Package 'hdf5r'

Description

A package that allows to interface with the HDF5 C-library. Provides access to most of its functionality from inside R using R6 classes. For more details please see the README at the github page https://github.com/hhoeflin/hdf5r.

Examples

test_file <- tempfile(fileext=".h5")
file.h5 <- H5File$new(test_file, mode="w")

data(cars)
file.h5$create_group("test")
file.h5[["test/cars"]] <- cars
cars_ds <- file.h5[["test/cars"]]
h5attr(cars_ds, "rownames") <- rownames(cars)

# Close the file at the end
# the 'close' method closes only the file-id, but leaves object inside the file open
# This may prevent re-opening of the file. 'close_all' closes the file and all objects in it
file.h5$close_all()
# now re-open it 
file.h5 <- H5File$new(test_file, mode="r+")

# lets look at the content
file.h5$ls(recursive=TRUE)

cars_ds <- file.h5[["test/cars"]]
# note that for now tables in HDF5 are 1-dimensional, not 2-dimensional
mycars <- cars_ds[]
h5attr_names(cars_ds)
h5attr(cars_ds, "rownames")

file.h5$close_all()

Description

Retrieving a copy of a type

Usage

## S3 method for class 'types_env'
x$name

## S3 method for class 'types_env'
x[[name]]

Arguments

Details

The types are stored in the environment h5types. These types should not be accessed directly. Therefor, the $-operator is overloaded to ensure that every type that is accessed is a copy of the original type

Value

Returns an object that is a copy of a type that was requested

Author(s)

Holger Hoefling

Description

Convert a double or integer to hex

Usage

as_hex(x)

Arguments

Details

Converts a double or integer to hex. Contrary to the built-in format, this is done without any conversion of integers in double-format to integers in integer format.

Value

Character string with the hex value

Author(s)

Holger Hoefling

Description

Create an empty R-object according to a given HDF5 datatype

Usage

create_empty(nelem, dtype)

Arguments

Details

With complex datatypes it can be useful to have a template that can be used so that the data input into a dataset conforms to expectations.

Given a datatype, this function creates an object of length nelem. Here, an empty datatype refers to objects with value 0 for numeric objects and empty strings.

Value

An empty R object corresponding to the datatype that was passed in

Author(s)

Holger Hoefling

Description

Create an extended factor

Usage

factor_ext(x, values, levels, drop = FALSE)

Arguments

Details

An extended version of a regular factor variable. Instead of the levels having values from 1 to n where n is the number of levels, any integer value can be used for any level (including 64bit integers). If all values are in the range of a regular 32-bit integer, it is coerced to int. Automatic coercion of extended factors to factors in H5ToR_Post for enums only works for 32-bit integer base types. In this page this is heavily used, as constants in HDF5 can be arbitrary integer values.

Value

An object of S3 class factor_ext

Author(s)

Holger Hoefling

Description

Various functions for factor_ext objects

Usage

values(x, ...)

## S3 method for class 'factor_ext'
values(x, ...)

## S3 method for class 'factor'
values(x, ...)

## Default S3 method:
values(x, ...)

## S3 method for class 'factor_ext'
as.character(x, ...)

## S3 method for class 'factor_ext'
x[[...]]

## S3 replacement method for class 'factor_ext'
x[[...]] <- value

## S3 method for class 'factor_ext'
x[..., drop = FALSE]

## S3 replacement method for class 'factor_ext'
x[...] <- value

is.factor_ext(x)

coercible_to_factor(x)

coerce_to_factor(x)

## S3 method for class 'factor_ext'
print(x, quote = FALSE, max.levels = NULL,
  width = getOption("width"), ...)

## S3 method for class 'factor_ext'
e1 == e2

## S3 method for class 'factor_ext'
e1 != e2

## S3 method for class 'factor_ext'
c(...)

Arguments

Details

values

Extracts the underlying values of an object (the generic here)

values.factor_ext

Extracts the underlying values of a factor_ext object

values.factor

Extracts the underlying values of a factor

values.default

Default of the values function; currently returns an error

as.character

Coerces factor_ext to a character-representation using it levels, not values

[[.factor_ext

Single-item subsetting of a factor_ext object

[[<-.factor_ext

Single-item subset assignment to a factor_ext object

[.factor_ext

Subsetting of a factor_ext object

[<-.factor_ext

Subset assignment to a factor_ext object

is.factor_ext

Check if it is a factor_ext object. Returns a logical

coercible_to_factor

Checks if a factor_ext could be coerced to a factor. Return a logical.

coerce_to_factor

Coerces to a factor, otherwise throws an error if not possible.

print.factor_ext

Prints a factor_ext object.

==.factor_ext

Compare two factor_ext for equality.

!=.factor_ext

Compare two factor_ext for inequality.

c.factor_ext

Concatenate objects of type factor_ext.

Value

Depending on the function

Author(s)

Holger Hoefling

Description

Flatten a nested data.frame

Usage

flatten_df(df, factor_ext_to_char = FALSE)

Arguments

Details

HDF5 Compounds allow for nesting. Correspondingly, nested data.frames are being produced. This function flattens such a nested data.frame.

For easier printing to the screen, it also allows for coercion of factor_ext to character variables.

Value

A flattened data.frame

Author(s)

Holger Hoefling

Description

Guess the dimension of a chunk

Usage

guess_chunks(space_maxdims, dtype_size,
  chunk_size = getOption("hdf5r.chunk_size"))

Arguments

Details

The size of the chunk in bytes is first divided by the size of the datatype, giving the number of elements to be stored in each chunk. This is taken as a rough guideline. Then, the number of dimensions of the dataset is used. By default, the chunk is assumed to have the same size in each dimension, yielding an initial guess.

If the resulting chunk is larger than the entire dataset for a maximal dimension, this dimension of the chunk is reduced and redistributed to the other dimensions.

As a chunk is never allowed to be larger than the maximum dimension of the dataset itself,

Value

An integer vector giving the dimension of the chunk

Author(s)

Holger Hoefling

Description

Guess the HDF5 datatype of an R object

Usage

guess_nelem(x, dtype)

guess_dim(x)

guess_dtype(x, ds_dim = NULL, scalar = FALSE,
  string_len = getOption("hdf5r.default_string_len"))

Arguments

Details

Given an object, it creates a datatype in HDF5 that would match this object. For simple datasets like arrays, this function is not so useful, but is very good for creating dataframes or hierarchical objects (like lists of dataframes) etc.

Value

An object of class H5T that represents the HDF5-type of the Robj that was passed in

Author(s)

Holger Hoefling

Description

Guess the dataspace of an object

Usage

guess_space(x, dtype, chunked = TRUE)

Arguments

Details

Creates a dataspace that fits an R object so that it can be written into a dataset. This is used for example in dataset creation based on an R-object, not a specifically defined dimensions.

Value

An object of type H5S

Author(s)

Holger Hoefling

Description

The functions listed below provide a wrapper-interface compatible to functions specified in the h5 package. The author(s) have decided to deprecate h5 and join forces and still make the transition for h5 users as smooth as possible. Additionally, almost all testcases could be transferred to hdf5r to improve test coverage even more.

Usage

h5file(...)

createGroup(object, name, ...)

openLocation(object, name)

openGroup(object, name)

createDataSet(object, name, ...)

readDataSet(object)

h5close(object)

h5flush(object)

existsGroup(object, name)

is.h5file(name)

extendDataSet(object, dims)

## S3 method for class 'H5D'
rbind(x, mat, ..., deparse.level = 1)

## S3 method for class 'H5D'
cbind(x, mat, ..., deparse.level = 1)

## S3 method for class 'H5D'
c(x, ...)

h5unlink(object, name)

list.attributes(object)

Arguments

Details

Below you can find a list of all h5 functions including hdf5r mappings.

h5file

Directly maps to H5File$new, see also H5File.

createGroup

Maps to object$create_group where object implements CommonFG.

openLocation

Uses object$open where object implements CommonFG.

createDataSet

Maps to object$create_dataset where object implements CommonFG.

readDataSet

Maps to object$read, see also H5D.

h5close

Maps to object$close_all for H5File and object$close for other.

h5flush

Maps to object$flush where object implements CommonFGDTA.

The following interfaces are defined:

CommonFG

Implemented by objects of class H5File and H5Group.

CommonFGDTA

Implemented by objects of class H5File, H5Group, H5D, H5T and H5A.

References

Mario Annau (2017). h5: Interface to the 'HDF5' Library. R package version 0.9.9. https://github.com/mannau/h5

Description

This class represents an HDF5 attribute. Usually it is easier to read and write attributes for groups, datasets and committed datatypes using the functions documented in h5attributes.

Details

Otherwise, the functionality for attributes is very similar to that of datasets (H5D), however with the notable exception that attributes always have to be read and written as a whole.

Value

Object of class H5A.

Methods

get_info()

This function implements the HDF5-API function H5Aget_info. Please see the documentation at https://docs.hdfgroup.org/hdf5/v1_10/group___h5_a.html for details.

attr_name()

This function implements the HDF5-API function H5Aget_name. Please see the documentation at https://docs.hdfgroup.org/hdf5/v1_10/group___h5_a.html for details.

get_space()

This function implements the HDF5-API function H5Aget_space. Please see the documentation at https://docs.hdfgroup.org/hdf5/v1_10/group___h5_a.html for details.

get_type(native = TRUE)

This function implements the HDF5-API function H5Aget_type. Please see the documentation at https://docs.hdfgroup.org/hdf5/v1_10/group___h5_a.html for details.

get_storage_size()

This function implements the HDF5-API function H5Aget_storage_size. Please see the documentation at https://docs.hdfgroup.org/hdf5/v1_10/group___h5_a.html for details.

read_low_level(buffer, mem_type, duplicate_buffer = FALSE)

Only for advanced users. See documentation for read instead. This function implements the HDF5-API function H5Aread. Please see the documentation at https://docs.hdfgroup.org/hdf5/v1_10/group___h5_a.html for details.

read(flags = getOption("hdf5r.h5tor_default"), drop = TRUE)

Reads the data of the attribute and returns it as an R-object

Parameters

flags

Conversion rules for integer values. See also h5const

drop

Logical. Should dimensions of length 1 be dropped (R-default for arrays)

write_low_level(buffer, mem_type)

Only for advanced users. See documentation for write instead. This function implements the HDF5-API function H5Awrite. Please see the documentation at https://docs.hdfgroup.org/hdf5/v1_10/group___h5_a.html for details.

write(robj, mem_type = NULL, flush = getOption("hdf5r.flush_on_write"))

Writes the data of robj to the attribute

Parameters

robj

The object to write into the attribute

mem_type

The memory data type to use when transferring from HDF5 to intermediate storage. This is an advanced development feature and may be removed in the future.

print(...)

Prints information for the dataset

Parameters

...

ignored

flush(scope = h5const$H5F_SCOPE_GLOBAL)

This function implements the HDF5-API function H5Fflush. Please see the documentation at https://docs.hdfgroup.org/hdf5/v1_10/group___h5_f.html for details.

get_filename()

This function implements the HDF5-API function H5Fget_name. Please see the documentation at https://docs.hdfgroup.org/hdf5/v1_10/group___h5_f.html for details.

Author(s)

Holger Hoefling

Examples

fname <- tempfile(fileext = ".h5")
file <- H5File$new(fname, mode = "a")
h5attr(file, "attr_numeric") <- rnorm(10)
a <- file$attr_open("attr_numeric")
a$get_info()
a$attr_name()
a$get_space()
a$get_type()
a$get_storage_size()
a$read()
a$write(10:1)
a$print()
a$close()
file$close_all()

Description

Interface for HDF5 attributes

Usage

h5attributes(x)

h5attr_names(x)

h5attr(x, which)

h5attr(x, which) <- value

Arguments

Details

Implements high-level functions that allows interactions with HDF5-attributes in a way very similar to regular R-object attributes in R are handled.

Value

For h5attributes, a named list with the content of the attributes read out. For h5attr_names, a vector of names of the attributes attached to the object x. For h5attr, the content of the attribute and for h5attr<-, the assignment, the original object to which the attributes are attached (so that chaining is possible).

Author(s)

Holger Hoefling

Description

These are all constants used in HDF5. They are stored in an environment with locked bindings so that they cannot be changed. An overview of all constants can be seen with h5const$overview, listing all of them. Each constant can be accessed using $ and the name of the constant. See the examples below.

Details

There are also some flags that govern 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 all start with the term H5TOR. There are currently possible values

H5TOR_CONV_NONE

Doesn't do any conversion. Every integer datatype with more than 32 bit is returned as 64bit integers. For unsigned 64bit integers, the conversion to signed 64bit integers is done by truncation

H5TOR_CONV_INT64_INT_NOLOSS

Under this setting, whenever a 64 bit integer would be returned, it is checked if it would also fit into a 32 bit integer without data loss and returned as such if possible

H5TOR_CONV_INT64_FLOAT_NOLOSS

Under this setting, whenever a 64 bit integer would be returned, it is checked if it would also fit into a 64 bit floating point value without data loss and returned as such if possible

H5TOR_CONV_INT64_NOLOSS

Combines H5TOR_CONV_INT64_INT_NOLOSS and H5TOR_CONV_INT64_FLOAT_NOLOSS and is set as the default in the hdf5r.h5tor_default option.

H5TOR_CONV_INT64_FLOAT_FORCE

Under this setting, whenever a 64 bit integer would be returned, it is coerced to a double even if this results in a loss of precision. If a loss of precision occurs, a warning is issued. Please note that this also overrides the use of H5TOR_CONV_UNIT64_NA. As loss of precision is already accepted, UINT64-values that are larger than LLONG_MAX will be represented as their next possible floating point value.

H5TOR_CONV_UINT64_NA

When converting an unsigned 64bit integer, any values that don't fit into a signed 64bit integer are set to NA. If this flag is not set, then the values will be truncated to LLONG_MAX, the largest 64bit signed integer.

H5TOR_CONV_DEFAULT

Is both H5TOR_CONV_INT64_INT and H5TOR_CONV_UNIT64_FLOAT

Author(s)

Holger Hoefling

Examples

h5const$overview
h5const$H5F_ACC_RDWR
h5const$H5F_ACC_DEFAULT
# Combining flags
bitwOr(h5const$H5TOR_CONV_UINT64_NA, h5const$H5TOR_CONV_INT64_INT_NOLOSS)

Description

In HDF5, datasets can be located in a group (see H5Group) or at the root of a file (see 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 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).

Details

In order to create a dataset, the create_dataset methods of either H5Group or H5File should be used. Please see the documentation there for how to create them.

The most important parts of a dataset are the

Space

The space of the dataset. It describes the dimension of the dataset as well as the maximum dimensions. Can be obtained using the get_space of the H5S object.

Datatype

The datatypes that is being used in the dataset. Can be obtained using the get_type method. See H5T to get more information about using datatypes.

In order to read and write datasets, the read and write methods are available. In addition, the standard way of using [ to access arrays is supported as well (see H5S_H5D_subset_assign for more help).

Other information/action of possible interest are

Storage size

The size of the dataset can be extracted using get_storage_size

Size change

The size of the dataset can be changed using the set_extent method

Please also note the active methods

dims

Dimension of the dataset

maxdims

Maximum dimensions of the dataset

chunk_dims

Dimension of the chunks

key_info

Returns the space, type, property-list and dimensions

Value

Object of class H5D.

Methods

new(id = NULL)

Initializes a new dataset-object. Only for internal use. Use the create_dataset function for H5Group and H5File objects

Parameters

id

For internal use only

get_space()

This function implements the HDF5-API function H5Dget_space. Please see the documentation at https://docs.hdfgroup.org/hdf5/v1_10/group___h5_d.html for details.

get_space_status()

This function implements the HDF5-API function H5Dget_space_status. Please see the documentation at https://docs.hdfgroup.org/hdf5/v1_10/group___h5_d.html for details.

get_type(native = TRUE)

This function implements the HDF5-API function H5Dget_type. Please see the documentation at https://docs.hdfgroup.org/hdf5/v1_10/group___h5_d.html for details.

get_create_plist()

This function implements the HDF5-API function H5Dget_create_plist. Please see the documentation at https://docs.hdfgroup.org/hdf5/v1_10/group___h5_d.html for details.

get_access_plist()

This function implements the HDF5-API function H5Dget_access_plist. Please see the documentation at https://docs.hdfgroup.org/hdf5/v1_10/group___h5_d.html for details.

get_offset()

This function implements the HDF5-API function H5Dget_offset. Please see the documentation at https://docs.hdfgroup.org/hdf5/v1_10/group___h5_d.html for details.

get_storage_size()

This function implements the HDF5-API function H5Dget_storage_size. Please see the documentation at https://docs.hdfgroup.org/hdf5/v1_10/group___h5_d.html for details.

vlen_get_buf_size(type, space)

This function implements the HDF5-API function H5Dvlen_get_buf_size. Please see the documentation at https://docs.hdfgroup.org/hdf5/v1_10/group___h5_d.html for details.

vlen_reclaim(buffer, type, space, dataset_xfer_pl = h5const$H5P_DEFAULT)

This function implements the HDF5-API function H5Dvlen_reclaim. Please see the documentation at https://docs.hdfgroup.org/hdf5/v1_10/group___h5_d.html for details.

read_low_level(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 read instead or the [ interface. This function implements the HDF5-API function H5Dread, with minor changes to the API to accommodate R. Please see the documentation at https://docs.hdfgroup.org/hdf5/v1_10/group___h5_d.html for details. It reads the data in the dataset as specified by mem_space and return it as an R-obj

Parameters

file_space

An HDF5-space, represented as class H5S that determines which part of the dataset is being read. Can also be given as an id

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.

mem_type

Memory type; extracted from the dataset if null (can be passed in for efficiency reasons Can also be given as an id.

dataset_xfer_pl

Dataset transfer property list. See H5P_DATASET_XFER

flags

Conversion rules for integer values. See also h5const

set_dim

If TRUE, the dimension attribute is set in the return value. How it is set is determined by dim_to_set.

dim_to_set

The dimension to set; Has to be numeric and needs to be specified if set_dim is 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.

drop

Logical. Should dimensions of length 1 be dropped (R-default for arrays)

read(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 [, where all indices are being passed in the parameter args.

Parameters

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 [ operator. If set to NULL, the entire dataset will be read.

envir

The environment in which to evaluate args

dataset_xfer_pl

An object of class H5P_DATASET_XFER.

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 h5const. The relevant ones start with the term 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 bit64 package otherwise. For 64bit unsigned int that are larger than 64bit signed int, it return a double. This looses precision, however.

drop

Logical. When reading data, should dimensions of size 1 be dropped.

Return

The data that was read as an R object

write_low_level(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 read instead or the [<- interface as used for arrays. This function implements the HDF5-API function H5Dwrite, with some changes to accommodate R. Please see the documentation at https://docs.hdfgroup.org/hdf5/v1_10/group___h5_d.html for details. It writes that data from the robj into the dataset.

Parameters

robj

The object to write into the dataset

mem_space

The space as it is represented in memory; advanced feature; may be removed in the future

mem_type

Memory type; extracted from the dataset if null (can be passed in for efficiency reasons

file_space

An HDF5-space, represented as class H5S that determines which part of the dataset is being written.

dataset_xfer_pl

Dataset transfer property list. See H5P_DATASET_XFER

flush

Should a flush be done after the write

write(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 [<-, where all indices are being passed in the parameter args.

Parameters

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 [ operator. If set to NULL, the entire dataset will be read.

value

The data to write to the dataset

envir

The environment in which to evaluate args

dataset_xfer_pl

An object of class H5P_DATASET_XFER.

Return

The HDF5 dataset object, returned invisibly

set_extent(dims)

This function implements the HDF5-API function H5Dset_extent. Please see the documentation at https://docs.hdfgroup.org/hdf5/v1_10/group___h5_d.html for details.

get_fill_value()

This function implements the HDF5-API function H5Pget_fill_value, automatically supplying the datatype of the dataset for convenience. Please see the documentation at https://docs.hdfgroup.org/hdf5/v1_10/group___h5_p.html for details.

create_reference(...)

This function implements the HDF5-API function H5Rcreate. The parameters are interpreted as in '['. The function always create H5R_DATASET_REGION references Please see the documentation at https://docs.hdfgroup.org/hdf5/v1_10/group___h5_r.html for details.

print(..., max.attributes = 10)

Prints information for the dataset

Parameters

...

ignored

max.attributes

Maximum number of attribute names to print

obj_info(remove_internal_use_only = TRUE)

This function implements the HDF5-API function H5Oget_info. Please see the documentation at https://docs.hdfgroup.org/hdf5/v1_10/group___h5_o.html for details.

get_obj_name()

This function implements the HDF5-API function H5Iget_name. Please see the documentation at https://docs.hdfgroup.org/hdf5/v1_10/group___h5_i.html for details.

create_attr(attr_name, robj = NULL, dtype = NULL, space = NULL)

This function implements the HDF5-API function H5Acreate2. Please see the documentation at https://docs.hdfgroup.org/hdf5/v1_10/group___h5_a.html for details.

attr_open(attr_name)

This function implements the HDF5-API function H5Aopen. Please see the documentation at https://docs.hdfgroup.org/hdf5/v1_10/group___h5_a.html for details.

create_attr_by_name(attr_name, obj_name, robj = NULL, dtype = NULL, space = NULL, link_access_pl = h5const$H5P_DEFAULT)

This function implements the HDF5-API function H5Acreate_by_name. Please see the documentation at https://docs.hdfgroup.org/hdf5/v1_10/group___h5_a.html for details.

attr_open_by_name(attr_name, obj_name, link_access_pl = h5const$H5P_DEFAULT)

This function implements the HDF5-API function H5Aopen_by_name. Please see the documentation at https://docs.hdfgroup.org/hdf5/v1_10/group___h5_a.html for details.

attr_open_by_idx(n, obj_name, idx_type = h5const$H5_INDEX_NAME, order = h5const$H5_ITER_NATIVE, link_access_pl = h5const$H5P_DEFAULT)

This function implements the HDF5-API function H5Aopen_by_idx. Please see the documentation at https://docs.hdfgroup.org/hdf5/v1_10/group___h5_a.html for details.

attr_exists_by_name(attr_name, obj_name, link_access_pl = h5const$H5P_DEFAULT)

This function implements the HDF5-API function H5Aexists_by_name. Please see the documentation at https://docs.hdfgroup.org/hdf5/v1_10/group___h5_a.html for details.

attr_exists(attr_name)

This function implements the HDF5-API function H5Aexists. Please see the documentation at https://docs.hdfgroup.org/hdf5/v1_10/group___h5_a.html for details.

attr_rename_by_name(old_attr_name, new_attr_name, obj_name, link_access_pl = h5const$H5P_DEFAULT)

This function implements the HDF5-API function H5Arename_by_name. Please see the documentation at https://docs.hdfgroup.org/hdf5/v1_10/group___h5_a.html for details.

attr_rename(old_attr_name, new_attr_name)

This function implements the HDF5-API function H5Arename. Please see the documentation at https://docs.hdfgroup.org/hdf5/v1_10/group___h5_a.html for details.

attr_delete(attr_name)

This function implements the HDF5-API function H5Adelete. Please see the documentation at https://docs.hdfgroup.org/hdf5/v1_10/group___h5_a.html for details.

attr_delete_by_name(attr_name, obj_name, link_access_pl = h5const$H5P_DEFAULT)

This function implements the HDF5-API function H5Adelete_by_name. Please see the documentation at https://docs.hdfgroup.org/hdf5/v1_10/group___h5_a.html for details.

attr_delete_by_idx(n, obj_name, idx_type = h5const$H5_INDEX_NAME, order = h5const$H5_ITER_NATIVE, link_access_pl = h5const$H5P_DEFAULT)

This function implements the HDF5-API function H5Adelete_by_idx. Please see the documentation at https://docs.hdfgroup.org/hdf5/v1_10/group___h5_a.html for details.

attr_info_by_name(attr_name, obj_name, link_access_pl = h5const$H5P_DEFAULT)

This function implements the HDF5-API function H5Aget_info_by_name. Please see the documentation at https://docs.hdfgroup.org/hdf5/v1_10/group___h5_a.html for details.

attr_info_by_idx(n, obj_name, idx_type = h5const$H5_INDEX_NAME, order = h5const$H5_ITER_NATIVE, link_access_pl = h5const$H5P_DEFAULT)

This function implements the HDF5-API function H5Aget_info_by_idx. Please see the documentation at https://docs.hdfgroup.org/hdf5/v1_10/group___h5_a.html for details.

attr_name_by_idx(n, obj_name, idx_type = h5const$H5_INDEX_NAME, order = h5const$H5_ITER_NATIVE, link_access_pl = h5const$H5P_DEFAULT)

This function implements the HDF5-API function H5Aget_name_by_idx. Please see the documentation at https://docs.hdfgroup.org/hdf5/v1_10/group___h5_a.html for details.

attr_get_number()

This function implements the HDF5-API function H5Aget_num_attrs. Please see the documentation at https://support.hdfgroup.org/HDF5/doc/RM/RM_H5A.html#Annot-NumAttrs for details.

flush(scope = h5const$H5F_SCOPE_GLOBAL)

This function implements the HDF5-API function H5Fflush. Please see the documentation at https://docs.hdfgroup.org/hdf5/v1_10/group___h5_f.html for details.

get_filename()

This function implements the HDF5-API function H5Fget_name. Please see the documentation at https://docs.hdfgroup.org/hdf5/v1_10/group___h5_f.html for details.

dims()

Get the dimension of the dataset

maxdims()

Get the maximal dimension of the dataset

chunk_dims()

Return the dimension of the chunks. NA if the dataset is not chunked

key_info()

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 Inf for type_size_variable and the underlying size for type_size_raw

Author(s)

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)

Description

H5File objects are are the main entry point to access HDF5 data from binary files. This class represents an open HDF5 File-id. It inherits all functions of the H5RefClass.

Details

HDF5 files can be opened or generated using the H5File$new() function and a specified file access mode. H5File$new() returns a H5File object which can be used to access H5Groups and Datasets (see H5D) using subsetting parameters or according class methods.

HDF5 files which have been created or opened through H5File$new() need to be closed afterwards using $close_all(). $close_all() not only closes the file itself, but also all objects that are still open inside it (such as groups or datasets). $flush() can be used to flush unwritten data to an HDF5 file.

HDF5 Files typically contain the following objects:

Groups

Similar to a file system folder, used to organize HDF5 objects in a hierarchical way, see also H5Group

Datasets

Objects to store actual data, see also H5D

Attributes

Meta data objects to store extra information about Files, Groups and Datasets, see also H5A

Value

Object of class H5File.

Methods

new(filename = NULL, mode = c("a", "r", "r+", "w", "w-", "x"), file_create_pl = h5const$H5P_DEFAULT, file_access_pl = h5const$H5P_DEFAULT, id = NULL)

Opens or creates a new HDF5 File

Parameters

filename

Name of the file

mode

How to open it. a creates a new file or opens an existing one for read/write. r opens an existing file for reading, r+ opens an existing file for read/write. w creates a file, truncating any existing ones and w-/x are synonyms, creating a file and failing if it already exists.

get_obj_count(types = h5const$H5F_OBJ_ALL)

This function implements the HDF5-API function H5Fget_obj_count. Please see the documentation at https://docs.hdfgroup.org/hdf5/v1_10/group___h5_f.html for details.

get_obj_ids(types = h5const$H5F_OBJ_ALL)

This function implements the HDF5-API function H5Fget_obj_ids. Please see the documentation at https://docs.hdfgroup.org/hdf5/v1_10/group___h5_f.html for details.

get_filesize()

This function implements the HDF5-API function H5Fget_filesize. Please see the documentation at https://docs.hdfgroup.org/hdf5/v1_10/group___h5_f.html for details.

file_info()

This function implements the HDF5-API function H5Fget_info2. Please see the documentation at https://docs.hdfgroup.org/hdf5/v1_10/group___h5_f.html for details. Please note that the returned information differs if HDF5 Version 1.8.16 or HDF5 Version >= 1.10.0 is being used

get_intent()

This function implements the HDF5-API function H5Fget_intent. Please see the documentation at https://docs.hdfgroup.org/hdf5/v1_10/group___h5_f.html for details.

close_all(close_self = TRUE)

Closes the file, flushes it and also closes all open objects that are still open in it. This is the recommended way of closing any file. If not all objects in a file are closed, the file remains open and cannot be re-opened the regular way.

print(..., max.attributes = 10, max.listing = 10)

Prints information for the file

Parameters

max.attributes

Maximum number of attribute names to print

max.listing

Maximum number of ls-items to print

...

ignored

open(name, link_access_pl = h5const$H5P_DEFAULT, dataset_access_pl = h5const$H5P_DEFAULT, type_access_pl = h5const$H5P_DEFAULT)

Opens groups, datasets or types using the appropriate HDF5-API functions. Please see the documentation at https://docs.hdfgroup.org/hdf5/v1_10/group___h5_d.html for datasets, https://docs.hdfgroup.org/hdf5/v1_10/group___h5_o.html for types and https://docs.hdfgroup.org/hdf5/v1_10/group___h5_o.html for general objects.

open_by_idx(n, group_name = ".", index_type = h5const$H5_INDEX_NAME, order = h5const$H5_ITER_NATIVE, link_access_pl = h5const$H5P_DEFAULT)

This function implements the HDF5-API function H5Oopen_by_idx. Please see the documentation at https://docs.hdfgroup.org/hdf5/v1_10/group___h5_o.html for details.

ls(recursive = FALSE, detailed = FALSE, index_type = h5const$H5_INDEX_NAME, order = h5const$H5_ITER_NATIVE, link_access_pl = h5const$H5P_DEFAULT, dataset_access_pl = h5const$H5P_DEFAULT, type_access_pl = h5const$H5P_DEFAULT)

Returns the contents of a file or group as a data.frame.

exists(name, link_access_pl = h5const$H5P_DEFAULT)

This function implements the HDF5-API function H5Lexists. Please see the documentation at https://docs.hdfgroup.org/hdf5/v1_10/group___h5_l.html for details.

path_valid(path, check_object_valid = TRUE)

This function implements the HDF5-API function H5LTpath_valid. Please see the documentation at https://support.hdfgroup.org/HDF5/doc/HL/RM_H5LT.html#H5LTpath_valid for details.

link(obj, new_link_name, link_create_pl = h5const$H5P_DEFAULT, link_access_pl = h5const$H5P_DEFAULT)

This function implements the HDF5-API function H5Olink. Please see the documentation at https://docs.hdfgroup.org/hdf5/v1_10/group___h5_o.html for details.

obj_copy_to(dst_loc, dst_name, src_name, object_copy_pl = h5const$H5P_DEFAULT, link_create_pl = h5const$H5P_DEFAULT)

This function implements the HDF5-API function H5Ocopy. Please see the documentation at https://docs.hdfgroup.org/hdf5/v1_10/group___h5_o.html for details.

obj_copy_from(src_loc, src_name, dst_name, object_copy_pl = h5const$H5P_DEFAULT, link_create_pl = h5const$H5P_DEFAULT)

This function implements the HDF5-API function H5Ocopy. Please see the documentation at https://docs.hdfgroup.org/hdf5/v1_10/group___h5_o.html for details.

obj_info_by_idx(n, group_name = ".", index_field = h5const$H5_INDEX_NAME, order = h5const$H5_ITER_NATIVE, remove_internal_use_only = TRUE)

This function implements the HDF5-API function H5Oget_info_by_idx. Please see the documentation at https://docs.hdfgroup.org/hdf5/v1_10/group___h5_o.html for details.

obj_info_by_name(object_name, remove_internal_use_only = TRUE)

This function implements the HDF5-API function H5Oget_info_by_name. Please see the documentation at https://docs.hdfgroup.org/hdf5/v1_10/group___h5_o.html for details.

group_info()

This function implements the HDF5-API function H5Gget_info. Please see the documentation at https://docs.hdfgroup.org/hdf5/v1_10/group___h5_g.html for details.

group_info_by_name(name, link_access_pl = h5const$H5P_DEFAULT)

This function implements the HDF5-API function H5Gget_info_by_name. Please see the documentation at https://docs.hdfgroup.org/hdf5/v1_10/group___h5_g.html for details.

group_info_by_idx(n, group_name = ".", index_field = h5const$H5_INDEX_NAME, order = h5const$H5_ITER_NATIVE, link_access_pl = h5const$H5P_DEFAULT)

This function implements the HDF5-API function H5Gget_info_by_idx. Please see the documentation at https://docs.hdfgroup.org/hdf5/v1_10/group___h5_g.html for details.

create_group(name, link_create_pl = h5const$H5P_DEFAULT, group_create_pl = h5const$H5P_DEFAULT, group_access_pl = h5const$H5P_DEFAULT)

This function implements the HDF5-API function H5Gcreate2 and H5Gcreate_anon (if name is NULL). Please see the documentation at https://docs.hdfgroup.org/hdf5/v1_10/group___h5_g.html for regular groups and https://docs.hdfgroup.org/hdf5/v1_10/group___h5_g.html for anonymous groups for details.

create_dataset(name, robj = NULL, dtype = NULL, space = NULL, dims = NULL, chunk_dims = "auto", gzip_level = 4, link_create_pl = h5const$H5P_DEFAULT, dataset_create_pl = h5const$H5P_DEFAULT, dataset_access_pl = h5const$H5P_DEFAULT)

This function is the main interface to create a new dataset. Its parameters allow for customization of the default behavior, i.e. in order to get a specific datatype, a certain chunk size or dataset dimensionality. Also note that this function implements the HDF5-API function H5Dcreate2 and H5Dcreate_anon (if name is NULL). Please see the documentation at https://docs.hdfgroup.org/hdf5/v1_10/group___h5_d.html for regular groups and https://docs.hdfgroup.org/hdf5/v1_10/group___h5_d.html for anonymous groups for details.

Parameters

name

The name of the new dataset. If missing, an anonymous dataset is created

robj

An R-object to take as a template for creating the dataset. Either robj or both dtype and space have to be provided

dtype

The datatype to use for the creation of the object. Can be null if robj is given.

space

The space to use for the object creation. Can be null if robj is given. Otherwise an object of type H5S which specifies the dimensions of the dataset.

dims

Dimension of the new dataset; used if space is NULL. overwrite the dimension guessed from robj if robj is given.

chunk_dims

Size of the chunk. Has to have the same length as the dataset dimension. If "auto" then the size of each chunk is estimated so that each chunk is roughly as large in bytes as the value in the hdf5r.chunk_size option. See also guess_chunks for a more detailed explanation. If set to NULL, then no chunking is used, unless explicitly set in dataset_create_pl.

gzip_level

Only if chunk_dims is not null. If given, then the dataset_create_pl is set to enable zipping at the level given here. If set to NULL, then gzip is not set (but could be set otherwise in dataset_create_pl

link_create_pl

Link creation property list. See H5P_LINK_CREATE

dataset_create_pl

Dataset creation property list. See H5P_DATASET_CREATE

dataset_access_pl

Dataset access property list. See H5P_DATASET_ACCESS

commit(name, dtype, link_create_pl = h5const$H5P_DEFAULT, type_create_pl = h5const$H5P_DEFAULT, type_access_pl = h5const$H5P_DEFAULT)

This function implements the HDF5-API function H5Tcommit2. Please see the documentation at https://docs.hdfgroup.org/hdf5/v1_10/group___h5_t.html for details.

link_create_hard(obj_loc, obj_name, link_name, link_create_pl = h5const$H5P_DEFAULT, link_access_pl = h5const$H5P_DEFAULT)

This function implements the HDF5-API function H5Lcreate_hard. Please see the documentation at https://docs.hdfgroup.org/hdf5/v1_10/group___h5_l.html for details.

link_create_soft(target_path, link_name, link_create_pl = h5const$H5P_DEFAULT, link_access_pl = h5const$H5P_DEFAULT)

This function implements the HDF5-API function H5Lcreate_soft. Please see the documentation at https://docs.hdfgroup.org/hdf5/v1_10/group___h5_l.html for details.

link_create_external(target_filename, target_obj_name, link_name, link_create_pl = h5const$H5P_DEFAULT, link_access_pl = h5const$H5P_DEFAULT)

This function implements the HDF5-API function H5Lcreate_external. Please see the documentation at https://docs.hdfgroup.org/hdf5/v1_10/group___h5_l.html for details.

link_exists(name, link_access_pl = h5const$H5P_DEFAULT)

This function implements the HDF5-API function H5Lexists. Please see the documentation at https://docs.hdfgroup.org/hdf5/v1_10/group___h5_l.html for details.

link_move_from(src_loc, src_name, dst_name, link_create_pl = h5const$H5P_DEFAULT, link_access_pl = h5const$H5P_DEFAULT)

This function implements the HDF5-API function H5Lmove. Please see the documentation at https://docs.hdfgroup.org/hdf5/v1_10/group___h5_l.html for details.

link_move_to(dst_loc, dst_name, src_name, link_create_pl = h5const$H5P_DEFAULT, link_access_pl = h5const$H5P_DEFAULT)

This function implements the HDF5-API function H5Lmove. Please see the documentation at https://docs.hdfgroup.org/hdf5/v1_10/group___h5_l.html for details.

link_copy_from(src_loc, src_name, dst_name, link_create_pl = h5const$H5P_DEFAULT, link_access_pl = h5const$H5P_DEFAULT)

This function implements the HDF5-API function H5Lcopy. Please see the documentation at https://docs.hdfgroup.org/hdf5/v1_10/group___h5_l.html for details.

link_copy_to(dst_loc, dst_name, src_name, link_create_pl = h5const$H5P_DEFAULT, link_access_pl = h5const$H5P_DEFAULT)

This function implements the HDF5-API function H5Lcopy. Please see the documentation at https://docs.hdfgroup.org/hdf5/v1_10/group___h5_l.html for details.

link_delete(name, link_access_pl = h5const$H5P_DEFAULT)

This function implements the HDF5-API function H5Ldelete. Please see the documentation at https://docs.hdfgroup.org/hdf5/v1_10/group___h5_l.html for details.

link_delete_by_idx(n, group_name = ".", index_field = h5const$H5_INDEX_NAME, order = h5const$H5_ITER_NATIVE, link_access_pl = h5const$H5P_DEFAULT)

This function implements the HDF5-API function H5Ldelete_by_idx. Please see the documentation at https://docs.hdfgroup.org/hdf5/v1_10/group___h5_l.html for details.

link_info(name, link_access_pl = h5const$H5P_DEFAULT)

This function implements the HDF5-API function H5Lget_info. Please see the documentation at https://docs.hdfgroup.org/hdf5/v1_10/group___h5_l.html for details.

link_info_by_idx(n, group_name = ".", index_field = h5const$H5_INDEX_NAME, order = h5const$H5_ITER_NATIVE, link_access_pl = h5const$H5P_DEFAULT)

This function implements the HDF5-API function H5Lget_info_by_idx. Please see the documentation at https://docs.hdfgroup.org/hdf5/v1_10/group___h5_l.html for details.

link_value(name, link_access_pl = h5const$H5P_DEFAULT)

This function implements the HDF5-API function H5Lget_val. Please see the documentation at https://docs.hdfgroup.org/hdf5/v1_10/group___h5_l.html for details.

link_value_by_idx(n, group_name = ".", index_field = h5const$H5_INDEX_NAME, order = h5const$H5_ITER_NATIVE, link_access_pl = h5const$H5P_DEFAULT)

This function implements the HDF5-API function H5Lget_val_by_idx. Please see the documentation at https://docs.hdfgroup.org/hdf5/v1_10/group___h5_l.html for details.

link_name_by_idx(n, group_name, idx_type = h5const$H5_INDEX_NAME, order = h5const$H5_ITER_NATIVE, link_access_pl = h5const$H5P_DEFAULT)

This function implements the HDF5-API function H5Lget_name_by_idx. Please see the documentation at https://docs.hdfgroup.org/hdf5/v1_10/group___h5_l.html for details.

mount(name, child)

This function implements the HDF5-API function H5Fmount. Please see the documentation at https://docs.hdfgroup.org/hdf5/v1_10/group___h5_f.html for details.

unmount(name)

This function implements the HDF5-API function H5Funmount. Please see the documentation at https://docs.hdfgroup.org/hdf5/v1_10/group___h5_f.html for details.

create_reference(name = ".", space = NULL)

This function implements the HDF5-API function H5Rcreate. If space=NULL then a H5R_OBJECT reference is created, otherwise a H5R_DATASET_REGION reference Please see the documentation at https://docs.hdfgroup.org/hdf5/v1_10/group___h5_r.html for details.

obj_info(remove_internal_use_only = TRUE)

This function implements the HDF5-API function H5Oget_info. Please see the documentation at https://docs.hdfgroup.org/hdf5/v1_10/group___h5_o.html for details.

get_obj_name()

This function implements the HDF5-API function H5Iget_name. Please see the documentation at https://docs.hdfgroup.org/hdf5/v1_10/group___h5_i.html for details.

create_attr(attr_name, robj = NULL, dtype = NULL, space = NULL)

This function implements the HDF5-API function H5Acreate2. Please see the documentation at https://docs.hdfgroup.org/hdf5/v1_10/group___h5_a.html for details.

attr_open(attr_name)

This function implements the HDF5-API function H5Aopen. Please see the documentation at https://docs.hdfgroup.org/hdf5/v1_10/group___h5_a.html for details.

create_attr_by_name(attr_name, obj_name, robj = NULL, dtype = NULL, space = NULL, link_access_pl = h5const$H5P_DEFAULT)

This function implements the HDF5-API function H5Acreate_by_name. Please see the documentation at https://docs.hdfgroup.org/hdf5/v1_10/group___h5_a.html for details.

attr_open_by_name(attr_name, obj_name, link_access_pl = h5const$H5P_DEFAULT)

This function implements the HDF5-API function H5Aopen_by_name. Please see the documentation at https://docs.hdfgroup.org/hdf5/v1_10/group___h5_a.html for details.

attr_open_by_idx(n, obj_name, idx_type = h5const$H5_INDEX_NAME, order = h5const$H5_ITER_NATIVE, link_access_pl = h5const$H5P_DEFAULT)

This function implements the HDF5-API function H5Aopen_by_idx. Please see the documentation at https://docs.hdfgroup.org/hdf5/v1_10/group___h5_a.html for details.

attr_exists_by_name(attr_name, obj_name, link_access_pl = h5const$H5P_DEFAULT)

This function implements the HDF5-API function H5Aexists_by_name. Please see the documentation at https://docs.hdfgroup.org/hdf5/v1_10/group___h5_a.html for details.

attr_exists(attr_name)

This function implements the HDF5-API function H5Aexists. Please see the documentation at https://docs.hdfgroup.org/hdf5/v1_10/group___h5_a.html for details.

attr_rename_by_name(old_attr_name, new_attr_name, obj_name, link_access_pl = h5const$H5P_DEFAULT)

This function implements the HDF5-API function H5Arename_by_name. Please see the documentation at https://docs.hdfgroup.org/hdf5/v1_10/group___h5_a.html for details.

attr_rename(old_attr_name, new_attr_name)

This function implements the HDF5-API function H5Arename. Please see the documentation at https://docs.hdfgroup.org/hdf5/v1_10/group___h5_a.html for details.

attr_delete(attr_name)

This function implements the HDF5-API function H5Adelete. Please see the documentation at https://docs.hdfgroup.org/hdf5/v1_10/group___h5_a.html for details.

attr_delete_by_name(attr_name, obj_name, link_access_pl = h5const$H5P_DEFAULT)

This function implements the HDF5-API function H5Adelete_by_name. Please see the documentation at https://docs.hdfgroup.org/hdf5/v1_10/group___h5_a.html for details.

attr_delete_by_idx(n, obj_name, idx_type = h5const$H5_INDEX_NAME, order = h5const$H5_ITER_NATIVE, link_access_pl = h5const$H5P_DEFAULT)

This function implements the HDF5-API function H5Adelete_by_idx. Please see the documentation at https://docs.hdfgroup.org/hdf5/v1_10/group___h5_a.html for details.

attr_info_by_name(attr_name, obj_name, link_access_pl = h5const$H5P_DEFAULT)

This function implements the HDF5-API function H5Aget_info_by_name. Please see the documentation at https://docs.hdfgroup.org/hdf5/v1_10/group___h5_a.html for details.

attr_info_by_idx(n, obj_name, idx_type = h5const$H5_INDEX_NAME, order = h5const$H5_ITER_NATIVE, link_access_pl = h5const$H5P_DEFAULT)

This function implements the HDF5-API function H5Aget_info_by_idx. Please see the documentation at https://docs.hdfgroup.org/hdf5/v1_10/group___h5_a.html for details.

attr_name_by_idx(n, obj_name, idx_type = h5const$H5_INDEX_NAME, order = h5const$H5_ITER_NATIVE, link_access_pl = h5const$H5P_DEFAULT)

This function implements the HDF5-API function H5Aget_name_by_idx. Please see the documentation at https://docs.hdfgroup.org/hdf5/v1_10/group___h5_a.html for details.

attr_get_number()

This function implements the HDF5-API function H5Aget_num_attrs. Please see the documentation at https://support.hdfgroup.org/HDF5/doc/RM/RM_H5A.html#Annot-NumAttrs for details.

flush(scope = h5const$H5F_SCOPE_GLOBAL)

This function implements the HDF5-API function H5Fflush. Please see the documentation at https://docs.hdfgroup.org/hdf5/v1_10/group___h5_f.html for details.

get_filename()

This function implements the HDF5-API function H5Fget_name. Please see the documentation at https://docs.hdfgroup.org/hdf5/v1_10/group___h5_f.html for details.

names(link_access_pl = h5const$H5P_DEFAULT)

Returns the names of the items in the group or at the root of the file

Parameters

link_access_pl

The link-access property list. See https://docs.hdfgroup.org/hdf5/v1_10/group___l_a_p_l.html for more detail.

Extract/List File Contents

The following functions are defined to extract HDF5 file contents:

list.groups

List HDF5 groups in file.

list.datasets

List HDF5 datasets in file.

names

List all items in a file or group (applicable for H5File and H5Group)

list.attributes

List Attributes of HDF5 object (file, group or dataset).

h5attr_names

Attribute names of an HDF5 object; similar to list.attributes

Author(s)

Holger Hoefling, Mario Annau

See Also

h5file

Examples

# The following examples generates a HDF5 file with the different HDF5 
# Objects and shows its contents:
fname <- tempfile(fileext = ".h5")
file <- H5File$new(fname, mode = "a")
file[["testdataset"]] <- 1:10
h5attr(file, "testattrib") <- LETTERS[1:10]
file$create_group("testgroup")
file[["testgroup/testdataset2"]] <- 1:10
# Show contents of file
file
# Close file and delete
file$close_all()

# The following example shows hdf5 file contents and how to use them to iterate over HDF5 elements:
file <- h5file(fname, mode = "a")
sapply(c("testgroup1", "testgroup2", "testgroup3"), file$create_group)
file[["testgroup1/testset1"]] <- 1:10
file[["testgroup2/testset2"]] <- 11:20
file[["testgroup3/testset3"]] <- 21:30

# Extract first 3 elements from each dataset and combine result to matrix
sapply(list.datasets(file, recursive = TRUE), function(x) file[[x]][1:3])
# Close file
file$close_all()
file.remove(fname)

Description

Trigger the HDF5 garbage collection

Usage

h5garbage_collect()

Details

This function triggers the HDF5 internal garbage collection. It is independent of the R garbage collection and currently has to be triggered by hand.

Value

Invisible NULL

Author(s)

Holger Hoefling

Description

Retrieve object from a group of file

Usage

## S3 method for class 'H5Group'
x[[name, ..., link_access_pl = h5const$H5P_DEFAULT,
  dataset_access_pl = h5const$H5P_DEFAULT,
  type_access_pl = h5const$H5P_DEFAULT]]

## S3 method for class 'H5File'
x[[name, ..., link_access_pl = h5const$H5P_DEFAULT,
  dataset_access_pl = h5const$H5P_DEFAULT,
  type_access_pl = h5const$H5P_DEFAULT]]

## S3 replacement method for class 'H5Group'
x[[name, ...]] <- value

## S3 replacement method for class 'H5File'
x[[name, ...]] <- value

Arguments

Details

Works similar to retrieving objects in a list. x[["my_name"]] retrieves object my_name from the HDF5-File or HDF5-Group x.

One can also assign objects under a not yet existing name. For either a H5Group or H5D, a hard link is created. If it is a datatype, H5T, this is committed under the chosen name name.

Value

A H5Group, H5D or H5T, depending on the object saved in the group under the requested name.

Author(s)

Holger Hoefling

Description

HDF5-Groups are essentially equivalent to directories in a file system. Inside the groups, other groups or datasets can be created. For the most parts, groups behave like files, so please also look at the documentation of H5File.

Value

Object of class H5Group.

Methods

print(..., max.attributes = 10, max.listing = 10)

Prints information for the group

Parameters

max.attributes

Maximum number of attribute names to print

max.listing

Maximum number of ls-items to print

...

ignored

open(name, link_access_pl = h5const$H5P_DEFAULT, dataset_access_pl = h5const$H5P_DEFAULT, type_access_pl = h5const$H5P_DEFAULT)

Opens groups, datasets or types using the appropriate HDF5-API functions. Please see the documentation at https://docs.hdfgroup.org/hdf5/v1_10/group___h5_d.html for datasets, https://docs.hdfgroup.org/hdf5/v1_10/group___h5_o.html for types and https://docs.hdfgroup.org/hdf5/v1_10/group___h5_o.html for general objects.

open_by_idx(n, group_name = ".", index_type = h5const$H5_INDEX_NAME, order = h5const$H5_ITER_NATIVE, link_access_pl = h5const$H5P_DEFAULT)

This function implements the HDF5-API function H5Oopen_by_idx. Please see the documentation at https://docs.hdfgroup.org/hdf5/v1_10/group___h5_o.html for details.

ls(recursive = FALSE, detailed = FALSE, index_type = h5const$H5_INDEX_NAME, order = h5const$H5_ITER_NATIVE, link_access_pl = h5const$H5P_DEFAULT, dataset_access_pl = h5const$H5P_DEFAULT, type_access_pl = h5const$H5P_DEFAULT)

Returns the contents of a file or group as a data.frame.

exists(name, link_access_pl = h5const$H5P_DEFAULT)

This function implements the HDF5-API function H5Lexists. Please see the documentation at https://docs.hdfgroup.org/hdf5/v1_10/group___h5_l.html for details.

path_valid(path, check_object_valid = TRUE)

This function implements the HDF5-API function H5LTpath_valid. Please see the documentation at https://support.hdfgroup.org/HDF5/doc/HL/RM_H5LT.html#H5LTpath_valid for details.

link(obj, new_link_name, link_create_pl = h5const$H5P_DEFAULT, link_access_pl = h5const$H5P_DEFAULT)

This function implements the HDF5-API function H5Olink. Please see the documentation at https://docs.hdfgroup.org/hdf5/v1_10/group___h5_o.html for details.

obj_copy_to(dst_loc, dst_name, src_name, object_copy_pl = h5const$H5P_DEFAULT, link_create_pl = h5const$H5P_DEFAULT)

This function implements the HDF5-API function H5Ocopy. Please see the documentation at https://docs.hdfgroup.org/hdf5/v1_10/group___h5_o.html for details.

obj_copy_from(src_loc, src_name, dst_name, object_copy_pl = h5const$H5P_DEFAULT, link_create_pl = h5const$H5P_DEFAULT)

This function implements the HDF5-API function H5Ocopy. Please see the documentation at https://docs.hdfgroup.org/hdf5/v1_10/group___h5_o.html for details.

obj_info_by_idx(n, group_name = ".", index_field = h5const$H5_INDEX_NAME, order = h5const$H5_ITER_NATIVE, remove_internal_use_only = TRUE)

This function implements the HDF5-API function H5Oget_info_by_idx. Please see the documentation at https://docs.hdfgroup.org/hdf5/v1_10/group___h5_o.html for details.

obj_info_by_name(object_name, remove_internal_use_only = TRUE)

This function implements the HDF5-API function H5Oget_info_by_name. Please see the documentation at https://docs.hdfgroup.org/hdf5/v1_10/group___h5_o.html for details.

group_info()

This function implements the HDF5-API function H5Gget_info. Please see the documentation at https://docs.hdfgroup.org/hdf5/v1_10/group___h5_g.html for details.

group_info_by_name(name, link_access_pl = h5const$H5P_DEFAULT)

This function implements the HDF5-API function H5Gget_info_by_name. Please see the documentation at https://docs.hdfgroup.org/hdf5/v1_10/group___h5_g.html for details.

group_info_by_idx(n, group_name = ".", index_field = h5const$H5_INDEX_NAME, order = h5const$H5_ITER_NATIVE, link_access_pl = h5const$H5P_DEFAULT)

This function implements the HDF5-API function H5Gget_info_by_idx. Please see the documentation at https://docs.hdfgroup.org/hdf5/v1_10/group___h5_g.html for details.

create_group(name, link_create_pl = h5const$H5P_DEFAULT, group_create_pl = h5const$H5P_DEFAULT, group_access_pl = h5const$H5P_DEFAULT)

This function implements the HDF5-API function H5Gcreate2 and H5Gcreate_anon (if name is NULL). Please see the documentation at https://docs.hdfgroup.org/hdf5/v1_10/group___h5_g.html for regular groups and https://docs.hdfgroup.org/hdf5/v1_10/group___h5_g.html for anonymous groups for details.

create_dataset(name, robj = NULL, dtype = NULL, space = NULL, dims = NULL, chunk_dims = "auto", gzip_level = 4, link_create_pl = h5const$H5P_DEFAULT, dataset_create_pl = h5const$H5P_DEFAULT, dataset_access_pl = h5const$H5P_DEFAULT)

This function is the main interface to create a new dataset. Its parameters allow for customization of the default behavior, i.e. in order to get a specific datatype, a certain chunk size or dataset dimensionality. Also note that this function implements the HDF5-API function H5Dcreate2 and H5Dcreate_anon (if name is NULL). Please see the documentation at https://docs.hdfgroup.org/hdf5/v1_10/group___h5_d.html for regular groups and https://docs.hdfgroup.org/hdf5/v1_10/group___h5_d.html for anonymous groups for details.

Parameters

name

The name of the new dataset. If missing, an anonymous dataset is created

robj

An R-object to take as a template for creating the dataset. Either robj or both dtype and space have to be provided

dtype

The datatype to use for the creation of the object. Can be null if robj is given.

space

The space to use for the object creation. Can be null if robj is given. Otherwise an object of type H5S which specifies the dimensions of the dataset.

dims

Dimension of the new dataset; used if space is NULL. overwrite the dimension guessed from robj if robj is given.

chunk_dims

Size of the chunk. Has to have the same length as the dataset dimension. If "auto" then the size of each chunk is estimated so that each chunk is roughly as large in bytes as the value in the hdf5r.chunk_size option. See also guess_chunks for a more detailed explanation. If set to NULL, then no chunking is used, unless explicitly set in dataset_create_pl.

gzip_level

Only if chunk_dims is not null. If given, then the dataset_create_pl is set to enable zipping at the level given here. If set to NULL, then gzip is not set (but could be set otherwise in dataset_create_pl

link_create_pl

Link creation property list. See H5P_LINK_CREATE

dataset_create_pl

Dataset creation property list. See H5P_DATASET_CREATE

dataset_access_pl

Dataset access property list. See H5P_DATASET_ACCESS

commit(name, dtype, link_create_pl = h5const$H5P_DEFAULT, type_create_pl = h5const$H5P_DEFAULT, type_access_pl = h5const$H5P_DEFAULT)

This function implements the HDF5-API function H5Tcommit2. Please see the documentation at https://docs.hdfgroup.org/hdf5/v1_10/group___h5_t.html for details.

link_create_hard(obj_loc, obj_name, link_name, link_create_pl = h5const$H5P_DEFAULT, link_access_pl = h5const$H5P_DEFAULT)

This function implements the HDF5-API function H5Lcreate_hard. Please see the documentation at https://docs.hdfgroup.org/hdf5/v1_10/group___h5_l.html for details.

link_create_soft(target_path, link_name, link_create_pl = h5const$H5P_DEFAULT, link_access_pl = h5const$H5P_DEFAULT)

This function implements the HDF5-API function H5Lcreate_soft. Please see the documentation at https://docs.hdfgroup.org/hdf5/v1_10/group___h5_l.html for details.

link_create_external(target_filename, target_obj_name, link_name, link_create_pl = h5const$H5P_DEFAULT, link_access_pl = h5const$H5P_DEFAULT)

This function implements the HDF5-API function H5Lcreate_external. Please see the documentation at https://docs.hdfgroup.org/hdf5/v1_10/group___h5_l.html for details.

link_exists(name, link_access_pl = h5const$H5P_DEFAULT)

This function implements the HDF5-API function H5Lexists. Please see the documentation at https://docs.hdfgroup.org/hdf5/v1_10/group___h5_l.html for details.

link_move_from(src_loc, src_name, dst_name, link_create_pl = h5const$H5P_DEFAULT, link_access_pl = h5const$H5P_DEFAULT)

This function implements the HDF5-API function H5Lmove. Please see the documentation at https://docs.hdfgroup.org/hdf5/v1_10/group___h5_l.html for details.

link_move_to(dst_loc, dst_name, src_name, link_create_pl = h5const$H5P_DEFAULT, link_access_pl = h5const$H5P_DEFAULT)

This function implements the HDF5-API function H5Lmove. Please see the documentation at https://docs.hdfgroup.org/hdf5/v1_10/group___h5_l.html for details.

link_copy_from(src_loc, src_name, dst_name, link_create_pl = h5const$H5P_DEFAULT, link_access_pl = h5const$H5P_DEFAULT)

This function implements the HDF5-API function H5Lcopy. Please see the documentation at https://docs.hdfgroup.org/hdf5/v1_10/group___h5_l.html for details.

link_copy_to(dst_loc, dst_name, src_name, link_create_pl = h5const$H5P_DEFAULT, link_access_pl = h5const$H5P_DEFAULT)

This function implements the HDF5-API function H5Lcopy. Please see the documentation at https://docs.hdfgroup.org/hdf5/v1_10/group___h5_l.html for details.

link_delete(name, link_access_pl = h5const$H5P_DEFAULT)

This function implements the HDF5-API function H5Ldelete. Please see the documentation at https://docs.hdfgroup.org/hdf5/v1_10/group___h5_l.html for details.

link_delete_by_idx(n, group_name = ".", index_field = h5const$H5_INDEX_NAME, order = h5const$H5_ITER_NATIVE, link_access_pl = h5const$H5P_DEFAULT)

This function implements the HDF5-API function H5Ldelete_by_idx. Please see the documentation at https://docs.hdfgroup.org/hdf5/v1_10/group___h5_l.html for details.

link_info(name, link_access_pl = h5const$H5P_DEFAULT)

This function implements the HDF5-API function H5Lget_info. Please see the documentation at https://docs.hdfgroup.org/hdf5/v1_10/group___h5_l.html for details.

link_info_by_idx(n, group_name = ".", index_field = h5const$H5_INDEX_NAME, order = h5const$H5_ITER_NATIVE, link_access_pl = h5const$H5P_DEFAULT)

This function implements the HDF5-API function H5Lget_info_by_idx. Please see the documentation at https://docs.hdfgroup.org/hdf5/v1_10/group___h5_l.html for details.

link_value(name, link_access_pl = h5const$H5P_DEFAULT)

This function implements the HDF5-API function H5Lget_val. Please see the documentation at https://docs.hdfgroup.org/hdf5/v1_10/group___h5_l.html for details.

link_value_by_idx(n, group_name = ".", index_field = h5const$H5_INDEX_NAME, order = h5const$H5_ITER_NATIVE, link_access_pl = h5const$H5P_DEFAULT)

This function implements the HDF5-API function H5Lget_val_by_idx. Please see the documentation at https://docs.hdfgroup.org/hdf5/v1_10/group___h5_l.html for details.

link_name_by_idx(n, group_name, idx_type = h5const$H5_INDEX_NAME, order = h5const$H5_ITER_NATIVE, link_access_pl = h5const$H5P_DEFAULT)

This function implements the HDF5-API function H5Lget_name_by_idx. Please see the documentation at https://docs.hdfgroup.org/hdf5/v1_10/group___h5_l.html for details.

mount(name, child)

This function implements the HDF5-API function H5Fmount. Please see the documentation at https://docs.hdfgroup.org/hdf5/v1_10/group___h5_f.html for details.

unmount(name)

This function implements the HDF5-API function H5Funmount. Please see the documentation at https://docs.hdfgroup.org/hdf5/v1_10/group___h5_f.html for details.

create_reference(name = ".", space = NULL)

This function implements the HDF5-API function H5Rcreate. If space=NULL then a H5R_OBJECT reference is created, otherwise a H5R_DATASET_REGION reference Please see the documentation at https://docs.hdfgroup.org/hdf5/v1_10/group___h5_r.html for details.

obj_info(remove_internal_use_only = TRUE)

This function implements the HDF5-API function H5Oget_info. Please see the documentation at https://docs.hdfgroup.org/hdf5/v1_10/group___h5_o.html for details.

get_obj_name()

This function implements the HDF5-API function H5Iget_name. Please see the documentation at https://docs.hdfgroup.org/hdf5/v1_10/group___h5_i.html for details.

create_attr(attr_name, robj = NULL, dtype = NULL, space = NULL)

This function implements the HDF5-API function H5Acreate2. Please see the documentation at https://docs.hdfgroup.org/hdf5/v1_10/group___h5_a.html for details.

attr_open(attr_name)

This function implements the HDF5-API function H5Aopen. Please see the documentation at https://docs.hdfgroup.org/hdf5/v1_10/group___h5_a.html for details.

create_attr_by_name(attr_name, obj_name, robj = NULL, dtype = NULL, space = NULL, link_access_pl = h5const$H5P_DEFAULT)

This function implements the HDF5-API function H5Acreate_by_name. Please see the documentation at https://docs.hdfgroup.org/hdf5/v1_10/group___h5_a.html for details.

attr_open_by_name(attr_name, obj_name, link_access_pl = h5const$H5P_DEFAULT)

This function implements the HDF5-API function H5Aopen_by_name. Please see the documentation at https://docs.hdfgroup.org/hdf5/v1_10/group___h5_a.html for details.

attr_open_by_idx(n, obj_name, idx_type = h5const$H5_INDEX_NAME, order = h5const$H5_ITER_NATIVE, link_access_pl = h5const$H5P_DEFAULT)

This function implements the HDF5-API function H5Aopen_by_idx. Please see the documentation at https://docs.hdfgroup.org/hdf5/v1_10/group___h5_a.html for details.

attr_exists_by_name(attr_name, obj_name, link_access_pl = h5const$H5P_DEFAULT)

This function implements the HDF5-API function H5Aexists_by_name. Please see the documentation at https://docs.hdfgroup.org/hdf5/v1_10/group___h5_a.html for details.

attr_exists(attr_name)

This function implements the HDF5-API function H5Aexists. Please see the documentation at https://docs.hdfgroup.org/hdf5/v1_10/group___h5_a.html for details.

attr_rename_by_name(old_attr_name, new_attr_name, obj_name, link_access_pl = h5const$H5P_DEFAULT)

This function implements the HDF5-API function H5Arename_by_name. Please see the documentation at https://docs.hdfgroup.org/hdf5/v1_10/group___h5_a.html for details.

attr_rename(old_attr_name, new_attr_name)

This function implements the HDF5-API function H5Arename. Please see the documentation at https://docs.hdfgroup.org/hdf5/v1_10/group___h5_a.html for details.

attr_delete(attr_name)

This function implements the HDF5-API function H5Adelete. Please see the documentation at https://docs.hdfgroup.org/hdf5/v1_10/group___h5_a.html for details.

attr_delete_by_name(attr_name, obj_name, link_access_pl = h5const$H5P_DEFAULT)

This function implements the HDF5-API function H5Adelete_by_name. Please see the documentation at https://docs.hdfgroup.org/hdf5/v1_10/group___h5_a.html for details.

attr_delete_by_idx(n, obj_name, idx_type = h5const$H5_INDEX_NAME, order = h5const$H5_ITER_NATIVE, link_access_pl = h5const$H5P_DEFAULT)

This function implements the HDF5-API function H5Adelete_by_idx. Please see the documentation at https://docs.hdfgroup.org/hdf5/v1_10/group___h5_a.html for details.

attr_info_by_name(attr_name, obj_name, link_access_pl = h5const$H5P_DEFAULT)

This function implements the HDF5-API function H5Aget_info_by_name. Please see the documentation at https://docs.hdfgroup.org/hdf5/v1_10/group___h5_a.html for details.

attr_info_by_idx(n, obj_name, idx_type = h5const$H5_INDEX_NAME, order = h5const$H5_ITER_NATIVE, link_access_pl = h5const$H5P_DEFAULT)

This function implements the HDF5-API function H5Aget_info_by_idx. Please see the documentation at https://docs.hdfgroup.org/hdf5/v1_10/group___h5_a.html for details.

attr_name_by_idx(n, obj_name, idx_type = h5const$H5_INDEX_NAME, order = h5const$H5_ITER_NATIVE, link_access_pl = h5const$H5P_DEFAULT)

This function implements the HDF5-API function H5Aget_name_by_idx. Please see the documentation at https://docs.hdfgroup.org/hdf5/v1_10/group___h5_a.html for details.

attr_get_number()

This function implements the HDF5-API function H5Aget_num_attrs. Please see the documentation at https://support.hdfgroup.org/HDF5/doc/RM/RM_H5A.html#Annot-NumAttrs for details.

flush(scope = h5const$H5F_SCOPE_GLOBAL)

This function implements the HDF5-API function H5Fflush. Please see the documentation at https://docs.hdfgroup.org/hdf5/v1_10/group___h5_f.html for details.

get_filename()

This function implements the HDF5-API function H5Fget_name. Please see the documentation at https://docs.hdfgroup.org/hdf5/v1_10/group___h5_f.html for details.

names(link_access_pl = h5const$H5P_DEFAULT)

Returns the names of the items in the group or at the root of the file

Parameters

link_access_pl

The link-access property list. See https://docs.hdfgroup.org/hdf5/v1_10/group___l_a_p_l.html for more detail.

Author(s)

Holger Hoefling

Examples

fname <- tempfile(fileext = ".h5")
file <- H5File$new(fname, mode = "a")
group <- file$create_group("testgroup")
group$print()
group$close()
file$close_all()

Description

It inherits all functions of the H5P.

Value

Object of class H5P_ATTRIBUTE_CREATE.

Methods

new(id = NULL)

Create a new class of type H5P_ATTRIBUTE_CREATE

Parameters

id

Internal use only

set_char_encoding(encoding = h5const$H5T_CSET_UTF8)

This function implements the HDF5-API function H5Pset_char_encoding. Please see the documentation at https://docs.hdfgroup.org/hdf5/v1_10/group___h5_p.html for details.

get_char_encoding()

This function implements the HDF5-API function H5Pget_char_encoding. Please see the documentation at https://docs.hdfgroup.org/hdf5/v1_10/group___h5_p.html for details.

Author(s)

Holger Hoefling

See Also

H5P

Description

It inherits all functions of the H5RefClass. The intent of this class is to provide a mechanism to compare the class of HDF5 property classes. This is mainly intended for internal use to get the class type of an HDF5 identifier that is known to be a property list, but not of which type.

Value

Object of class H5P_CLASS.

Methods

equal(cmp)

This function implements the HDF5-API function H5Pequal. Please see the documentation at https://docs.hdfgroup.org/hdf5/v1_10/group___h5_p.html for details.

Author(s)

Holger Hoefling

See Also

H5P

Description

It inherits all functions of the H5P.

Value

Object of class H5P_DATASET_ACCESS.

Methods

set_chunk_cache(rdcc_nslots = -1, rdcc_nbytes = -1, rdcc_w0 = -1)

This function implements the HDF5-API function H5Pset_chunk_cache. Please see the documentation at https://docs.hdfgroup.org/hdf5/v1_10/group___h5_p.html for details.

get_chunk_cache()

This function implements the HDF5-API function H5Pget_chunk_cache. Please see the documentation at https://docs.hdfgroup.org/hdf5/v1_10/group___h5_p.html for details.

Author(s)

Holger Hoefling

See Also

H5P

Description

It inherits all functions of the H5P.

Value

Object of class H5P_DATASET_CREATE.

Methods

new(id = NULL)

Create a new class of type H5P_DATASET_CREATE

Parameters

id

Internal use only

set_layout(layout = h5const$H5D_CHUNKED)

This function implements the HDF5-API function H5Pset_layout. Please see the documentation at https://docs.hdfgroup.org/hdf5/v1_10/group___h5_p.html for details.

get_layout()

This function implements the HDF5-API function H5Pget_layout. Please see the documentation at https://docs.hdfgroup.org/hdf5/v1_10/group___h5_p.html for details.

set_chunk(chunk)

This function implements the HDF5-API function H5Pset_chunk. Please see the documentation at https://docs.hdfgroup.org/hdf5/v1_10/group___h5_p.html for details.

get_chunk(max_ndims)

This function implements the HDF5-API function H5Pget_chunk. If the layout is not chunked, returns NA. Please see the documentation at https://docs.hdfgroup.org/hdf5/v1_10/group___h5_p.html for details.

set_deflate(level)

This function implements the HDF5-API function H5Pset_deflate. Please see the documentation at https://docs.hdfgroup.org/hdf5/v1_10/group___h5_p.html for details.

set_fill_value(dtype, value)

This function implements the HDF5-API function H5Pset_fill_value. Please see the documentation at https://docs.hdfgroup.org/hdf5/v1_10/group___h5_p.html for details.

get_fill_value(dtype)

This function implements the HDF5-API function H5Pget_fill_value. Please see the documentation at https://docs.hdfgroup.org/hdf5/v1_10/group___h5_p.html for details.

set_fill_time(fill_time = h5const$H5D_FILL_TIME_IFSET)

This function implements the HDF5-API function H5Pset_fill_time. Please see the documentation at https://docs.hdfgroup.org/hdf5/v1_10/group___h5_p.html for details.

get_fill_time()

This function implements the HDF5-API function H5Pget_fill_time. Please see the documentation at https://docs.hdfgroup.org/hdf5/v1_10/group___h5_p.html for details.

set_alloc_time(alloc_time = h5const$H5D_ALLOC_TIME_DEFAULT)

This function implements the HDF5-API function H5Pset_alloc_time. Please see the documentation at https://docs.hdfgroup.org/hdf5/v1_10/group___h5_p.html for details.

get_alloc_time()

This function implements the HDF5-API function H5Pget_alloc_time. Please see the documentation at https://docs.hdfgroup.org/hdf5/v1_10/group___h5_p.html for details.

set_filter(filter = h5const$H5Z_FILTER_DEFLATE, flags = h5const$H5Z_FLAG_OPTIONAL, cd_values = integer(0))

This function implements the HDF5-API function H5Pset_filter. Please see the documentation at https://docs.hdfgroup.org/hdf5/v1_10/group___h5_p.html for details.

all_filters_avail()

This function implements the HDF5-API function H5Pall_filters_avail. Please see the documentation at https://docs.hdfgroup.org/hdf5/v1_10/group___h5_p.html for details.

get_nfilters()

This function implements the HDF5-API function H5Pget_nfilters. Please see the documentation at https://docs.hdfgroup.org/hdf5/v1_10/group___h5_p.html for details.

get_filter(idx)

This function implements the HDF5-API function H5Pget_filter2. Please see the documentation at https://docs.hdfgroup.org/hdf5/v1_10/group___h5_p.html for details.

modify_filter(filter = h5const$H5Z_FILTER_DEFLATE, flags = h5const$H5Z_FLAG_OPTIONAL, cd_values = integer(0))

This function implements the HDF5-API function H5Pmodify_filter. Please see the documentation at https://docs.hdfgroup.org/hdf5/v1_10/group___h5_p.html for details.

remove_filter(filter = h5const$H5Z_FILTER_ALL)

This function implements the HDF5-API function H5Premove_filter. Please see the documentation at https://docs.hdfgroup.org/hdf5/v1_10/group___h5_p.html for details.

set_fletcher32()

This function implements the HDF5-API function H5Pset_fletcher32. Please see the documentation at https://docs.hdfgroup.org/hdf5/v1_10/group___h5_p.html for details.

set_nbit()

This function implements the HDF5-API function H5Pset_nbit. Please see the documentation at https://docs.hdfgroup.org/hdf5/v1_10/group___h5_p.html for details.

set_scaleoffset(scale_type = h5const$H5Z_SO_FLOAT_DSCALE, scale_factor = 0)

This function implements the HDF5-API function H5Pset_scaleoffset. Please see the documentation at https://docs.hdfgroup.org/hdf5/v1_10/group___h5_p.html for details.

set_shuffle()

This function implements the HDF5-API function H5Pset_shuffle. Please see the documentation at https://docs.hdfgroup.org/hdf5/v1_10/group___h5_p.html for details.

set_szip()

This function implements the HDF5-API function H5Pset_szip. Please see the documentation at https://docs.hdfgroup.org/hdf5/v1_10/group___h5_p.html for details.

set_external(filename, offset, size)

This function implements the HDF5-API function H5Pset_external. Please see the documentation at https://docs.hdfgroup.org/hdf5/v1_10/group___h5_p.html for details.

get_external_count()

This function implements the HDF5-API function H5Pget_external_count. Please see the documentation at https://docs.hdfgroup.org/hdf5/v1_10/group___h5_p.html for details.

get_external(idx)

This function implements the HDF5-API function H5Pget_external. Please see the documentation at https://docs.hdfgroup.org/hdf5/v1_10/group___h5_p.html for details.

Author(s)

Holger Hoefling

See Also

H5P

Description

It inherits all functions of the H5P.

Value

Object of class H5P_DATASET_XFER.

Methods

new(id = NULL)

Create a new class of type H5P_DATASET_XFER

Parameters

id

Internal use only

set_buffer(size = 2^20)

This function implements the HDF5-API function H5Pset_buffer. Please see the documentation at https://docs.hdfgroup.org/hdf5/v1_10/group___h5_p.html for details.

set_edc_check(check = h5const$H5Z_ENABLE_EDC)

This function implements the HDF5-API function H5Pset_edc_check. Please see the documentation at https://docs.hdfgroup.org/hdf5/v1_10/group___h5_p.html for details.

get_edc_check()

This function implements the HDF5-API function H5Pget_edc_check. Please see the documentation at https://docs.hdfgroup.org/hdf5/v1_10/group___h5_p.html for details.

set_hyper_vector_size(size = 2^10)

This function implements the HDF5-API function H5Pset_hyper_vector_size. Please see the documentation at https://docs.hdfgroup.org/hdf5/v1_10/group___h5_p.html for details.

get_hyper_vector_size()

This function implements the HDF5-API function H5Pget_hyper_vector_size. Please see the documentation at https://docs.hdfgroup.org/hdf5/v1_10/group___h5_p.html for details.

set_btree_ratios(left, middle, right)

This function implements the HDF5-API function H5Pset_btree_ratios. Please see the documentation at https://docs.hdfgroup.org/hdf5/v1_10/group___h5_p.html for details.

get_btree_ratios()

This function implements the HDF5-API function H5Pget_btree_ratios. Please see the documentation at https://docs.hdfgroup.org/hdf5/v1_10/group___h5_p.html for details.

Author(s)

Holger Hoefling

See Also

H5P

Description

It inherits all functions of the H5P.

Value

Object of class H5P_FILE_ACCESS.

Methods

new(id = NULL)

Create a new class of type H5P_FILE_ACCESS

Parameters

id

Internal use only

set_cache(rdcc_nslots = 521, rdcc_nbytes = 2^20, rdcc_w0 = 0.75)

This function implements the HDF5-API function H5Pset_cache. Please see the documentation at https://docs.hdfgroup.org/hdf5/v1_10/group___h5_p.html for details.

get_cache()

This function implements the HDF5-API function H5Pget_cache. Please see the documentation at https://docs.hdfgroup.org/hdf5/v1_10/group___h5_p.html for details.

Author(s)

Holger Hoefling

See Also

H5P

Description

It inherits all functions of the H5P.

Value

Object of class H5P_FILE_CREATE.

Methods

new(id = NULL)

Create a new class of type H5P_FILE_CREATE

Parameters

id

Internal use only

set_userblock(size)

This function implements the HDF5-API function H5Pset_userblock. Please see the documentation at https://docs.hdfgroup.org/hdf5/v1_10/group___h5_p.html for details.

get_userblock()

This function implements the HDF5-API function H5Pget_userblock. Please see the documentation at https://docs.hdfgroup.org/hdf5/v1_10/group___h5_p.html for details.

set_sizes(sizeof_addr, sizeof_size)

This function implements the HDF5-API function H5Pset_sizes. Please see the documentation at https://docs.hdfgroup.org/hdf5/v1_10/group___h5_p.html for details.

get_sizes()

This function implements the HDF5-API function H5Pget_sizes. Please see the documentation at https://docs.hdfgroup.org/hdf5/v1_10/group___h5_p.html for details.

set_sym_k(ik, lk)

This function implements the HDF5-API function H5Pset_sym_k. Please see the documentation at https://docs.hdfgroup.org/hdf5/v1_10/group___h5_p.html for details.

get_sym_k()

This function implements the HDF5-API function H5Pget_sym_k. Please see the documentation at https://docs.hdfgroup.org/hdf5/v1_10/group___h5_p.html for details.

set_istore_k(ik)

This function implements the HDF5-API function H5Pset_istore_k. Please see the documentation at https://docs.hdfgroup.org/hdf5/v1_10/group___h5_p.html for details.

get_istore_k()

This function implements the HDF5-API function H5Pget_istore_k. Please see the documentation at https://docs.hdfgroup.org/hdf5/v1_10/group___h5_p.html for details.

set_file_space(strategy, threshold)

This function implements the HDF5-API function H5Pset_file_space. Please see the documentation at https://docs.hdfgroup.org/hdf5/v1_10/group___h5_p.html for details.

get_file_space()

This function implements the HDF5-API function H5Pget_file_space. Please see the documentation at https://docs.hdfgroup.org/hdf5/v1_10/group___h5_p.html for details.

Author(s)

Holger Hoefling

See Also

H5P

Description

It inherits all functions of the H5P.

Value

Object of class H5P_LINK_ACCESS.

Methods

new(id = NULL)

Create a new class of type H5P_LINK_ACCESS

Parameters

id

Internal use only

set_nlinks(nlinks)

This function implements the HDF5-API function H5Pset_nlinks. Please see the documentation at https://docs.hdfgroup.org/hdf5/v1_10/group___h5_p.html for details.

get_nlinks()

This function implements the HDF5-API function H5Pget_nlinks. Please see the documentation at https://docs.hdfgroup.org/hdf5/v1_10/group___h5_p.html for details.

set_elink_prefix(elink_prefix)

This function implements the HDF5-API function H5Pset_elink_prefix. Please see the documentation at https://docs.hdfgroup.org/hdf5/v1_10/group___h5_p.html for details.

get_elink_prefix()

This function implements the HDF5-API function H5Pget_elink_prefix. Please see the documentation at https://docs.hdfgroup.org/hdf5/v1_10/group___h5_p.html for details.

set_elink_acc_flags(elink_acc_flags = h5const$H5F_ACC_RDWR)

This function implements the HDF5-API function H5Pset_elink_acc_flags. Please see the documentation at https://docs.hdfgroup.org/hdf5/v1_10/group___h5_p.html for details.

get_elink_acc_flags()

This function implements the HDF5-API function H5Pget_elink_acc_flags. Please see the documentation at https://docs.hdfgroup.org/hdf5/v1_10/group___h5_p.html for details.

Author(s)

Holger Hoefling

See Also

H5P

Description

It inherits all functions of the H5P.

Value

Object of class H5P_LINK_CREATE.

Methods

new(id = NULL)

Create a new class of type H5P_LINK_CREATE

Parameters

id

Internal use only

set_char_encoding(encoding = h5const$H5T_CSET_UTF8)

This function implements the HDF5-API function H5Pset_char_encoding. Please see the documentation at https://docs.hdfgroup.org/hdf5/v1_10/group___h5_p.html for details.

get_char_encoding()

This function implements the HDF5-API function H5Pget_char_encoding. Please see the documentation at https://docs.hdfgroup.org/hdf5/v1_10/group___h5_p.html for details.

set_create_intermediate_group(create = TRUE)

This function implements the HDF5-API function H5Pset_create_intermediate_group. Please see the documentation at https://docs.hdfgroup.org/hdf5/v1_10/group___h5_p.html for details.

get_create_intermediate_group()

This function implements the HDF5-API function H5Pget_create_intermediate_group. Please see the documentation at https://docs.hdfgroup.org/hdf5/v1_10/group___h5_p.html for details.

Author(s)

Holger Hoefling

See Also

H5P

Description

It inherits all functions of the H5P.

Value

Object of class H5P_OBJECT_COPY.

Methods

new(id = NULL)

Create a new class of type H5P_OBJECT_COPY

Parameters

id

Internal use only

set_copy_obj(copy_options = 0)

This function implements the HDF5-API function H5Pset_copy_object. Please see the documentation at https://docs.hdfgroup.org/hdf5/v1_10/group___h5_p.html for details.

get_copy_obj()

This function implements the HDF5-API function H5Pget_copy_object. Please see the documentation at https://docs.hdfgroup.org/hdf5/v1_10/group___h5_p.html for details.

Author(s)

Holger Hoefling

See Also

H5P

Description

It inherits all functions of the H5P.

Value

Object of class H5P_OBJECT_CREATE.

Methods

new(id = NULL)

Create a new class of type H5P_OBJECT_CREATE

Parameters

id

Internal use only

set_obj_track_times(track_times = TRUE)

This function implements the HDF5-API function H5Pset_obj_track_times. Please see the documentation at https://docs.hdfgroup.org/hdf5/v1_10/group___h5_p.html for details.

get_obj_track_times()

This function implements the HDF5-API function H5Pget_obj_track_times. Please see the documentation at https://docs.hdfgroup.org/hdf5/v1_10/group___h5_p.html for details.

set_attr_phase_change(max_compact, min_dense)

This function implements the HDF5-API function H5Pset_attr_phase_change. Please see the documentation at https://docs.hdfgroup.org/hdf5/v1_10/group___h5_p.html for details.

get_attr_phase_change()

This function implements the HDF5-API function H5Pget_attr_phase_change. Please see the documentation at https://docs.hdfgroup.org/hdf5/v1_10/group___h5_p.html for details.

set_attr_creation_order(crt_order_flags = 0)

This function implements the HDF5-API function H5Pset_attr_creation_order. Please see the documentation at https://docs.hdfgroup.org/hdf5/v1_10/group___h5_p.html for details.

get_attr_creation_order()

This function implements the HDF5-API function H5Pget_attr_creation_order. Please see the documentation at https://docs.hdfgroup.org/hdf5/v1_10/group___h5_p.html for details.

Author(s)

Holger Hoefling

See Also

H5P

Description

This is the base class for all property lists, but most have a specialized class. It inherits all functions of the H5RefClass. It is also the base class for many other classes, specifically

Dataset Creation

H5P_DATASET_CREATE

Dataset Access

H5P_DATASET_ACCESS

Dataset Transfer

H5P_DATASET_XFER

Link Creation

H5P_LINK_CREATE

Link Access

H5P_LINK_ACCESS

Object Creation

H5P_OBJECT_CREATE

Object Copy

H5P_OBJECT_COPY

Attribute Creation

H5P_ATTRIBUTE_CREATE

The base class is unlikely to be needed by users - they should use the appropriate subclass required.

Value

Object of class H5P.

Methods

new(id = NULL)

Create a new property list; this function itself is unlikely to be needed by users. Users should use the classes of the type they actually require

Parameters

id

Internal use only

get_class()

This function implements the HDF5-API function H5Pget_class. Please see the documentation at https://docs.hdfgroup.org/hdf5/v1_10/group___h5_p.html for details.

get_class_name()

This function implements the HDF5-API function H5Pget_class_name. Please see the documentation at https://docs.hdfgroup.org/hdf5/v1_10/group___h5_p.html for details.

copy()

This function implements the HDF5-API function H5Pcopy. Please see the documentation at https://docs.hdfgroup.org/hdf5/v1_10/group___h5_p.html for details.

equal(cmp)

This function implements the HDF5-API function H5Pequal. Please see the documentation at https://docs.hdfgroup.org/hdf5/v1_10/group___h5_p.html for details.

Author(s)

Holger Hoefling

Examples

fname <- tempfile(fileext = ".h5")
file <- H5File$new(fname, mode = "a")
file[["testdataset"]] <- 1:10
p <- file[["testdataset"]]$get_create_plist()
p$get_class()
p$get_class_name()
p$copy()
p$equal(p)
file$close_all()

Description

H5R_DATASET_REGION is the reference class for dataset regions. Users should not create this class by themselves, but use the appropriate and instead use the create_reference methods of H5D, H5Group or H5File classes.

Value

Object of class H5R_DATASET_REGION.

Methods

new(num = 0, id = NULL)

Create a new reference for dataset regions; Usually, users shouldn't have to call this, but use the create_reference method of a dataset.

dereference(object_access_pl = h5const$H5P_DEFAULT, obj = NULL, get_value = FALSE)

Dereference an H5R reference for a dataset region. The file the reference is pointing to is assigned automatically. It returns a list where each item is a list with components dataset, being an H5D object and space being a H5S object. When setting get_value=TRUE, then instead of these objects The data itself is returned This function implements the HDF5-API function H5Rdereference. Please see the documentation at https://docs.hdfgroup.org/hdf5/v1_10/group___h5_r.html for details.

Parameters

obj

Overriding the default file the reference is referring to

object_access_pl

The object-access property list. Currently always the default

Author(s)

Holger Hoefling

Description

Various functions for H5R objects

Usage

is.H5R(x)

is.H5R_OBJECT(x)

is.H5R_DATASET_REGION(x)

## S3 method for class 'H5R'
names(x)

## S3 method for class 'H5R'
length(x)

## S3 method for class 'H5R'
x[i, j, ..., drop = TRUE]

## S3 replacement method for class 'H5R'
x[i, ...] <- value

## S3 method for class 'H5R'
c(..., recursive = FALSE)

## S3 method for class 'H5R'
dim(x)

## S3 replacement method for class 'H5R'
dim(x) <- value

## S3 method for class 'H5R'
t(x)

## S3 method for class 'H5R'
dimnames(x)

## S3 replacement method for class 'H5R'
dimnames(x) <- value

## S3 method for class 'H5R'
cbind(..., deparse.level = 1)

## S3 method for class 'H5R'
rbind(..., deparse.level = 1)

## S3 method for class 'H5R'
print(x, ...)

## S3 method for class 'H5R'
format(x, ...)

## S3 method for class 'H5R'
as.data.frame(x, row.names = NULL, optional = FALSE, ...,
  nm = paste(deparse(substitute(x), width.cutoff = 500L), collapse =
  " "))

## S3 method for class 'H5R'
as.vector(x, mode = "any")

Arguments

Details

is.H5R

Check if object inherits from H5R

is.H5R_OBJECT

Check if object inherits from H5R_OBJECT

is.H5R_DATASET_REGION

Check if object inherits from H5R_DATASET_REGION

names.H5R

Returns the names of the elements of the vector

length.H5R

Returns the length of the vector

[.H5R

Array subsetting function

[<-.H5R

Array subset assignment

c.H5R

Concatenation of H5R vectors

dim.H5R

Dimensionality of the object

dim<-.H5R

Assign dimension of the object

t.H5R

Transpose a matrix of H5R objects

dimnames.H5R

Get the dimnames of the object

dimnames<-.H5R

Set the dimnames of the object

cbind.H5R

cbind functionality for H5R objects

rbind.H5R

rbind functionality for H5R objects

print.H5R

Printing of an object of class h5R

format.H5R

Formatting of an H5R object

as.data.frame.H5R

Coerce an H5R object to a data.frame

as.vector.H5R

Coerce to a vector

as.data.frame.H5R

Coerces the object to a data.frame

as.vector.H5R

Coerces to a vector

Value

Depending on the function

Author(s)

Holger Hoefling

Description

H5R_OBJECT is the reference class for objects. Users should not create this class by themselves, but use the appropriate and instead use the create_reference methods of H5D, H5Group or H5File classes.

Value

Object of class H5R_OBJECT.

Methods

new(num = 0, id = NULL)

Create a new reference for object; Usually, users shouldn't have to call this, but use the create_reference method of a dataset, group of committed datatype

dereference(object_access_pl = h5const$H5P_DEFAULT, obj = NULL)

Dereference an H5R reference. The file the reference is pointing to is assigned automatically This function implements the HDF5-API function H5Rdereference. Please see the documentation at https://docs.hdfgroup.org/hdf5/v1_10/group___h5_r.html for details.

Parameters

obj

Overriding the default file the reference is referring to

object_access_pl

The object-access property list. Currently always the default

Author(s)

Holger Hoefling

Description

H5R is only the common base class and is never used. User should not create objects of this class by themselves and instead use the create_reference methods of H5D, H5Group or H5File classes. Sub-classes are H5R_OBJECT and H5R_DATASET_REGION

Value

Object of class H5R.

Methods

subset_read(dim_index, drop = TRUE)

Method that returns a subset of the data in the H5R-object

Parameters

dim_index

A list of dimension indices as usually pasted into [

drop

Logical. Should dimensions of size 1 be dropped.

subset2_read(i, exact = TRUE)

Method to read a single item

Parameters

i

The single item to read

exact

Is the item name exact or should partial matching be allowed?

subset_assign(dim_index, value)

Assign values into a subset of the H5R-vector

Parameters

dim_index

A list of dimension indices as usually passed into [

value

The value to assign

subset2_assign(i, exact = TRUE, value)

Assign a value to a single value in the array

Parameters

i

the index where to assign the value

value

The value to assign

t()

Transpose the object if it is a matrix (i.e. has rank 2

length()

Get the length of the object

ref(ref)

Get or assign the internal raw-vector representation of the data. Usually, user's shouldn't have to use this.

dim(x)

Get or assign the dimensionality of the object

dimnames(x)

Get or assign the dimnames of the object

names(x)

Get or assign the names of the object

rank()

Get the rank of the object

Author(s)

Holger Hoefling

Examples

fname <- tempfile(fileext = ".h5")
file <- H5File$new(fname, mode = "a")
file[["testset"]] <- matrix(rnorm(9), nrow = 3)
dset <- file[["testset"]]
r <- file$create_reference("testset")
file$close_all()

Description

This class is not intended for creating objects, but as a base class for all other H5-derived classes to provide common functionality for id tracking

Value

Object of reference class H5RefClass.

Fields

id

Returns the id of the object as an integer

Methods

new(id = NULL)

Constructor for the basic class for hdf5 objects. Takes an id and stores it appropriately, including the necessary counting of object references that the package implements. This reference counting is included in addition to R's internal method in order to allow for the invalidation of objects in R itself when all open handles in an R-file are being closed.

close()

Closes an object and calls the appropriate HDF5 function for the type of object

print(...)

Prints the class of the object and the id

methods()

Prints available methods on the screen

get_file_id()

This function implements the HDF5-API function H5Iget_file_id. Please see the documentation at https://docs.hdfgroup.org/hdf5/v1_10/group___h5_i.html for details.

get_obj_type()

This function implements the HDF5-API function H5Iget_type. Please see the documentation at https://docs.hdfgroup.org/hdf5/v1_10/group___h5_i.html for details.

get_ref()

This function implements the HDF5-API function H5Iget_ref. Please see the documentation at https://docs.hdfgroup.org/hdf5/v1_10/group___h5_i.html for details.

inc_ref()

This function implements the HDF5-API function H5Iinc_ref. Please see the documentation at https://docs.hdfgroup.org/hdf5/v1_10/group___h5_i.html for details.

dec_ref()

This function implements the HDF5-API function H5Idec_ref. Please see the documentation at https://docs.hdfgroup.org/hdf5/v1_10/group___h5_i.html for details.

id()

Returns the id of the object

is_valid()

This function implements the HDF5-API function H5Iis_valid. Please see the documentation at https://docs.hdfgroup.org/hdf5/v1_10/group___h5_i.html for details. Additionally, the R-object representing the HDF5-id can be invalidated as well. In this case, the class id is set to NA and is_valid returns FALSE.

message()

Legacy function; currently not used; may be removed

Author(s)

Holger Hoefling

Description

Selecting and assigning subsets of HDF5-Spaces and HDF5-Datasets

Usage

subset_h5.H5S(x, d1, ..., op = h5const$H5S_SELECT_SET,
  envir = parent.frame())

## S3 method for class 'H5S'
x[d1, ..., op = h5const$H5S_SELECT_SET,
  envir = parent.frame()]

subset_h5.H5D(x, d1, ..., dataset_xfer_pl = h5const$H5P_DEFAULT,
  flags = getOption("hdf5r.h5tor_default"), drop = TRUE,
  envir = parent.frame())

## S3 method for class 'H5D'
x[d1, ..., dataset_xfer_pl = h5const$H5P_DEFAULT,
  flags = getOption("hdf5r.h5tor_default"), drop = TRUE,
  envir = parent.frame()]

subset_assign_h5.H5D(x, d1, ..., dataset_xfer_pl = h5const$H5P_DEFAULT,
  envir = parent.frame(), value)

## S3 replacement method for class 'H5D'
x[d1, ..., dataset_xfer_pl = h5const$H5P_DEFAULT,
  envir = parent.frame()] <- value

Arguments

Details

Used for subsetting HDF5-Datasets or HDF5-Spaces or for assigning data into HDF5-Datasets. There are some differences to consider with R itself.

Most importantly HDF5-COMPOUND objects only have a single dimension internally to HDF5 (a vector), but they correspond to R-data.frames, which are 2 dimensional. For an HDF5 COMPOUND object, it is currently not possible to only sub-select a specific column. All columns have to be extracted (using 1-dimensional access with [ and can then be subset in R itself. The same is true for writing a COMPOUND object (H5T_COMPOUND). A complete data-frame is needed, not just a subset of the columns.

Another important differences is for datasets of HDF5-ARRAY type H5T_ARRAY where the access to the object is only for the dimension of the object itself, not including the dimensions of the underlying array type.

Value

For x being a H5S, the same object is returned, but with the selection set as requested. For H5D it retrieves the subset of data requested or sets the subset of data assigned, as for any n-dimensional array in R.

Author(s)

Holger Hoefling

Description

This class represents Spaces in HDF5. These are mostly useful to define the dimensions of a dataset as well as the maximum dimensions to which it can grow. By default, the maximum dimension is equal to the initial dimension. If you want the array to be able to grow arbitrarily large in one dimension, set the maximum dimension for this index to Inf. See the examples below for code how to do this.

Value

Object of class H5S.

Methods

new(type = c("simple", "scalar", "null"), dims = NULL, maxdims = dims, decode_buf = NULL, id = NULL)

Create a new HDF5-space. This can be done by either specifying a space with appropriate dimensions or by decoding a character string that represents an encoded space

Parameters

type

Either a simple space, for which dims and maxdims have to be given or a scalar or null space. See the HDF5 user guide on spaces to explain the differences.

dims

The dimension of the space in case it is of type simple

maxdims

The maximal dimensions of the space

decode_buf

The character string that holds the encoded representation of a space

id

An existing HDF5 id; internal use only

copy()

This function implements the HDF5-API function H5Scopy. Please see the documentation at https://docs.hdfgroup.org/hdf5/v1_10/group___h5_s.html for details.

encode()

This function implements the HDF5-API function H5Sencode. Please see the documentation at https://docs.hdfgroup.org/hdf5/v1_10/group___h5_s.html for details.

is_simple()

This function implements the HDF5-API function H5Sis_simple. Please see the documentation at https://docs.hdfgroup.org/hdf5/v1_10/group___h5_s.html for details.

get_simple_extent_ndims()

This function implements the HDF5-API function H5Sget_simple_extent_ndims. Please see the documentation at https://docs.hdfgroup.org/hdf5/v1_10/group___h5_s.html for details.

offset_simple(offset)

This function implements the HDF5-API function H5Soffset_simple. Please see the documentation at https://docs.hdfgroup.org/hdf5/v1_10/group___h5_s.html for details.

get_simple_extent_dims()

This function implements the HDF5-API function H5Sget_simple_extent_dims. Please see the documentation at https://docs.hdfgroup.org/hdf5/v1_10/group___h5_s.html for details.

get_simple_extent_npoints()

This function implements the HDF5-API function H5Sget_simple_extent_npoints. Please see the documentation at https://docs.hdfgroup.org/hdf5/v1_10/group___h5_s.html for details.

get_simple_extent_type()

This function implements the HDF5-API function H5Sget_simple_extent_type. Please see the documentation at https://docs.hdfgroup.org/hdf5/v1_10/group___h5_s.html for details.

extent_copy(h5s_source)

This function implements the HDF5-API function H5Sextent_copy. Please see the documentation at https://docs.hdfgroup.org/hdf5/v1_10/group___h5_s.html for details.

extent_equal(h5s_cmp)

This function implements the HDF5-API function H5Sextent_equal. Please see the documentation at https://docs.hdfgroup.org/hdf5/v1_10/group___h5_s.html for details.

set_extent_simple(dims, maxdims)

This function implements the HDF5-API function H5Sset_extent_simple. Please see the documentation at https://docs.hdfgroup.org/hdf5/v1_10/group___h5_s.html for details.

set_extent_none()

This function implements the HDF5-API function H5Sset_extent_none. Please see the documentation at https://docs.hdfgroup.org/hdf5/v1_10/group___h5_s.html for details.

get_select_type()

This function implements the HDF5-API function H5Sget_select_type. Please see the documentation at https://docs.hdfgroup.org/hdf5/v1_10/group___h5_s.html for details.

get_select_npoints()

This function implements the HDF5-API function H5Sget_select_npoints. Please see the documentation at https://docs.hdfgroup.org/hdf5/v1_10/group___h5_s.html for details.

get_select_hyper_nblocks()

This function implements the HDF5-API function H5Sget_select_hyper_nblocks. Please see the documentation at https://docs.hdfgroup.org/hdf5/v1_10/group___h5_s.html for details.

get_select_hyper_blocklist(startblock = 0, numblocks = (self$get_select_hyper_nblocks() - startblock))

This function implements the HDF5-API function H5Sget_select_hyper_blocklist. Please see the documentation at https://docs.hdfgroup.org/hdf5/v1_10/group___h5_s.html for details.

get_select_elem_npoints()

This function implements the HDF5-API function H5Sget_select_elem_npoints. Please see the documentation at https://docs.hdfgroup.org/hdf5/v1_10/group___h5_s.html for details.

get_select_elem_pointlist(startpoint = 0, numpoints = (self$get_select_elem_npoints() - startpoint))

This function implements the HDF5-API function H5Sget_select_elem_pointlist. Please see the documentation at https://docs.hdfgroup.org/hdf5/v1_10/group___h5_s.html for details.

get_select_bounds()

This function implements the HDF5-API function H5Sget_select_bounds. Please see the documentation at https://docs.hdfgroup.org/hdf5/v1_10/group___h5_s.html for details.

select_all()

This function implements the HDF5-API function H5Sselect_all. Please see the documentation at https://docs.hdfgroup.org/hdf5/v1_10/group___h5_s.html for details.

select_none()

This function implements the HDF5-API function H5Sselect_none. Please see the documentation at https://docs.hdfgroup.org/hdf5/v1_10/group___h5_s.html for details.

select_valid()

This function implements the HDF5-API function H5Sselect_valid. Please see the documentation at https://docs.hdfgroup.org/hdf5/v1_10/group___h5_s.html for details.

select_elements(coord, op = h5const$H5S_SELECT_SET, byrow = TRUE)

This function implements the HDF5-API function H5Sselect_elements. Please see the documentation at https://docs.hdfgroup.org/hdf5/v1_10/group___h5_s.html for details.

select_hyperslab(start, count, stride = NULL, block = NULL, op = h5const$H5S_SELECT_SET)

This function implements the HDF5-API function H5Sselect_hyperslab. Please see the documentation at https://docs.hdfgroup.org/hdf5/v1_10/group___h5_s.html for details.

subset(args, op = h5const$H5S_SELECT_SET, envir = parent.frame())

Subsetting the space. This is mainly intended as a helper function for the '[' function, but can also be used on its own.

Parameters

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 [ operator.

op

The operator to use. Same as for the other HDF5 space selection functions. One of the elements shown in h5const$H5S_seloper_t

envir

The environment in which to evaluate args

print(...)

Prints information for the group

Parameters

...

ignored

dims()

Get the dimensions of the space. Return NULL if the space is not simple (i.e. NULL-space) or a length-0 integer if it is a scalar

maxdims()

Get the maximal dimensions of the space.Return NULL if the space is not simple (i.e. NULL-space) or a length-0 integer if it is a scalar

rank()

This function implements the HDF5-API function H5Sget_simple_extent_ndims. Please see the documentation at https://docs.hdfgroup.org/hdf5/v1_10/group___h5_s.html for details.

Author(s)

Holger Hoefling

Examples

h5s_fixed <- H5S$new("simple", dims=c(5, 2))
h5s_fixed

h5s_variable <- H5S$new("simple", dims=c(5,2), maxdims=c(Inf,2))
h5s_variable
h5s_variable$set_extent_simple(c(10,2), c(Inf, 2))
h5s_variable

# now select a subset of points
# argument evaluation has a heuristic; here it chooses point selection
h5s_variable[c(1, 3, 8), 1]
h5s_variable$get_select_type()
h5s_variable$get_select_elem_pointlist()

# and a hyperslab (chosen by the argument heuristic)
h5s_variable[2:7, 1:2]
h5s_variable$get_select_type()
h5s_variable$get_select_hyper_blocklist()

Description

Inherits from class 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 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 data.frame has to be an array. So please use with care.

Value

Object of class H5T_ARRAY.

Methods

new(dims, dtype_base, id = NULL)

Create an array datatype.

Parameters

dims

The dimension of the datatype

dtype_base

The datatype that makes up the elements of the array

id

internal use only

get_array_ndims()

This function implements the HDF5-API function H5Tget_array_ndims. Please see the documentation at https://docs.hdfgroup.org/hdf5/v1_10/group___h5_t.html for details.

get_array_dims()

This function implements the HDF5-API function H5Tget_array_dims2. Please see the documentation at https://docs.hdfgroup.org/hdf5/v1_10/group___h5_t.html for details.

get_super()

This function implements the HDF5-API function H5Tget_super. Please see the documentation at https://docs.hdfgroup.org/hdf5/v1_10/group___h5_t.html for details.

describe()

Print a detailed description of the datatype; this is experimental

Author(s)

Holger Hoefling

See Also

H5T

Description

In HDF5, complex numbers don't actually exist. They are represented as H5T_COMPOUND with two columns named Real and Imaginary. Inherits from class H5T_COMPOUND.

Value

Object of class H5T_COMPLEX.

Methods

new(id = NULL)

Create a new complex datatype

Parameters

id

Internal use only

Author(s)

Holger Hoefling

See Also

H5T, H5T_COMPOUND

Description

Inherits from class H5T.

Value

Object of class H5T_COMPOUND.

Methods

new(labels, dtypes, size = NULL, offset = NULL, id = NULL)

Create at compound type that is the HDF5 equivalent of a table

Parameters

labels

The labels of the columns of the compound object

dtypes

The datatypes of the columns of the object; this is usually a list of objects of class H5T

size

The size of each datatype; if NULL, automatically inferred

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 NULL, inferred automatically

id

Internal use only

pack()

This function implements the HDF5-API function H5Tpack. Please see the documentation at https://docs.hdfgroup.org/hdf5/v1_10/group___h5_t.html for details.

get_cpd_types()

Return H5T objects that represent the datatypes of the columns of the compound object. Returned as a list if more than 1

get_cpd_labels()

Return the labels of the columns as a character vector

get_cpd_classes()

Return the classes of the columns as an object of type factor_ext

get_cpd_offsets()

Return the offsets of the datatypes

describe()

Print a detailed description of the datatype; this is experimental

Author(s)

Holger Hoefling

See Also

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

Description

Inherits from class H5T.

Value

Object of class H5T_ENUM.

Methods

new(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.

Parameters

labels

The labels of the ENUM-type

values

The values corresponding to the labels

id

Internal use only

get_labels()

Return all the labels of the enumeration type

get_values()

Return the values of the enumeration type

set_size(size)

Base type of every enum is H5T_INTEGER. This disables the set_size function

get_super()

Returns H5T_INTEGER that is the base type of the enumeration

describe()

Print a detailed description of the datatype; this is experimental

Author(s)

Holger Hoefling

See Also

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()

Description

Inherits from class H5T. Users should not create float types with this class, but instead use e.g. h5types$H5T_NATIVE_DOUBLE. Using the functions of this class, many aspects of the representation of the floating point number can then be manipulated.

Value

Object of class H5T_FLOAT.

Methods

set_fields(spos, epos, esize, mpos, msize)

This function implements the HDF5-API function H5Tset_fields. Please see the documentation at https://docs.hdfgroup.org/hdf5/v1_10/group___h5_t.html for details.

get_fields()

This function implements the HDF5-API function H5Tget_fields. Please see the documentation at https://docs.hdfgroup.org/hdf5/v1_10/group___h5_t.html for details.

set_ebias(ebias)

This function implements the HDF5-API function H5Tset_ebias. Please see the documentation at https://docs.hdfgroup.org/hdf5/v1_10/group___h5_t.html for details.

get_ebias()

This function implements the HDF5-API function H5Tget_ebias. Please see the documentation at https://docs.hdfgroup.org/hdf5/v1_10/group___h5_t.html for details.

set_norm(norm)

This function implements the HDF5-API function H5Tset_norm. Please see the documentation at https://docs.hdfgroup.org/hdf5/v1_10/group___h5_t.html for details.

get_norm()

This function implements the HDF5-API function H5Tget_norm. Please see the documentation at https://docs.hdfgroup.org/hdf5/v1_10/group___h5_t.html for details.

set_inpad(inpad)

This function implements the HDF5-API function H5Tset_inpad. Please see the documentation at https://docs.hdfgroup.org/hdf5/v1_10/group___h5_t.html for details.

get_inpad()

This function implements the HDF5-API function H5Tget_inpad. Please see the documentation at https://docs.hdfgroup.org/hdf5/v1_10/group___h5_t.html for details.

describe()

Print a detailed description of the datatype; this is experimental

Author(s)

Holger Hoefling

See Also

H5T

Description

Inherits from class H5T. Users should not create integer datatypes themselves using this class. Instead, integer should be derived from one of the base-types such as h5types$H5T_NATIVE_INT (which internally automatically creates a copy of the type). For a complete list of types see h5types$overview.

Value

Object of class H5T_INTEGER.

Methods

set_sign(sign)

This function implements the HDF5-API function H5Tset_sign. Please see the documentation at https://docs.hdfgroup.org/hdf5/v1_10/group___h5_t.html for details.

get_sign()

This function implements the HDF5-API function H5Tget_sign. Please see the documentation at https://docs.hdfgroup.org/hdf5/v1_10/group___h5_t.html for details.

describe()

Return a vector that describes the key features of the datatype

Author(s)

Holger Hoefling

See Also

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()

Description

Inherits from class H5T.

Value

Object of class H5T_LOGICAL.

Methods

new(include_NA = TRUE, id = NULL)

Create a logical datatype. This is internally represented by an ENUM-type

Parameters

id

Internal use only

Author(s)

Holger Hoefling

See Also

H5T, H5T_ENUM

Description

Inherits from class H5T.

Value

Object of class H5T_STRING.

Methods

new(type = c("c", "fortran"), size = 1, id = NULL)

Create a string datatype

Parameters

A

C or fortran type string

size

Size of the string object. Set to Inf for variable size strings

id

internal use only

get_size(variable_as_inf = TRUE)

Retrieves the length of the string, setting it to Inf it is of variable length. This function implements the HDF5-API function H5Tis_variable_str. Please see the documentation at https://docs.hdfgroup.org/hdf5/v1_10/group___h5_t.html for details.

get_cset()

This function implements the HDF5-API function H5Tget_cset. Please see the documentation at https://docs.hdfgroup.org/hdf5/v1_10/group___h5_t.html for details.

set_cset(cset = c("unknown", "UTF-8"))

This function implements the HDF5-API function H5Tset_cset. Please see the documentation at https://docs.hdfgroup.org/hdf5/v1_10/group___h5_t.html for details.

set_strpad(strpad)

This function implements the HDF5-API function H5Tset_strpad. Please see the documentation at https://docs.hdfgroup.org/hdf5/v1_10/group___h5_t.html for details.

get_strpad()

This function implements the HDF5-API function H5Tget_strpad. Please see the documentation at https://docs.hdfgroup.org/hdf5/v1_10/group___h5_t.html for details.

describe()

Print a detailed description of the datatype; this is experimental

Author(s)

Holger Hoefling

See Also

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

Description

Inherits from class H5T. This can make any datatype a variable length datatype. This would mostly be intended for storing ragged arrays.

Value

Object of class H5T_VLEN.

Methods

new(dtype_base, id = NULL)

Create a variable length datatype

Parameters

dtype_base

The basis-type of the variable length datatype

id

Internal use only

get_super()

This function implements the HDF5-API function H5Tget_super. Please see the documentation at https://docs.hdfgroup.org/hdf5/v1_10/group___h5_t.html for details.

describe()

Print a detailed description of the datatype; this is experimental

Author(s)

Holger Hoefling

See Also

H5T

Examples

vlen_int <- H5T_VLEN$new(h5types$H5T_NATIVE_INT)
vlen_int

Description

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 H5RefClass. It is also the base class for many other classes well, specifically

Integer

H5T_INTEGER

Bitfield

H5T_BITFIELD (currently identical to the integer class)

Float

H5T_FLOAT

Enum

H5T_ENUM

Compound

H5T_COMPOUND

String

H5T_STRING

Complex

H5T_COMPLEX

Array

H5T_ARRAY

Variable Length

H5T_VLEN

Value

Object of class H5T.

Methods

new(id)

Internal use only

get_class()

This function implements the HDF5-API function H5Tget_class. Please see the documentation at https://docs.hdfgroup.org/hdf5/v1_10/group___h5_t.html for details.

get_size(...)

This function implements the HDF5-API function H5Tget_size. Please see the documentation at https://docs.hdfgroup.org/hdf5/v1_10/group___h5_t.html for details.

Parameters

...

ignored

set_size(size)

This function implements the HDF5-API function H5Tset_size. Please see the documentation at https://docs.hdfgroup.org/hdf5/v1_10/group___h5_t.html for details.

set_precision(precision)

This function implements the HDF5-API function H5Tset_precision. Please see the documentation at https://docs.hdfgroup.org/hdf5/v1_10/group___h5_t.html for details.

get_precision()

This function implements the HDF5-API function H5Tget_precision. Please see the documentation at https://docs.hdfgroup.org/hdf5/v1_10/group___h5_t.html for details.

set_order(order)

This function implements the HDF5-API function H5Tset_order. Please see the documentation at https://docs.hdfgroup.org/hdf5/v1_10/group___h5_t.html for details.

get_order()

This function implements the HDF5-API function H5Tget_order. Please see the documentation at https://docs.hdfgroup.org/hdf5/v1_10/group___h5_t.html for details.

set_offset(offset)

This function implements the HDF5-API function H5Tset_offset. Please see the documentation at https://docs.hdfgroup.org/hdf5/v1_10/group___h5_t.html for details.

get_offset()

This function implements the HDF5-API function H5Tget_offset. Please see the documentation at https://docs.hdfgroup.org/hdf5/v1_10/group___h5_t.html for details.

set_pad(pad)

This function implements the HDF5-API function H5Tset_pad. Please see the documentation at https://docs.hdfgroup.org/hdf5/v1_10/group___h5_t.html for details.

get_pad()

This function implements the HDF5-API function H5Tget_pad. Please see the documentation at https://docs.hdfgroup.org/hdf5/v1_10/group___h5_t.html for details.

copy()

This function implements the HDF5-API function H5Tcopy. Please see the documentation at https://docs.hdfgroup.org/hdf5/v1_10/group___h5_t.html for details.

is_committed()

This function implements the HDF5-API function H5Tcommitted. Please see the documentation at https://docs.hdfgroup.org/hdf5/v1_10/group___h5_t.html for details.

equal(dtype)

This function implements the HDF5-API function H5Tequal. Please see the documentation at https://docs.hdfgroup.org/hdf5/v1_10/group___h5_t.html for details.

is_vlen()

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

detect_class(dtype_class)

This function implements the HDF5-API function H5Tdetect_class. Please see the documentation at https://docs.hdfgroup.org/hdf5/v1_10/group___h5_t.html for details.

get_native_type(direction = h5const$H5T_DIR_ASCEND)

This function implements the HDF5-API function H5Tget_native_type. Please see the documentation at https://docs.hdfgroup.org/hdf5/v1_10/group___h5_t.html for details.

get_create_plist()

This function implements the HDF5-API function H5Tget_create_plist. Please see the documentation at https://docs.hdfgroup.org/hdf5/v1_10/group___h5_t.html for details.

to_text(lang_type = h5const$H5LT_DDL)

This function implements the HDF5-API function H5LTdtype_to_text.

print(...)

Prints information for the group

Parameters

...

ignored

obj_info(remove_internal_use_only = TRUE)

This function implements the HDF5-API function H5Oget_info. Please see the documentation at https://docs.hdfgroup.org/hdf5/v1_10/group___h5_o.html for details.

get_obj_name()

This function implements the HDF5-API function H5Iget_name. Please see the documentation at https://docs.hdfgroup.org/hdf5/v1_10/group___h5_i.html for details.

create_attr(attr_name, robj = NULL, dtype = NULL, space = NULL)

This function implements the HDF5-API function H5Acreate2. Please see the documentation at https://docs.hdfgroup.org/hdf5/v1_10/group___h5_a.html for details.

attr_open(attr_name)

This function implements the HDF5-API function H5Aopen. Please see the documentation at https://docs.hdfgroup.org/hdf5/v1_10/group___h5_a.html for details.

create_attr_by_name(attr_name, obj_name, robj = NULL, dtype = NULL, space = NULL, link_access_pl = h5const$H5P_DEFAULT)

This function implements the HDF5-API function H5Acreate_by_name. Please see the documentation at https://docs.hdfgroup.org/hdf5/v1_10/group___h5_a.html for details.

attr_open_by_name(attr_name, obj_name, link_access_pl = h5const$H5P_DEFAULT)

This function implements the HDF5-API function H5Aopen_by_name. Please see the documentation at https://docs.hdfgroup.org/hdf5/v1_10/group___h5_a.html for details.

attr_open_by_idx(n, obj_name, idx_type = h5const$H5_INDEX_NAME, order = h5const$H5_ITER_NATIVE, link_access_pl = h5const$H5P_DEFAULT)

This function implements the HDF5-API function H5Aopen_by_idx. Please see the documentation at https://docs.hdfgroup.org/hdf5/v1_10/group___h5_a.html for details.

attr_exists_by_name(attr_name, obj_name, link_access_pl = h5const$H5P_DEFAULT)

This function implements the HDF5-API function H5Aexists_by_name. Please see the documentation at https://docs.hdfgroup.org/hdf5/v1_10/group___h5_a.html for details.

attr_exists(attr_name)

This function implements the HDF5-API function H5Aexists. Please see the documentation at https://docs.hdfgroup.org/hdf5/v1_10/group___h5_a.html for details.

attr_rename_by_name(old_attr_name, new_attr_name, obj_name, link_access_pl = h5const$H5P_DEFAULT)

This function implements the HDF5-API function H5Arename_by_name. Please see the documentation at https://docs.hdfgroup.org/hdf5/v1_10/group___h5_a.html for details.

attr_rename(old_attr_name, new_attr_name)

This function implements the HDF5-API function H5Arename. Please see the documentation at https://docs.hdfgroup.org/hdf5/v1_10/group___h5_a.html for details.

attr_delete(attr_name)

This function implements the HDF5-API function H5Adelete. Please see the documentation at https://docs.hdfgroup.org/hdf5/v1_10/group___h5_a.html for details.

attr_delete_by_name(attr_name, obj_name, link_access_pl = h5const$H5P_DEFAULT)

This function implements the HDF5-API function H5Adelete_by_name. Please see the documentation at https://docs.hdfgroup.org/hdf5/v1_10/group___h5_a.html for details.

attr_delete_by_idx(n, obj_name, idx_type = h5const$H5_INDEX_NAME, order = h5const$H5_ITER_NATIVE, link_access_pl = h5const$H5P_DEFAULT)

This function implements the HDF5-API function H5Adelete_by_idx. Please see the documentation at https://docs.hdfgroup.org/hdf5/v1_10/group___h5_a.html for details.

attr_info_by_name(attr_name, obj_name, link_access_pl = h5const$H5P_DEFAULT)

This function implements the HDF5-API function H5Aget_info_by_name. Please see the documentation at https://docs.hdfgroup.org/hdf5/v1_10/group___h5_a.html for details.

attr_info_by_idx(n, obj_name, idx_type = h5const$H5_INDEX_NAME, order = h5const$H5_ITER_NATIVE, link_access_pl = h5const$H5P_DEFAULT)

This function implements the HDF5-API function H5Aget_info_by_idx. Please see the documentation at https://docs.hdfgroup.org/hdf5/v1_10/group___h5_a.html for details.

attr_name_by_idx(n, obj_name, idx_type = h5const$H5_INDEX_NAME, order = h5const$H5_ITER_NATIVE, link_access_pl = h5const$H5P_DEFAULT)

This function implements the HDF5-API function H5Aget_name_by_idx. Please see the documentation at https://docs.hdfgroup.org/hdf5/v1_10/group___h5_a.html for details.

attr_get_number()

This function implements the HDF5-API function H5Aget_num_attrs. Please see the documentation at https://support.hdfgroup.org/HDF5/doc/RM/RM_H5A.html#Annot-NumAttrs for details.

create_reference(name = ".", space = NULL)

This function implements the HDF5-API function H5Rcreate. If space=NULL then a H5R_OBJECT reference is created, otherwise a H5R_DATASET_REGION reference Please see the documentation at https://docs.hdfgroup.org/hdf5/v1_10/group___h5_r.html for details.

Author(s)

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)

Description

HDF5 provides many native datatypes. These are all stored in the h5types environment. An overview of all available types can be seen using h5types$overview. Any specific type can be accessed using the $-operator. See also the examples below.

Author(s)

Holger Hoefling

Examples

h5types$overview
h5types$H5T_NATIVE_INT
h5types$H5T_NATIVE_DOUBLE

Description

Return the version of the HDF5-API

Usage

h5version(verbose = TRUE)

Arguments

Details

Return the version of the HDF5-API and print it to the screen if requested

Value

Version of the underlying HDF5 API as a string

Author(s)

Holger Hoefling

Description

Check if a file is an HDF5 file

Usage

is_hdf5(name)

Arguments

Details

Uses the HDF5 function H5Fis_hdf5 to check if a file is of type HDF5.

Value

Logical, TRUE if file is of type HDF5

Author(s)

Holger Hoefling

Description

List all Group (H5Group) and Dataset (H5D) names in the current object. This function is part of the h5 wrapper classes and uses $ls() to retrieve group names.

Usage

list.groups(object, path = "/", full.names = FALSE, recursive = TRUE,
  ...)

list.datasets(object, path = "/", full.names = FALSE,
  recursive = TRUE, ...)

list.objects(object, obj_type = c("H5I_GROUP", "H5I_DATASET",
  "H5I_DATATYPE"), path = "/", full.names = FALSE, recursive = TRUE,
  ...)

Arguments

Value

character

Description

Get the names of the items in the group or at the / root of the file

Usage

## S3 method for class 'H5Group'
names(x)

## S3 method for class 'H5File'
names(x)

Arguments

Details

Works similar to the regular names function for a list. The names of the items of either a H5File at the root or a H5Group are returned as a character vector. The items are then accessed, again similar to a list, using [[.

Value

A character vector with the names of the items in the group/file.

Author(s)

Holger Hoefling

Description

Print a data frame that includes extended factor objects

Usage

## S3 method for class 'data.frame_ext'
print(x, ...)

Arguments

Details

The regular print function for data-frames has special methods built-in for factors so that the label is printed instead of the constant. This function is intended to provide the same functionality for data frames with extended factors, by adding the class data.frame_ext to the class vector.

Value

The object to print itself, invisibly

Author(s)

Holger Hoefling

Description

Convert a text description to a datatype

Usage

text_to_dtype(text, lang_type = h5const$H5LT_DDL)

Arguments

Details

Converts a text to a datatype using the HDF5 function H5LT_text_to_dtype.

Value

A datatype corresponding to the text with the appropriate class inheriting from H5T.

Author(s)

Holger Hoefling