval_res <- args_regularity_evaluation(args=args, ds_dims=simple_extent$dims, envir=envir)
## need to check if maximum dimension in indices are larger than dataset dimensions
## if yes need to throw an error
if(any(reg_eval_res$max_dims > simple_extent$dims)) {
stop("The following coordinates are outside the dataset dimensions: ",
paste(which(reg_eval_res$max_dims > simple_extent$dims), sep=", "))
}
robj_dim <- private$get_robj_dim(reg_eval_res)
selection <- regularity_eval_to_selection(reg_eval_res=reg_eval_res)
apply_selection(space_id=self_space_id, selection=selection)
## create the memory space
mem_space_dims <- reg_eval_res$result_dims_pre_shuffle
mem_space_rank <- length(mem_space_dims)
mem_space_id <- as.integer64(.Call("R_H5Screate_simple", mem_space_rank, rev(mem_space_dims), rev(mem_space_dims),
PACKAGE="hdf5r")$return_val)
if(mem_space_id < 0) {
stop("Error creating simple dataspace")
}
on.exit(.Call("R_H5Sclose", mem_space_id, PACKAGE = "hdf5r"), add=TRUE)
## check if we have a compound, where we don't have to set
dim_to_set <- robj_dim$robj_dim_pre_shuffle
res <- self$read_low_level(file_space=self_space_id, mem_space=mem_space_id,
dataset_xfer_pl=dataset_xfer_pl, set_dim=TRUE, dim_to_set=dim_to_set, drop=drop)
if(any(reg_eval_res$needs_reshuffle)) {
res <- do_reshuffle(res, reg_eval_res)
}
}
return(res)
},
write_low_level=function(robj, file_space=h5const$H5S_ALL, mem_space=NULL, mem_type=NULL, dataset_xfer_pl=h5const$H5P_DEFAULT,
flush=getOption("hdf5r.flush_on_write")) {
"This function is for advanced users. It is recommended to use \\code{read} instead or the \\code{[<-} interface"
"as used for arrays."
"This function implements the HDF5-API function H5Dwrite, with some changes to accommodate R."
"Please see the documentation at \\url{https://portal.hdfgroup.org/display/HDF5/H5D_WRITE} for details."
"It writes that data from the \\code{robj} into the dataset."
"@param robj The object to write into the dataset"
"@param mem_space The space as it is represented in memory; advanced feature; may be removed in the future"
"@param mem_type Memory type; extracted from the dataset if null (can be passed in for efficiency reasons"
"@param file_space An HDF5-space, represented as class \\code{\\link{H5S}} that determines which part"
"of the dataset is being written."
"@param dataset_xfer_pl Dataset transfer property list. See \\code{\\link{H5P_DATASET_XFER}}"
"@param flush Should a flush be done after the write"
## first ensure that file_space of the correct types and extract the id
if(!inherits(file_space, "H5S") && !(is.integer64(file_space) && length(file_space) == 1)) {
stop("file_space has to be an id or of type H5T")
}
file_space_id <- get_id(file_space)
if(file_space_id==h5const$H5S_ALL$id) {
## get the actual file-space and ascertain its size
file_space_id <- .Call("R_H5Dget_space", self$id, PACKAGE="hdf5r")$return_val
on.exit(.Call("R_H5Sclose", file_space_id, PACKAGE = "hdf5r"), add=TRUE)
.Call("R_H5Sselect_all", file_space_id, PACKAGE = "hdf5r")
nelem_file <- .Call("R_H5Sget_select_npoints", file_space_id, PACKAGE = "hdf5r")$return_val
## in this case, we ignore what mem_space is set to
mem_space_id <- h5const$H5S_ALL$id
}
else {
## else, just get a linear space
nelem_file <- .Call("R_H5Sget_select_npoints", file_space_id, PACKAGE = "hdf5r")$return_val
if(is.null(mem_space)) {
## use this simple space; this may come with some speed penalties
## arguements are rank, dims, maxdims
mem_space_id <- as.integer64(.Call("R_H5Screate_simple", 1, nelem_file, nelem_file, PACKAGE="hdf5r")$return_val)
if(mem_space_id < 0) {
stop("Error creating simple dataspace")
}
on.exit(.Call("R_H5Sclose", mem_space_id, PACKAGE = "hdf5r"), add=TRUE)
}
else {
if(!inherits(mem_space, "H5S") && !(is.integer64(mem_space) && length(mem_space) == 1)) {
stop("mem_space has to be an id or of type H5T")
}
## extract the id that was given
mem_space_id <- get_id(mem_space)
}
}
if(is.null(mem_type)) {
mem_type_id <- standalone_H5D_get_type(h5d_id=self$id, native=TRUE)
on.exit(.Call("R_H5Tclose", mem_type_id, PACKAGE = "hdf5r"), add=TRUE)
}
else {
if(!inherits(mem_type, "H5T") && !(is.integer64(mem_type) && length(mem_type) == 1)) {
stop("mem_type has to be an id or of type H5T")
}
## now extract the ids
mem_type_id <- get_id(mem_type)
}
nelem_robj <- .Call("R_guess_nelem", robj, mem_type_id, PACKAGE="hdf5r")
if(nelem_robj != nelem_file && (nelem_file %% nelem_robj != 0 || nelem_file < nelem_robj)) {
stop("Number of objects in robj is not the same and not a multiple of number of elements selected in file: expected are ",
nelem_file, " but provided are ", nelem_robj)
}
buffer <- .Call("R_RToH5", robj, mem_type_id, nelem_robj, PACKAGE="hdf5r")
if(nelem_robj != nelem_file) {
## need to multiply input buffer
buffer <- rep(buffer, times=nelem_file / nelem_robj)
}
res <- .Call("R_H5Dwrite", self$id, mem_type_id, mem_space_id, file_space_id, dataset_xfer_pl$id,
buffer, PACKAGE="hdf5r")
if(res$return_val < 0) {
stop("Error writing dataset")
}
if(flush) {
self$flush
}
return(invisible(self))
},
write=function(args, value, dataset_xfer_pl=h5const$H5P_DEFAULT, envir=parent.frame()) {
"Main interface for writing data to the dataset. It is the function that is used by \\code{[<-}, where"
"all indices are being passed in the parameter \\code{args}."
"@param args The indices for each dimension to subset given as a list. This makes this easier to use as a programmatic API."
"For interactive use we recommend the use of the \\code{[} operator. If set to \\code{NULL}, the entire dataset will be read."
"@param value The data to write to the dataset"
"@param envir The environment in which to evaluate \\code{args}"
"@param dataset_xfer_pl An object of class \\code{\\link{H5P_DATASET_XFER}}."
"@return The HDF5 dataset object, returned invisibly"
self_space_id <- as.integer64(.Call("R_H5Dget_space", self$id, PACKAGE="hdf5r")$return_val)
on.exit(.Call("R_H5Sclose", self_space_id, PACKAGE = "hdf5r"), add=TRUE)
self_space_is_simple <- as.logical(.Call("R_H5Sis_simple", self_space_id, PACKAGE = "hdf5r")$return_val)
if(!self_space_is_simple) {
stop("Dataspace has to be simple for a selection to occur")
}
simple_extent <- standalone_H5S_get_simple_extent_dims(self_space_id)
## distinguish between scalar and non-scalar
if(simple_extent$rank == 0) {
if(is.null(args)) {
args <- list(quote(expr=))
}
## is a scalar
if(are_args_scalar(args)) {
return(self$write_low_level(value, file_space=self_space_id, mem_space=self_space_id, dataset_xfer_pl=dataset_xfer_pl))
}
else {
stop("Scalar dataspace; arguments have to be of length 1 and empty or equal to 1")
}
}
else {
if(is.null(args)) {
## create arguments that are missing in every dimension, i.e. represent all
args <- rep(list(quote(expr=)), simple_extent$rank)
}
reg_eval_res <- args_regularity_evaluation(args=args, ds_dims=simple_extent$dims, envir=envir, post_read=FALSE)
robj_dim <- private$get_robj_dim(reg_eval_res)
if(any(reg_eval_res$needs_reshuffle)) {
## need to ensure that the input has the right dimensions attached in case it is just a vector)
## and dimensions doesn't need to be reset for data.frames; there they are automatically correct
if(!inherits(value, "data.frame")) {
dim(value) <- robj_dim$robj_dim_pre_shuffle
}
value <- do_reshuffle(value, reg_eval_res)
}
## need to check if maximum dimension in indices are larger than dataset dimensions
## if yes need to throw an error
if(any(reg_eval_res$max_dims > simple_extent$dims)) {
## need to reset the extent of the arguments
if(any(reg_eval_res$max_dims > simple_extent$maxdims)) {
stop("The following coordinates are larger than the largest possible dataset dimensions (maxdims): ",
paste(which(reg_eval_res$max_dims > simple_extent$maxdims), sep=", "))
}
## need to check that value conforms to the right dimension for the arguments
## this is needed before a possible expansion of arguments
mem_type_id <- standalone_H5D_get_type(h5d_id=self$id, native=TRUE)
nelem_value <- .Call("R_guess_nelem", value, mem_type_id, PACKAGE="hdf5r")
.Call("R_H5Tclose", mem_type_id, PACKAGE = "hdf5r")
num_args_elem <- prod(reg_eval_res$result_dims_post_shuffle)
if(nelem_value != num_args_elem && (num_args_elem %% nelem_value != 0 || num_args_elem < nelem_value)) {
stop("Number of objects in robj is not the same and not a multiple of number of elements selected in file")
}
self$set_extent(pmax(reg_eval_res$max_dims, simple_extent$dims))
.Call("R_H5Sclose", self_space_id, PACKAGE = "hdf5r")
self_space_id <- as.integer64(.Call("R_H5Dget_space", self$id, PACKAGE="hdf5r")$return_val)
on.exit(.Call("R_H5Sclose", self_space_id, PACKAGE = "hdf5r"), add=FALSE)
}
## create the memory space
## go through all the robj-dimension
selection <- regularity_eval_to_selection(reg_eval_res=reg_eval_res)
apply_selection(space_id=self_space_id, selection=selection)
mem_space_dims <- reg_eval_res$result_dims_post_shuffle
mem_space_rank <- length(mem_space_dims)
mem_space_id <- as.integer64(.Call("R_H5Screate_simple", mem_space_rank, rev(mem_space_dims), rev(mem_space_dims),
PACKAGE="hdf5r")$return_val)
if(mem_space_id < 0) {
stop("Error creating simple dataspace")
}
on.exit(.Call("R_H5Sclose", mem_space_id, PACKAGE = "hdf5r"), add=TRUE)
return(self$write_low_level(value, file_space=self_space_id, mem_space=mem_space_id, dataset_xfer_pl=dataset_xfer_pl))
}
},
set_extent=function(dims) {
"This function implements the HDF5-API function H5Dset_extent."
"Please see the documentation at \\url{https://portal.hdfgroup.org/display/HDF5/H5D_SET_EXTENT} for details."
rank <- self$get_space()$get_simple_extent_ndims()
if(length(dims) != rank) {
stop(paste("Length of dims is", length(dims), "but has to be equal to the rank of the dataspace:", rank))
}
res <- .Call("R_H5Dset_extent", self$id, rev(dims), PACKAGE="hdf5r")$return_val
if(res < 0) {
stop("Error setting new extent")
}
return(invisible(self))
},
get_fill_value=function() {
"This function implements the HDF5-API function H5Pget_fill_value, automatically"
"supplying the datatype of the dataset for convenience."
"Please see the documentation at \\url{https://portal.hdfgroup.org/display/HDF5/H5P_GET_FILL_VALUE} for details."
dtype <- self$get_type()
create_plist <- self$get_create_plist()
value_h5 <- H5ToR_Pre(dtype, 1)
res <- .Call("R_H5Pget_fill_value", create_plist$id, dtype$id, value_h5, FALSE, PACKAGE="hdf5r")
if(res$return_val < 0) {
stop("Error retrieving fill value")
}
return(H5ToR_Post(value_h5, dtype, 1, -1))
},
create_reference=function(...) {
"This function implements the HDF5-API function H5Rcreate. The parameters are interpreted as in '['."
"The function always create \\code{H5R_DATASET_REGION} references"
"Please see the documentation at \\url{https://portal.hdfgroup.org/display/HDF5/H5R_CREATE} for details."
space <- self$get_space()
do.call("[", c(list(space), list(...)))
ref_type <- h5const$H5R_DATASET_REGION
ref_obj <- H5R_DATASET_REGION$new(1, self)
res <- .Call("R_H5Rcreate", ref_obj$ref, self$id, ".", h5const$H5R_DATASET_REGION, space$id, FALSE, PACKAGE="hdf5r")
if(res$return_val < 0) {
stop("Error creating object reference")
}
ref_obj$ref <- res$ref
return(ref_obj)
},
print=function(..., max.attributes = 10){
"Prints information for the dataset"
"@param ... ignored"
"@param max.attributes Maximum number of attribute names to print"
is_valid <- self$is_valid
print_class_id(self, is_valid)
if(is_valid) {
## get information about the file
## get the dataset name
cat("Dataset: ", self$get_obj_name(), "\n", sep="")
## get information about the file
this_file <- self$get_file_id()
cat("Filename: ", normalizePath(this_file$filename, mustWork=FALSE), "\n", sep="")
cat("Access type: ", as.character(this_file$get_intent()), "\n", sep="")
this_file$close()
## get attributes
print_attributes(self, max_to_print=max.attributes)
## get the datatype
this_dtype <- self$get_type()
type_text <- this_dtype$to_text()
cat("Datatype: ", type_text, "\n", sep="")
this_dtype$close()
## get the dataspace
this_space <- self$get_space()
if(!this_space$is_simple()) {
## has to be a NULL space
cat("Space: Type=NULL\n")
}
else {
extent_res <- this_space$get_simple_extent_dims()
if(extent_res$rank == 0) {
cat("Space: Type=Scalar\n")
}
else {
cat("Space: Type=Simple ")
cat("Dims=", paste(extent_res$dims, collapse=" x "), " ", sep="")
cat("Maxdims=", paste(extent_res$maxdims, collapse=" x "), "\n", sep="")
}
}
this_space$close()
this_chunk_dims <- self$chunk_dims
if(length(this_chunk_dims) == 1 && is.na(this_chunk_dims)) {
cat("Not chunked\n")
}
else {
cat("Chunk: ", paste(this_chunk_dims, collapse=" x "), "\n", sep="")
}
}
return(invisible(self))
}
),
active=list(
dims=function() {
"Get the dimension of the dataset"
ds_space <- self$get_space()
res <- ds_space$dims
ds_space$close()
return(res)
},
maxdims=function() {
"Get the maximal dimension of the dataset"
ds_space <- self$get_space()
res <- ds_space$maxdims
ds_space$close()
return(res)
},
chunk_dims=function() {
"Return the dimension of the chunks. NA if the dataset is not chunked"
dataset_create_pl <- self$get_create_plist()
ds_space <- self$get_space()
ndims <- ds_space$get_simple_extent_ndims()
ds_space$close()
res <- dataset_create_pl$get_chunk(ndims)
dataset_create_pl$close()
return(res)
},
key_info=function() {
"Returns the key types as a list, consisting of type, space, dataset_create_pl,"
"type_size_raw, type_size_variable, dims and chunk_dims."
"type_size_raw versus variable differs for variable length types, which return \\code{Inf}"
"for type_size_variable and the underlying size for type_size_raw"
ds_space <- self$get_space()
ds_type <- self$get_type(native=TRUE)
ds_create_pl <- self$get_create_plist()
ds_dims <- ds_space$dims
return(list(space=ds_space, type=ds_type, create_pl=ds_create_pl,
type_size_raw=ds_type$get_size(variable_as_inf=FALSE), type_size_variable=ds_type$get_size(variable_as_inf=TRUE),
dims=ds_dims, chunk_dims=ds_create_pl$get_chunk(length(ds_dims))))
}
),
private=list(
closeFun=function(id) {
nrt <- NA
if(!is.na(id) && is.loaded("R_H5Dclose", PACKAGE="hdf5r")) {
invisible(.Call("R_H5Dclose", id, PACKAGE = "hdf5r"))
}
},
get_robj_dim=function(reg_eval_res) {
"Get the size of the resulting R object"
""
"For normal objects, just uses the size of the indices in the request, and evaluates"
"them bost pre- and post-shuffle. If the internal object is an array, additional dimensions"
"are appended at the end."
"@title Get the size of the resulting R object"
"@param reg_eval_res The result of the regularity evaluation"
"@param dtype The datatype under consideration"
"@return A list with the dimensions of the resulting object, pre- and post shuffle"
"@author Holger Hoefling"
"@keywords internal"
add_array_dims <- NULL
dtype_id <- standalone_H5D_get_type(h5d_id=self$id, native=TRUE)
on.exit(.Call("R_H5Tclose", dtype_id, PACKAGE = "hdf5r"), add=TRUE)
dtype_cls_id <- .Call("R_H5Tget_class", dtype_id, PACKAGE="hdf5r")$return_val
if(dtype_cls_id == h5const$H5T_ARRAY) {
## here we call the function separately for efficiency reasons
rank <- .Call("R_H5Tget_array_ndims", dtype_id, PACKAGE="hdf5r")$return_val
dims <- integer(rank)
add_array_dims <- .Call("R_H5Tget_array_dims2", dtype_id, dims, PACKAGE="hdf5r")$dims
}
robj_dim_pre_shuffle <- c(reg_eval_res$result_dims_pre_shuffle, add_array_dims)
robj_dim_post_shuffle <- c(reg_eval_res$result_dims_post_shuffle, add_array_dims)
return(list(robj_dim_pre_shuffle=robj_dim_pre_shuffle,
robj_dim_post_shuffle=robj_dim_post_shuffle, add_array_dims=add_array_dims))
}
),
cloneable=FALSE
)
R6_set_list_of_items(H5D, "public", commonFGDT, overwrite=TRUE)
R6_set_list_of_items(H5D, "public", commonFGDTA, overwrite=TRUE)
##' Get the id of an H5RefClass
##'
##' If it is a H5RefClass, returns the id, otherwise returns the
##' object itself as it assumes it is already an id.
##' @title Get the id of an H5RefClass
##' @param obj Object to get the id from
##' @return The id itself
##' @author Holger Hoefling
##' @keywords internal
get_id <- function(obj) {
if(inherits(obj, "H5RefClass")) {
return(obj$id)
}
else {
return(obj)
}
}
##' Get the id of a type of the dataset
##'
##' A function that just returns an id; it is written standalone so that
##' one can use it to avoid the creation of R6 classes that be a considerable overhead in
##' certain circumstances
##' @title Get the id of a type of the dataset
##' @param native Should it be ensured that it is a native type
##' @param h5d_id The id of the dataset to get the type from
##' @return An id; the user has to ensure that the id is eventually closed
##' @author Holger Hoefling
##' @keywords internal
standalone_H5D_get_type <- function(h5d_id, native=TRUE) {
id <- .Call("R_H5Dget_type", h5d_id, PACKAGE="hdf5r")$return_val
if(id < 0) {
stop("Error retrieving datatype of dataset")
}
if(native) {
## return the native type
id_native <- .Call("R_H5Tget_native_type", id, h5const$H5T_DIR_ASCEND, PACKAGE="hdf5r")$return_val
## have the new id, can close the old one
.Call("R_H5Tclose", id, PACKAGE="hdf5r")
if(id_native < 0) {
stop("Error retrieving native-c-type")
}
return(id_native)
}
else {
return(id)
}
}
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