h5 (version 0.9.4)

H5File: HDF5 File Objects

Description

*H5File* objects are are the main entry point to access HDF5 data from binary files. The *H5File* S4 class directly maps H5File{https://www.hdfgroup.org/HDF5/doc/cpplus_RM/class_h5_1_1_h5_file.html} objects from the C++ API to R. Through the implemented class hierarchy it shares common functionality with *H5Group*.

Usage

h5file(name, mode = "a")
H5File(name, mode = "a")
h5flush(.Object)
## S3 method for class 'H5File':
h5flush(.Object)
## S3 method for class 'H5File':
h5close(.Object)
is.h5file(name)

Arguments

name

character; File path pointing to H5File.

mode

mode used for file The following modes are supported by h5file: [object Object],[object Object],[object Object],[object Object],[object Object]

.Object

H5File; S4 object of class H5File;

Reading and Writing Files

HDF5 files can be created and accessed using h5file(): file <- h5file(name = "test.h5", mode = "a")

The following access-modes are defined:

cl{ Mode Description a Read/write if exists, create otherwise (default). r Read only, file must exist. r+ Read/write, file must exist. w Create file, truncate if exists. w- Create file, fail if exists. }

Show File Contents

HDF5 objects stored in a file are shown with the following symbols: cl{ Mode Description + HDF5 Group. D HDF5 Dataset. A HDF5 Attribute. }

Details

HDF5 files can be opened or generated using the h5file() function and a specified file access mode. h5file() returns a H5File object which can be used to access H5Groups and DataSets using subsetting parameters or according class methods.

HDF5 files which have been created or opened through h5file() need to be closed afterwards using h5close().

h5flush() can be used to flush unwritten data to an HDF5 file.

HDF5 Files can contain the following objects: [object Object],[object Object],[object Object]

See Also

CommonFG CommonFG-Group CommonFG-DataSet H5Location-Attribute

Examples

# The following examples generates a HDF5 file with the different HDF5
# Objects and shows its contents:
file <- h5file(name = "test1.h5", mode = "a")
file["testdataset"] <- 1:10
h5attr(file, "testattrib") <- LETTERS[1:10]
file["testgroup/testdataset2"] <- 1:10
file
# Close file and delete
h5close(file)
if(file.exists("test.h5")) file.remove("test.h5")

# The following example shows hdf5 file contents and how to use them to iterate over HDF5 elements:
file <- h5file(name = "test2.h5", mode = "a")
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])
# Add new dataset to each group in HDF5 file
for(g in list.groups(file)) {
  file[paste(g, "testsetx", collapse = "/")] <- 1:10
}
list.datasets(file, recursive = TRUE)
# Close file
h5close(file)