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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.
##
#############################################################################
##' Extract HDF5-ids and return as a vector
##'
##' Internal helper function. Given a list of id-type-objects, it extracts the
##' ids itself and returns them as a vector
##' @title Extract HDF5-ids and return as a vector
##' @param dtype_ids Ids itself or class objects to extract the ids from.
##' @return The ids as a integer64-vector
##' @author Holger Hoefling
##' @importFrom bit64 as.integer64
##' @keywords internal
H5T_extractID <- function(dtype_ids) {
if(inherits(dtype_ids, "H5T")) {
dtype_ids_out <- dtype_ids$id
}
else if(is.list(dtype_ids)) {
for(i in seq_along(dtype_ids)) {
dtype_ids[[i]] <- H5T_extractID(dtype_ids[[i]])
}
dtype_ids_out <- unlist(dtype_ids)
class(dtype_ids_out) <- "integer64"
}
else if(is.numeric(dtype_ids)) {
if(any(bit64::as.integer64(dtype_ids) != dtype_ids)) {
stop("Numeric values cannot be coerced to integer")
}
else {
dtype_ids_out <- bit64::as.integer64(dtype_ids)
names(dtype_ids_out) <- names(dtype_ids)
}
}
else {
stop("'dtype_ids' has to be a vector or list with elements of type 'H5T' or integer (or coercible to integer)")
}
return(dtype_ids_out)
}
##' Turn ids into \code{\link{H5T}} objects
##'
##' Gets the HDF5 internal class for an id and dispatches them so that the correct
##' R6es are being created.
##' @title Turn ids into \code{\link{H5T}} objects
##' @param ids The ids to return as objects
##' @param do_copy Should the ids be copied using HDF5s internal copy mechanism
##' @return An object of type R6 class \code{\link{H5T}}
##' @author Holger Hoefling
##' @importFrom bit64 as.integer64
##' @keywords internal
H5T_factory <- function(ids, do_copy=FALSE) {
if(!missing(ids)) {
ids <- H5T_extractID(ids)
## look at the ids and their class, and produce the appropriate H5T class
res <- vector("list", length=length(ids))
for(i in seq_along(ids)) {
if(do_copy) {
foo <- .Call("R_H5Tcopy", bit64::as.integer64(ids[i]), PACKAGE="hdf5r")$return_val
ids[i] <- foo
}
if(is.na(ids[i]) || ids[i] < 0) {
stop("Invalid ids")
}
cls_id <- .Call("R_H5Tget_class", bit64::as.integer64(ids[i]), PACKAGE="hdf5r")$return_val
if(cls_id == "H5T_NO_CLASS") {
stop("Unknown cls_id")
}
class_name <- as.character(cls_id)
## now if it is a compound, need to check if it should be a H5T_COMPLEX
if(class_name == "H5T_COMPOUND") {
labels <- .Call("h5get_compound_names", ids[i], PACKAGE="hdf5r")$return_val
if(length(labels) == 2 && all(labels == c("Real", "Imaginary"))) {
class_name <- "H5T_COMPLEX"
}
}
## if is enum, need to check if it is logical
if(class_name == "H5T_ENUM") {
labels = .Call("h5get_enum_labels", ids[i], PACKAGE="hdf5r")$return_val
values = .Call("h5get_enum_values", ids[i], PACKAGE="hdf5r")$return_val
if(length(labels) == 3 && length(values) == 3 && all(labels==c("FALSE", "TRUE", "NA")) && all(values==c(0,1,2))) {
class_name <- "H5T_LOGICAL"
}
else if(length(labels) == 2 && length(values) == 2 && all(labels==c("FALSE", "TRUE")) && all(values==c(0,1))) {
class_name <-"H5T_LOGICAL"
}
}
res[[i]] <- switch(class_name, H5T_COMPOUND=H5T_COMPOUND$new(id=ids[i]), H5T_COMPLEX=H5T_COMPLEX$new(id=ids[i]),
H5T_ENUM=H5T_ENUM$new(id=ids[i]), H5T_LOGICAL=H5T_LOGICAL$new(id=ids[i]),
H5T_ARRAY=H5T_ARRAY$new(id=ids[i]), H5T_STRING=H5T_STRING$new(id=ids[i]),
H5T_VLEN=H5T_VLEN$new(id=ids[i]), H5T_INTEGER=H5T_INTEGER$new(id=ids[i]), H5T_FLOAT=H5T_FLOAT$new(id=ids[i]),
H5T_BITFIELD=H5T_BITFIELD$new(id=ids[i]),
H5T$new(id=ids[i]))
}
if(length(ids)==1) {
return(res[[1]])
}
else {
names(res) <- names(ids)
return(res)
}
}
else {
return(list())
}
}
##' Convert a text description to a datatype
##'
##' Converts a text to a datatype using the HDF5 function H5LT_text_to_dtype. Documentation can be found at
##' \url{https://portal.hdfgroup.org/display/HDF5/H5LT_TEXT_TO_DTYPE}.
##' @title Convert a text description to a datatype
##' @param text The text to convert to the datatype
##' @param lang_type The type of language to use; currently only \code{H5LT_DDL} is supported.
##' @return A datatype corresponding to the text with the appropriate class inheriting from \code{\link{H5T}}.
##' @author Holger Hoefling
##' @export
text_to_dtype <- function(text, lang_type=h5const$H5LT_DDL) {
id <- .Call("R_H5LTtext_to_dtype", paste(as.character(text), collapse = "\n"), h5const$H5LT_DDL, PACKAGE = "hdf5r")$return_val
if(id < 0) {
stop("Error trying to convert text to a datatype")
}
return(H5T_factory(ids=id))
}
#' Class for HDF5 datatypes.
#'
#' This is the base class for all datatypes, but most have a specialised class.
#' This class represents an HDF5 datatype. It inherits all functions of the
#' \code{\link{H5RefClass}}. It is also the base class for many other classes well, specifically
#' \describe{
#' \item{Integer}{\code{\link{H5T_INTEGER}}}
#' \item{Bitfield}{\code{\link{H5T_BITFIELD}} (currently identical to the integer class)}
#' \item{Float}{\code{\link{H5T_FLOAT}}}
#' \item{Enum}{\code{\link{H5T_ENUM}}}
#' \item{Compound}{\code{\link{H5T_COMPOUND}}}
#' \item{String}{\code{\link{H5T_STRING}}}
#' \item{Complex}{\code{\link{H5T_COMPLEX}}}
#' \item{Array}{\code{\link{H5T_ARRAY}}}
#' \item{Variable Length}{\code{\link{H5T_VLEN}}}
#' }
#' @docType class
#' @importFrom R6 R6Class
#' @return Object of class \code{\link{H5T}}.
#' @author Holger Hoefling
#'
#' @examples
#' my_int <- h5types$H5T_NATIVE_INT
#' my_int$to_text()
#' my_int$get_size()
#'
#' # Show how to commit a datatype
#' fname <- tempfile(fileext = ".h5")
#' file <- H5File$new(fname, mode = "a")
#' my_int$is_committed()
#' file$commit("my_int", my_int)
#' my_int$is_committed()
#'
#' # can now also add attributes
#' h5attr(my_int, "test") <- "A string"
#' h5attributes(my_int)
#'
#' file$close_all()
#' file.remove(fname)
#' @export
H5T <- R6Class("H5T",
inherit=H5RefClass,
public=list(
initialize=function(id) {
"Internal use only"
super$initialize(id)
},
get_class=function() {
"This function implements the HDF5-API function H5Tget_class."
"Please see the documentation at \\url{https://portal.hdfgroup.org/display/HDF5/H5T_GET_CLASS} for details."
cls_id <- .Call("R_H5Tget_class", self$id, PACKAGE="hdf5r")$return_val
return(cls_id)
},
get_size=function(...) {
"This function implements the HDF5-API function H5Tget_size."
"Please see the documentation at \\url{https://portal.hdfgroup.org/display/HDF5/H5T_GET_SIZE} for details."
"@param ... ignored"
return(.Call("R_H5Tget_size", self$id, PACKAGE="hdf5r")$return_val)
},
set_size=function(size) {
"This function implements the HDF5-API function H5Tset_size."
"Please see the documentation at \\url{https://portal.hdfgroup.org/display/HDF5/H5T_SET_SIZE} for details."
if(size==Inf) {
if(self$get_class() != h5const$H5T_STRING) {
stop("Can only set to infinite size if datatype is a string; use H5T_VLEN instead for variable length data")
}
herr <- .Call("R_H5Tset_size", self$id, Inf, PACKAGE="hdf5r")$return_val
}
else {
herr <- .Call("R_H5Tset_size", self$id, as.integer(size), PACKAGE="hdf5r")$return_val
}
if(herr < 0) {
stop("Could not set size to specified value")
}
return(invisible(self))
},
set_precision=function(precision) {
"This function implements the HDF5-API function H5Tset_precision."
"Please see the documentation at \\url{https://portal.hdfgroup.org/display/HDF5/H5T_SET_PRECISION} for details."
herr <- .Call("R_H5Tset_precision", self$id, as.integer(precision), PACKAGE = "hdf5r")$return_val
if(herr < 0) {
stop("Could not set precision")
}
return(invisible(self))
},
get_precision=function() {
"This function implements the HDF5-API function H5Tget_precision."
"Please see the documentation at \\url{https://portal.hdfgroup.org/display/HDF5/H5T_GET_PRECISION} for details."
prec <- .Call("R_H5Tget_precision", self$id, PACKAGE = "hdf5r")$return_val
if(prec < 0) {
stop("There was an error retrieving the precision")
}
return(prec)
},
set_order=function(order) {
"This function implements the HDF5-API function H5Tset_order."
"Please see the documentation at \\url{https://portal.hdfgroup.org/display/HDF5/H5T_SET_ORDER} for details."
herr <- .Call("R_H5Tset_order", self$id, as.integer(order), PACKAGE = "hdf5r")$return_val
if(herr < 0) {
stop("Could not set order")
}
return(invisible(self))
},
get_order=function() {
"This function implements the HDF5-API function H5Tget_order."
"Please see the documentation at \\url{https://portal.hdfgroup.org/display/HDF5/H5T_GET_ORDER} for details."
order <- .Call("R_H5Tget_order", self$id, PACKAGE = "hdf5r")$return_val
if(order < 0) {
stop("There was an error retrieving the order")
}
return(order)
},
set_offset=function(offset) {
"This function implements the HDF5-API function H5Tset_offset."
"Please see the documentation at \\url{https://portal.hdfgroup.org/display/HDF5/H5T_SET_OFFSET} for details."
herr <- .Call("R_H5Tset_offset", self$id, as.integer(offset), PACKAGE = "hdf5r")$return_val
if(herr < 0) {
stop("Could not set offset")
}
return(invisible(self))
},
get_offset=function() {
"This function implements the HDF5-API function H5Tget_offset."
"Please see the documentation at \\url{https://portal.hdfgroup.org/display/HDF5/H5T_GET_OFFSET} for details."
offset <- .Call("R_H5Tget_offset", self$id, PACKAGE = "hdf5r")$return_val
if(offset < 0) {
stop("There was an error retrieving the offset")
}
return(offset)
},
set_pad=function(pad) {
"This function implements the HDF5-API function H5Tset_pad."
"Please see the documentation at \\url{https://portal.hdfgroup.org/display/HDF5/H5T_SET_PAD} for details."
herr <- .Call("R_H5Tset_pad", self$id, as.integer(pad), PACKAGE = "hdf5r")$return_val
if(herr < 0) {
stop("Could not set pad")
}
return(invisible(self))
},
get_pad=function() {
"This function implements the HDF5-API function H5Tget_pad."
"Please see the documentation at \\url{https://portal.hdfgroup.org/display/HDF5/H5T_GET_PAD} for details."
pad <- .Call("R_H5Tget_pad", self$id, PACKAGE = "hdf5r")$return_val
if(pad < 0) {
stop("There was an error retrieving the pad")
}
return(pad)
},
copy=function() {
"This function implements the HDF5-API function H5Tcopy."
"Please see the documentation at \\url{https://portal.hdfgroup.org/display/HDF5/H5T_COPY} for details."
id <- .Call("R_H5Tcopy", self$id, PACKAGE="hdf5r")$return_val
return(H5T_factory(id, do_copy=FALSE))
},
is_committed=function() {
"This function implements the HDF5-API function H5Tcommitted."
"Please see the documentation at \\url{https://portal.hdfgroup.org/display/HDF5/H5T_COMMITTED} for details."
htri <- .Call("R_H5Tcommitted", self$id, PACKAGE="hdf5r")$return_val
if(htri < 0) {
stop("Error checking if a datatype has been committed")
}
return(as.logical(htri))
},
equal=function(dtype) {
"This function implements the HDF5-API function H5Tequal."
"Please see the documentation at \\url{https://portal.hdfgroup.org/display/HDF5/H5T_EQUAL} for details."
if(is.numeric(dtype)) {
dtype <- bit64::as.integer64(dtype)
}
if(inherits(dtype, "H5T")) {
dtype <- dtype$id
}
if(!is.integer64(dtype)) {
stop("'dtype' has to be either numeric, coercible to integer of of class 'H5T'")
}
eq_res <- .Call("R_H5Tequal", self$id, dtype, PACKAGE="hdf5r")$return_val
if(eq_res < 0) {
stop("There was a problem in the comparison")
}
return(as.logical(eq_res))
},
is_vlen=function() {
"This function detects if the underlying type is H5T_VLEN or a variable length string. This is used to know if"
"after reading a dataset, memory has to be freed"
htri <- .Call("R_H5Tdetect_vlen", self$id, PACKAGE = "hdf5r")$return_val
if(htri < 0) {
stop("Error trying to detect if type is of variable length")
}
return(as.logical(htri))
},
detect_class=function(dtype_class) {
"This function implements the HDF5-API function H5Tdetect_class."
"Please see the documentation at \\url{https://portal.hdfgroup.org/display/HDF5/H5T_DETECT_CLASS} for details."
htri <- .Call("R_H5Tdetect_class", self$id, dtype_class, PACKAGE = "hdf5r")$return_val
if(htri < 0) {
stop("Error trying to detect if type is of variable length")
}
return(as.logical(htri))
},
get_native_type=function(direction=h5const$H5T_DIR_ASCEND) {
"This function implements the HDF5-API function H5Tget_native_type."
"Please see the documentation at \\url{https://portal.hdfgroup.org/display/HDF5/H5T_GET_NATIVE_TYPE} for details."
id <- .Call("R_H5Tget_native_type", self$id, direction, PACKAGE="hdf5r")$return_val
if(id < 0) {
stop("Error retrieving native-c-type")
}
return(H5T_factory(id=id))
},
get_create_plist=function() {
"This function implements the HDF5-API function H5Tget_create_plist."
"Please see the documentation at \\url{https://portal.hdfgroup.org/display/HDF5/H5T_GET_CREATE_PLIST} for details."
id <- .Call("R_H5Tget_create_plist", self$id, PACKAGE="hdf5r")$return_val
if(id < 0) {
stop("Error retrieving type_creation_plist")
}
return(H5P_TYPE_CREATE$new(id=id))
},
to_text=function(lang_type=h5const$H5LT_DDL) {
"This function implements the HDF5-API function H5LTdtype_to_text."
"Please see the documentation at \\url{https://portal.hdfgroup.org/display/HDF5/H5LT_DTYPE_TO_TEXT} for details."
res <- standalone_H5T_dtype_to_text(self$id, lang_type)
return(res)
},
print=function(...){
"Prints information for the group"
"@param ... ignored"
is_valid <- self$is_valid
print_class_id(self, is_valid)
if(is_valid) {
type_text <- self$to_text()
cat("Datatype: ", type_text, "\n", sep="")
}
return(invisible(self))
}
),
private=list(
closeFun=function(id) if(!is.na(id) && is.loaded("R_H5Tclose", PACKAGE="hdf5r")) {
invisible(.Call("R_H5Tclose", id, PACKAGE = "hdf5r"))
}
),
cloneable=FALSE
)
## add a common function
R6_set_list_of_items(H5T, "public", commonFGDT, overwrite=TRUE)
R6_set_list_of_items(H5T, "public", commonFGT, overwrite=TRUE)
standalone_H5T_dtype_to_text <- function(h5t_id, lang_type) {
res <- .Call("R_H5LTdtype_to_text", h5t_id, character(0), lang_type, request_empty(1), PACKAGE="hdf5r")
if(res$return_val < 0) {
stop("Could not retrieve the necessary size of the buffer to convert type to text")
}
char_buf <- paste(rep(" ", res$len + 1), collapse="")
res <- .Call("R_H5LTdtype_to_text", h5t_id, char_buf, lang_type, nchar(char_buf), PACKAGE="hdf5r")
if(res$return_val < 0) {
stop("Could not convert type to text")
}
return(res$str)
}
#' Class for HDF5 integer-datatypes.
#'
#' Inherits from class \code{\link[=H5T]{H5T}}.
#' Users should not create integer datatypes themselves using this class. Instead, integer should be derived
#' from one of the base-types such as \code{h5types$H5T_NATIVE_INT} (which internally automatically creates a copy of the type).
#' For a complete list of types see \code{h5types$overview}.
#' @docType class
#' @importFrom R6 R6Class
#' @return Object of class \code{\link[=H5T_INTEGER]{H5T_INTEGER}}.
#' @export
#' @aliases H5T_BITFIELD H5T_BITFIELD
#' @author Holger Hoefling
#' @seealso \code{\link[=H5T]{H5T}}
#'
#' @examples
#' my_int <- h5types$H5T_NATIVE_INT
#'
#' # make an int with 2 bit
#' my_int$set_sign(h5const$H5T_SGN_NONE)
#' my_int$set_size(1)
#' my_int$set_precision(2)
#' my_int$describe()
H5T_INTEGER <- R6Class("H5T_INTEGER",
inherit=H5T,
public=list(
set_sign=function(sign) {
"This function implements the HDF5-API function H5Tset_sign."
"Please see the documentation at \\url{https://portal.hdfgroup.org/display/HDF5/H5T_SET_SIGN} for details."
herr <- .Call("R_H5Tset_sign", self$id, as.integer(sign), PACKAGE = "hdf5r")$return_val
if(herr < 0) {
stop("Could not set sign")
}
return(invisible(self))
},
get_sign=function() {
"This function implements the HDF5-API function H5Tget_sign."
"Please see the documentation at \\url{https://portal.hdfgroup.org/display/HDF5/H5T_GET_SIGN} for details."
sign <- .Call("R_H5Tget_sign", self$id, PACKAGE = "hdf5r")$return_val
return(sign)
if(sign < 0) {
stop("There was an error retrieving the sign")
}
},
describe=function() {
"Return a vector that describes the key features of the datatype"
return(list(size=self$get_size(), precision=self$get_precision(), sign=self$get_sign(),
order=self$get_order()))
}
),
cloneable=FALSE)
H5T_BITFIELD <- H5T_INTEGER
#' Class for HDF5 floating point datatypes.
#'
#' Inherits from class \code{\link[=H5T]{H5T}}. Users should not create float types with this class, but instead
#' use e.g. \code{h5types$H5T_NATIVE_DOUBLE}. Using the functions of this class, many aspects of the representation of the
#' floating point number can then be manipulated.
#'
#' @docType class
#' @importFrom R6 R6Class
#' @return Object of class \code{\link[=H5T_FLOAT]{H5T_FLOAT}}.
#' @export
#' @author Holger Hoefling
#' @seealso \code{\link[=H5T]{H5T}}
H5T_FLOAT <- R6Class("H5T_FLOAT",
inherit=H5T,
public=list(
set_fields=function(spos, epos, esize, mpos, msize) {
"This function implements the HDF5-API function H5Tset_fields."
"Please see the documentation at \\url{https://portal.hdfgroup.org/display/HDF5/H5T_SET_FIELDS} for details."
herr <- .Call("R_H5Tset_fields", self$id, spos, epos, esize, mpos, msize, PACKAGE="hdf5r")$return_val
if(herr < 0) {
stop("Error setting fields")
}
},
get_fields=function() {
"This function implements the HDF5-API function H5Tget_fields."
"Please see the documentation at \\url{https://portal.hdfgroup.org/display/HDF5/H5T_GET_FIELDS} for details."
res <- .Call("R_H5Tget_fields", self$id, request_empty(1), request_empty(1), request_empty(1), request_empty(1),
request_empty(1), PACKAGE="hdf5r")
if(res$return_val < 0) {
stop("Error retrieving fields")
}
return(list(spos=res$spos, epos=res$epos, esize=res$esize, mpos=res$mpos, msize=res$msize))
},
set_ebias=function(ebias) {
"This function implements the HDF5-API function H5Tset_ebias."
"Please see the documentation at \\url{https://portal.hdfgroup.org/display/HDF5/H5T_SET_EBIAS} for details."
herr <- .Call("R_H5Tset_ebias", self$id, as.integer(ebias), PACKAGE = "hdf5r")$return_val
if(herr < 0) {
stop("Could not set ebias")
}
return(invisible(self))
},
get_ebias=function() {
"This function implements the HDF5-API function H5Tget_ebias."
"Please see the documentation at \\url{https://portal.hdfgroup.org/display/HDF5/H5T_GET_EBIAS} for details."
ebias <- .Call("R_H5Tget_ebias", self$id, PACKAGE = "hdf5r")$return_val
return(ebias)
if(ebias < 0) {
stop("There was an error retrieving the ebias")
}
},
set_norm=function(norm) {
"This function implements the HDF5-API function H5Tset_norm."
"Please see the documentation at \\url{https://portal.hdfgroup.org/display/HDF5/H5T_SET_NORM} for details."
herr <- .Call("R_H5Tset_norm", self$id, as.integer(norm), PACKAGE = "hdf5r")$return_val
if(herr < 0) {
stop("Could not set norm")
}
return(invisible(self))
},
get_norm=function() {
"This function implements the HDF5-API function H5Tget_norm."
"Please see the documentation at \\url{https://portal.hdfgroup.org/display/HDF5/H5T_GET_NORM} for details."
norm <- .Call("R_H5Tget_norm", self$id, PACKAGE = "hdf5r")$return_val
return(norm)
if(norm < 0) {
stop("There was an error retrieving the norm")
}
},
set_inpad=function(inpad) {
"This function implements the HDF5-API function H5Tset_inpad."
"Please see the documentation at \\url{https://portal.hdfgroup.org/display/HDF5/H5T_SET_INPAD} for details."
herr <- .Call("R_H5Tset_inpad", self$id, as.integer(inpad), PACKAGE = "hdf5r")$return_val
if(herr < 0) {
stop("Could not set inpad")
}
return(invisible(self))
},
get_inpad=function() {
"This function implements the HDF5-API function H5Tget_inpad."
"Please see the documentation at \\url{https://portal.hdfgroup.org/display/HDF5/H5T_GET_INPAD} for details."
inpad <- .Call("R_H5Tget_inpad", self$id, PACKAGE = "hdf5r")$return_val
return(inpad)
if(inpad < 0) {
stop("There was an error retrieving the inpad")
}
},
describe=function() {
"Print a detailed description of the datatype; this is experimental"
return(list(size=self$get_size(), precision=self$get_precision(),
fields=self$get_fields(), ebias=self$get_ebias(), norm=self$get_norm(),
inpad=self$get_inpad()))
}
),
cloneable=FALSE)
#' Class for HDF5 enumeration datatypes.
#'
#' Inherits from class \code{\link[=H5T]{H5T}}.
#' @docType class
#' @importFrom R6 R6Class
#' @importFrom utils compareVersion
#' @return Object of class \code{\link[=H5T_ENUM]{H5T_ENUM}}.
#' @export
#' @author Holger Hoefling
#' @seealso \code{\link[=H5T]{H5T}}
#'
#' @examples
#' nucleotide_enum <- H5T_ENUM$new(labels=c("A", "C", "G", "T"), values=0:3)
#' nucleotide_enum
#' # For HDF5 1.8.16 or higher, the size and precision are set optimally
#' nucleotide_enum$get_size()
#' nucleotide_enum$get_precision()
H5T_ENUM <- R6Class("H5T_ENUM",
inherit=H5T_INTEGER,
public=list(
initialize=function(labels, values=seq_along(labels), id=NULL) {
"Create an enumeration datatype. This is either a factor-like object or a logical variable (that is"
"internally represented as an ENUM-type."
"@param labels The labels of the ENUM-type"
"@param values The values corresponding to the labels"
"@param id Internal use only"
if(!is.null(id)) {
super$initialize(id=id)
return(self)
}
if(!missing(labels)) {
if(missing(values)) {
values <- seq_along(labels)
}
max_abs <- max(abs(values))
has_neg <- any(values < 0)
needed_precision <- ceiling(log2(max_abs + 1))
if(has_neg) {
needed_precision <- needed_precision + 1
}
size <- ceiling(needed_precision / 8)
if(has_neg) {
if(size <= 1) {
dtype_id <- h5types$H5T_NATIVE_CHAR
}
else if(size <= 2) {
dtype_id <- h5types$H5T_NATIVE_SHORT
}
else if(size <= 4) {
dtype_id <- h5types$H5T_NATIVE_INT
}
else {
dtype_id <- h5types$H5T_NATIVE_LLONG
}
}
else {
if(size <= 1) {
dtype_id <- h5types$H5T_NATIVE_UCHAR
}
else if(size <= 2) {
dtype_id <- h5types$H5T_NATIVE_USHORT
}
else if(size <= 4) {
dtype_id <- h5types$H5T_NATIVE_UINT
}
else {
if(needed_precision==64) {
stop("Can't support UINT64; unsigned precision of 64bit not possible")
}
else {
dtype_id <- h5types$H5T_NATIVE_LLONG
}
}
}
if(compareVersion(h5version(verbose=FALSE), "1.8.16") >= 0) {
## can only do this for 1.8.16 or above
## lower version have problems getting native type of an enum based on a non-native type
dtype_id$set_size(size)
dtype_id$set_precision(needed_precision)
}
id <- .Call("h5create_enum_type", as.character(labels), values, dtype_id$id, PACKAGE="hdf5r")$return_val
super$initialize(id=id)
return(self)
}
stop("None of the parameters were set")
},
get_labels=function() {
"Return all the labels of the enumeration type"
return(.Call("h5get_enum_labels", self$id, PACKAGE="hdf5r")$return_val)
},
get_values=function() {
"Return the values of the enumeration type"
return(.Call("h5get_enum_values", self$id, PACKAGE = "hdf5r")$return_val)
},
set_size=function(size) {
"Base type of every enum is \\code{H5T_INTEGER}. This disables the set_size function"
stop("Function 'set_size' not allowed for 'H5T_ENUM'")
},
get_super=function() {
"Returns \\code{\\link{H5T_INTEGER}} that is the base type of the enumeration"
id <- .Call("R_H5Tget_super", self$id, PACKAGE="hdf5r")$return_val
if(id < 0) {
stop("Error retrieving super_type")
}
return(H5T_factory(id=id))
},
describe=function() {
"Print a detailed description of the datatype; this is experimental"
return(list(super=self$get_super()$describe(), labels=self$get_labels(), values=self$get_values()))
}
),
cloneable=FALSE
)
#' Class for HDF5 logical datatypes. This is an enum with the 3 values FALSE, TRUE and NA mapped on values 0, 1 and 2.
#' Is transparently mapped onto a logical variable
#'
#' Inherits from class \code{\link[=H5T]{H5T}}.
#' @docType class
#' @importFrom R6 R6Class
#' @return Object of class \code{\link[=H5T_LOGICAL]{H5T_LOGICAL}}.
#' @export
#' @author Holger Hoefling
#' @seealso \code{\link[=H5T]{H5T}}, \code{\link[=H5T_ENUM]{H5T_ENUM}}
H5T_LOGICAL <- R6Class("H5T_LOGICAL",
inherit=H5T_ENUM,
public=list(
initialize=function(include_NA=TRUE, id=NULL) {
"Create a logical datatype. This is"
"internally represented by an ENUM-type"
"@param id Internal use only"
if(!is.null(id)) {
super$initialize(id=id)
return(self)
}
if(include_NA) {
dtype_id <- h5types$H5T_NATIVE_UCHAR
if(compareVersion(h5version(verbose=FALSE), "1.8.16") >= 0) {
## can only do this for 1.8.16 or above
## lower version have problems getting native type of an enum based on a non-native type
dtype_id$set_size(1)
dtype_id$set_precision(2)
}
id <- .Call("h5create_enum_type", as.character(c("FALSE","TRUE", "NA")), as.integer(c(0,1,2)), dtype_id$id, PACKAGE="hdf5r")$return_val
super$initialize(id=id)
return(self)
}
else {
dtype_id <- h5types$H5T_NATIVE_UCHAR
if(compareVersion(h5version(verbose=FALSE), "1.8.16") >= 0) {
## can only do this for 1.8.16 or above
## lower version have problems getting native type of an enum based on a non-native type
dtype_id$set_size(1)
dtype_id$set_precision(1)
}
id <- .Call("h5create_enum_type", as.character(c("FALSE","TRUE")), as.integer(c(0,1)), dtype_id$id, PACKAGE="hdf5r")$return_val
super$initialize(id=id)
return(self)
}
}),
cloneable=FALSE
)
#' Class for HDF5 compound datatypes.
#'
#' Inherits from class \code{\link[=H5T]{H5T}}.
#' @docType class
#' @importFrom R6 R6Class
#' @return Object of class \code{\link[=H5T_COMPOUND]{H5T_COMPOUND}}.
#' @export
#' @author Holger Hoefling
#' @seealso \code{\link[=H5T]{H5T}}
#'
#' @examples
#' # create a H5T_COMPOUND corresponding to a data-frame
#' my_cpd <- H5T_COMPOUND$new(c("name", "age", "salary"),
#' dtypes=list(H5T_STRING$new(size=200), h5types$H5T_NATIVE_INT, h5types$H5T_NATIVE_DOUBLE))
#' my_cpd
H5T_COMPOUND <- R6Class("H5T_COMPOUND",
inherit=H5T,
public=list(
initialize=function(labels, dtypes, size=NULL, offset=NULL, id=NULL) {
"Create at compound type that is the HDF5 equivalent of a table"
"@param labels The labels of the columns of the compound object"
"@param dtypes The datatypes of the columns of the object; this is usually a list of objects"
"of class \\code{\\link{H5T}}"
"@param size The size of each datatype; if \\code{NULL}, automatically inferred"
"@param offset The offset where each datatype starts; can be different from the sum of the individual sizes"
"so that datatypes are aligned with memory addresses. If \\code{NULL}, inferred automatically"
"@param id Internal use only"
if(is.null(id)) {
if(missing(dtypes) || missing(labels)) {
stop("Either 'id' or ('dtype_ids' and 'labels') have to be given")
}
dtype_ids <- H5T_extractID(dtypes)
if(length(labels) != length(dtype_ids)) {
stop("'labels' and 'dtype_ids' have to have the same length")
}
if(!is.character(labels)) {
stop("'labels' has to be a character vector")
}
labels <- as.character(labels)
id <- .Call("h5create_compound_type", labels, dtype_ids, as.integer(size), as.integer(offset), PACKAGE="hdf5r")$return_val
}
super$initialize(id)
},
pack=function() {
"This function implements the HDF5-API function H5Tpack."
"Please see the documentation at \\url{https://portal.hdfgroup.org/display/HDF5/H5T_PACK} for details."
herr <- .Call("R_H5Tpack", self$id, PACKAGE="hdf5r")$return_val
if(herr < 0) {
stop("Error removing padding")
}
return(invisible(self))
},
get_cpd_types=function() {
"Return \\code{\\link{H5T}} objects that represent the datatypes of the columns of the "
"compound object. Returned as a list if more than 1"
dtype_ids <- .Call("h5get_compound_types", self$id, PACKAGE="hdf5r")$return_val
return(H5T_factory(ids=dtype_ids))
},
get_cpd_labels=function() {
"Return the labels of the columns as a character vector"
return(.Call("h5get_compound_names", self$id, PACKAGE="hdf5r")$return_val)
},
get_cpd_classes=function() {
"Return the classes of the columns as an object of type \\code{\\link{factor_ext}}"
return(.Call("h5get_compound_classes", self$id, PACKAGE="hdf5r")$return_val)
},
get_cpd_offsets=function() {
"Return the offsets of the datatypes"
return(.Call("h5get_compound_offsets", self$id, PACKAGE="hdf5r")$return_val)
},
describe=function() {
"Print a detailed description of the datatype; this is experimental"
cpd_types <- self$get_cpd_types()
if(!is.list(cpd_types)) {
cpd_types <- list(cpd_types)
}
cpd_describe <- lapply(cpd_types, function(x) x$describe())
return(list(cpd_types=cpd_describe, labels=self$get_cpd_labels(),
classes=self$get_cpd_classes(), offsets=self$get_cpd_offsets(),
size=self$get_size()))
}
),
cloneable=FALSE
)
#' Class for HDF5 string datatypes.
#'
#' Inherits from class \code{\link[=H5T]{H5T}}.
#' @docType class
#' @importFrom R6 R6Class
#' @return Object of class \code{\link[=H5T_STRING]{H5T_STRING}}.
#' @export
#' @author Holger Hoefling
#' @seealso \code{\link[=H5T]{H5T}}
#'
#' @examples
#' # fixed width string
#' str_flen <- H5T_STRING$new(size=100)
#' str_flen$is_vlen()
#' str_flen
#'
#' # variable length string
#' str_vlen <- H5T_STRING$new(size=Inf)
#' str_vlen$is_vlen()
#' str_vlen
H5T_STRING <- R6Class("H5T_STRING",
inherit=H5T,
public=list(
initialize=function(type=c("c", "fortran"), size=1, id=NULL) {
"Create a string datatype"
"@param A C or fortran type string"
"@param size Size of the string object. Set to \\code{Inf} for variable size strings"
"@param id internal use only"
newid <- FALSE
if(is.null(id)) {
type <- match.arg(type)
id <- switch(type, c=h5types$H5T_C_S1, fortran=h5types$H5T_FORTRAN_S1)
## need to copy it through the low level function; copy function returns an
## object; and that object closes the id; so it needs to be copied this way
id <- .Call("R_H5Tcopy", id$id, PACKAGE="hdf5r")$return_val
newid <- TRUE
}
super$initialize(id=id)
if(newid) {
self$set_size(size)
}
return(self)
},
get_size=function(variable_as_inf=TRUE) {
"Retrieves the length of the string, setting it to \\code{Inf} it is of variable length."
"This function implements the HDF5-API function H5Tis_variable_str."
"Please see the documentation at \\url{https://portal.hdfgroup.org/display/HDF5/H5T_IS_VARIABLE_STR} for details."
## needs to be overloaded to properly assess if it is a variable length string
## first check if the string has variable length
if(variable_as_inf) {
is_var_string = .Call("R_H5Tis_variable_str", self$id, PACKAGE = "hdf5r")$return_val
if(is_var_string < 0) {
error("Could not determine if datatype is a variable length string")
}
if(is_var_string) {
return(Inf)
}
else {
return(super$get_size())
}
}
else {
return(super$get_size())
}
},
get_cset=function() {
"This function implements the HDF5-API function H5Tget_cset."
"Please see the documentation at \\url{https://portal.hdfgroup.org/display/HDF5/H5T_GET_CSET} for details."
cset_res = .Call("R_H5Tget_cset", self$id, PACKAGE = "hdf5r")$return_val
return(cset_res)
},
set_cset=function(cset=c("unknown", "UTF-8")) {
"This function implements the HDF5-API function H5Tset_cset."
"Please see the documentation at \\url{https://portal.hdfgroup.org/display/HDF5/H5T_SET_CSET} for details."
if(is.character(cset)) {
cset <- match.arg(cset)
cset <- switch(cset, unknown=h5const$H5T_CSET_ASCII, "UTF-8"=h5const$H5T_CSET_UTF8)
}
cset_res <- .Call("R_H5Tset_cset", self$id, as.integer(cset), PACKAGE = "hdf5r")$return_val
if(cset_res < 0) {
stop("Error when trying to set cset")
}
return(self)
},
set_strpad=function(strpad) {
"This function implements the HDF5-API function H5Tset_strpad."
"Please see the documentation at \\url{https://portal.hdfgroup.org/display/HDF5/H5T_SET_STRPAD} for details."
herr <- .Call("R_H5Tset_strpad", self$id, as.integer(strpad), PACKAGE = "hdf5r")$return_val
if(herr < 0) {
stop("Could not set strpad")
}
return(invisible(self))
},
get_strpad=function() {
"This function implements the HDF5-API function H5Tget_strpad."
"Please see the documentation at \\url{https://portal.hdfgroup.org/display/HDF5/H5T_GET_STRPAD} for details."
strpad <- .Call("R_H5Tget_strpad", self$id, PACKAGE = "hdf5r")$return_val
return(strpad)
if(strpad < 0) {
stop("There was an error retrieving the strpad")
}
},
describe=function() {
"Print a detailed description of the datatype; this is experimental"
return(list(size=self$get_size(), cset=self$get_cset(), strpad=self$get_strpad()))
}
),
cloneable=FALSE
)
#' Class for HDF5 complex datatypes
#'
#' In HDF5, complex numbers don't actually exist. They are represented as H5T_COMPOUND with two columns named \code{Real} and
#' \code{Imaginary}.
#' Inherits from class \code{\link[=H5T_COMPOUND]{H5T_COMPOUND}}.
#' @docType class
#' @importFrom R6 R6Class
#' @return Object of class \code{\link[=H5T_COMPLEX]{H5T_COMPLEX}}.
#' @export
#' @author Holger Hoefling
#' @seealso \code{\link[=H5T]{H5T}}, \code{\link[=H5T_COMPOUND]{H5T_COMPOUND}}
H5T_COMPLEX <- R6Class("H5T_COMPLEX",
inherit=H5T_COMPOUND,
public=list(
initialize=function(id=NULL) {
"Create a new complex datatype"
"@param id Internal use only"
if(is.null(id)) {
labels <- c("Real", "Imaginary")
dtypes <- rep(h5types$H5T_NATIVE_DOUBLE$id,2)
super$initialize(labels=labels, dtypes=dtypes, size=NULL, offset=NULL)
}
else {
super$initialize(id=id)
}
}
),
cloneable=FALSE
)
#' Class for HDF5 array datatypes.
#'
#' Inherits from class \code{\link[=H5T]{H5T}}. This class represents an array. As datasets in HDF5
#' are itself already arrays, this datatype is not needed there. It is mostly useful when a column in a
#' \code{H5T_COMPUND} object is intended to be an array. This however makes it difficult to work
#' with such objects in R - as a column of the corresponding \code{data.frame} has to be an array. So please
#' use with care.
#' @docType class
#' @importFrom R6 R6Class
#' @return Object of class \code{\link[=H5T_ARRAY]{H5T_ARRAY}}.
#' @export
#' @author Holger Hoefling
#' @seealso \code{\link[=H5T]{H5T}}
H5T_ARRAY <- R6Class("H5T_ARRAY",
inherit=H5T,
public=list(
initialize=function(dims, dtype_base, id=NULL) {
"Create an array datatype."
"@param dims The dimension of the datatype"
"@param dtype_base The datatype that makes up the elements of the array"
"@param id internal use only"
if(is.null(id)) {
## ok, check that we have the right base type available
if(missing(dims) || missing(dtype_base)) {
stop("When creating a new array datatype, either id has to be given (for an existing one), or dims and dtype_base")
}
if(inherits(dtype_base, "H5T")) {
dtype_base <- dtype_base$id
}
rank <- length(dims)
dims <- rev(dims)
id <- .Call("R_H5Tarray_create2", bit64::as.integer64(dtype_base), as.integer(rank), as.integer(dims), PACKAGE = "hdf5r")$return_val
}
super$initialize(id)
},
get_array_ndims=function() {
"This function implements the HDF5-API function H5Tget_array_ndims."
"Please see the documentation at \\url{https://portal.hdfgroup.org/display/HDF5/H5T_GET_ARRAY_NDIMS} for details."
res <- .Call("R_H5Tget_array_ndims", self$id, PACKAGE="hdf5r")$return_val
if(res < 0) {
stop("Error trying to get rank of array-type")
}
return(res)
},
get_array_dims=function() {
"This function implements the HDF5-API function H5Tget_array_dims2."
"Please see the documentation at \\url{https://portal.hdfgroup.org/display/HDF5/H5T_GET_ARRAY_DIMS2} for details."
rank <- self$get_array_ndims()
dims <- integer(rank)
res <- .Call("R_H5Tget_array_dims2", self$id, dims, PACKAGE="hdf5r")
if(res$return_val < 0) {
stop("Error trying to get array-type dimensions")
}
return(rev(res$dims))
},
get_super=function() {
"This function implements the HDF5-API function H5Tget_super."
"Please see the documentation at \\url{https://portal.hdfgroup.org/display/HDF5/H5T_GET_SUPER} for details."
id <- .Call("R_H5Tget_super", self$id, PACKAGE="hdf5r")$return_val
if(id < 0) {
stop("Error retrieving super_type")
}
return(H5T_factory(id=id))
},
describe=function() {
"Print a detailed description of the datatype; this is experimental"
return(list(super=self$get_super()$describe(), array_dims=self$get_array_dims()))
}
),
cloneable=FALSE
)
#' Class for HDF5 variable-length datatypes.
#'
#' Inherits from class \code{\link[=H5T]{H5T}}. This can make any datatype a variable length datatype.
#' This would mostly be intended for storing ragged arrays.
#' @docType class
#' @importFrom R6 R6Class
#' @return Object of class \code{\link[=H5T_VLEN]{H5T_VLEN}}.
#' @export
#' @author Holger Hoefling
#' @seealso \code{\link[=H5T]{H5T}}
#'
#' @examples
#' vlen_int <- H5T_VLEN$new(h5types$H5T_NATIVE_INT)
#' vlen_int
H5T_VLEN <- R6Class("H5T_VLEN",
inherit=H5T,
public=list(
initialize=function(dtype_base, id=NULL) {
"Create a variable length datatype"
"@param dtype_base The basis-type of the variable length datatype"
"@param id Internal use only"
if(is.null(id)) {
if(inherits(dtype_base, "H5T")) {
dtype_base <- dtype_base$id
}
id <- .Call("R_H5Tvlen_create", bit64::as.integer64(dtype_base), PACKAGE="hdf5r")$return_val
}
super$initialize(id=id)
},
get_super=function() {
"This function implements the HDF5-API function H5Tget_super."
"Please see the documentation at \\url{https://portal.hdfgroup.org/display/HDF5/H5T_GET_SUPER} for details."
id <- .Call("R_H5Tget_super", self$id, PACKAGE="hdf5r")$return_val
if(id < 0) {
stop("Error retrieving super_type")
}
return(H5T_factory(id=id))
},
describe=function() {
"Print a detailed description of the datatype; this is experimental"
return(list(super=self$get_super()$describe()))
}
),
cloneable=FALSE
)
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