HDF5 Tools

HDF5 Tool Interfaces

These tools enable the user to examine HDF5 files interactively.

h5dump -- A tool for displaying HDF5 file contents
h5ls -- A tool for listing specified features of HDF5 file contents
h5repart -- A tool for repartitioning a file, creating a family of files
h5toh4 -- A tool for converting an HDF5 file to an HDF4 file
h4toh5 -- A tool for converting an HDF4 file to an HDF5 file

Tool Name: h5dump

Syntax:

h5dump
        [

OPTIONS] file

Purpose:

Displays HDF5 file contents.

Description:

h5dump enables the user to interactively examine the contents of an HDF5 file and dump those contents, in human readable form, to an ASCII file.

h5dump displays HDF5 file content on standard output. It may display the content of the whole HDF5 file or selected objects, which can be groups, datasets, links, attributes, or data types.

The --header option displays object header information only.

Names are the absolute names of the objects. h5dump displays objects in the order same as the command order. If a name does not start with a slash, h5dump begins searching for the specified object starting at the root group.

If an object is hard linked with multiple names, h5dump displays the content of the object in the first occurrence. Only the link information is displayed in later occurrences.

h5dump assigns a name for any unnamed data type in the form of #oid1:oid2, where oid1 and oid2 are the object identifiers assigned by the library. The unnamed types are displayed within the root group.

Data types are displayed with standard type names. For example, if a data set is created with H5T_NATIVE_INT type and the standard type name for integer on that machine is H5T_STD_I32BE, h5dump displays H5T_STD_I32BE as the type of the data set.

The h5dump output is described in detail in the DDL for HDF5, the Data Description Language document.

Note: It is no longer permissable to specify multiple attributes, datasets, data types, groups, or soft links with one flag. For example, before one could issue the command:

h5dump -a /attr1 /attr2 foo.h5

and both /attr1 and /attr2 would be dumped. In order to do this now, one must issue the command:

h5dump -a /attr1 -a /attr2 foo.h5

Options and Parameters:

-h   or   --help

Print a usage message and exit.

-B   or   --bootblock

Print the content of the boot block.
(This option is not yet implemented.)

-H   or   --header

Print the header only; no data is displayed.

-i   or   --object-ids

Print the object ids.

-V   or   --version

Print version number and exit.

-a P   or   --attribute=P

Print the specified attribute.

-d P   or   --dataset=P

Print the specified dataset.

-g P   or   --group=P

Print the specified group and all members.

-l P   or   --soft-link=P

Print the value(s) of the specified soft link.

-o P   or   --output=F

Output raw data into file F.

-t P   or   --datatype=T

Print the specified named data type.

-w P   or   --width=#

Set the number of columns of output.

file

The file to be examined.

P - is the full path from the root group to the object.

T - is the name of the data type.

F - is a filename.

# - is an integer greater than 1.

Examples:

Dumping the group /GroupFoo/GroupBar in the file quux.h5:
h5dump -g /GroupFoo/GroupBar quux.h5

Dumping the dataset Fnord in the group /GroupFoo/GroupBar in the file quux.h5:
h5dump -d /GroupFoo/GroupBar/Fnord quux.h5

Dumping the attribute metadata of the dataset Fnord which is in group /GroupFoo/GroupBar in the file quux.h5:
h5dump -a /GroupFoo/GroupBar/Fnord/metadata quux.h5

Dumping the attribute metadata which is an attribute of the root group in the file quux.h5:
h5dump -a /metadata quux.h5

Current Status:

The current version of h5dump displays the following information:

Group

group attribute (see Attribute)
group member

Dataset

dataset attribute (see Attribute)
dataset type (see Data type)
dataset space (see Data space)
dataset data

Attribute

attribute type (see Data type)
attribute space (see Data space)
attribute data

Data type

integer type
- H5T_STD_I8BE, H5T_STD_I8LE, H5T_STD_I16BE, ...
floating point type
- H5T_IEEE_F32BE, H5T_IEEE_F32LE, H5T_IEEE_F64BE, ...
string type
compound type
- named, unnamed and transient compound type
- integer, floating or string type member
opaque types
reference type
- object references
- data regions
enum type
variable-length datatypes
- atomic types only
- scalar or single dimensional array of variable-length types supported

Data space

scalar and simple space

Soft link
Hard link
Loop detection

See Also:

HDF5 Data Description Language syntax (DDL for HDF5)

Tool Name: h5ls
Syntax:
h5ls [OPTIONS] file[OBJECTS...]
Purpose:
Prints information about a file or dataset.
Description:
h5ls prints selected information about file objects in the specified format.
Options and Parameters:

-h   or   -?   or   --help
Print a usage message and exit.
-a   or   --address
Print addresses for raw data.
-d   or   --data
Print the values of datasets.
-e   or   --errors
Show all HDF5 error reporting.
-f   or   --full
Print full path names instead of base names.
-g   or   --group
Show information about a group, not its contents.
-l   or   --label
Label members of compound datasets.
-r   or   --recursive
List all groups recursively, avoiding cycles.
-s   or   --string
Print 1-bytes integer datasets as ASCII.
-S   or   --simple
Use a machine-readable output format.
-wN   or   --width=N
Set the number of columns of output.
-v   or   --verbose
Generate more verbose output.
-V   or   --version
Print version number and exit.
-x   or   --hexdump
Show raw data in hexadecimal format.
file
The file name may include a printf(3C) integer format such as %%05d to open a file family.
objects
Each object consists of an HDF5 file name optionally followed by a slash and an object name within the file (if no object is specified within the file then the contents of the root group are displayed). The file name may include a printf(3C) integer format such as "%05d" to open a file family.

Tool Name: h5repart
Syntax:
h5repart [-v] [-V] [-[b|m]N[g|m|k]] source_file dest_file
Purpose:
Repartitions a file or family of files.
Description:
h5repart splits a single file into a family of files, joins a family of files into a single file, or copies one family of files to another while changing the size of the family members. h5repart can also be used to copy a single file to a single file with holes.
Sizes associated with the -b and -m options may be suffixed with g for gigabytes, m for megabytes, or k for kilobytes.
File family names include an integer printf format such as %d.
Options and Parameters:

-v
Produce verbose output.
-V
Print a version number and exit.
-bN
The I/O block size, defaults to 1kB
-mN
The destination member size or 1GB
source_file
The name of the source file
dest_file
The name of the destination files

Tool Name: h5toh4
Syntax:
h5toh4 -h
h5toh4 h5file h4file
h5toh4 h5file
h5toh4 -m h5file1 h5file2 h5file3 ...
Purpose:
Converts an HDF5 file into an HDF4 file.
Description:
h5toh4 is an HDF5 utility which reads an HDF5 file, h5file, and converts all supported objects and pathways to produce an HDF4 file, h4file. If h4file already exists, it will be replaced.
If only one file name is given, the name must end in .h5 and is assumed to represent the HDF5 input file. h5toh4 replaces the .h5 suffix with .hdf to form the name of the resulting HDF4 file and proceeds as above. If a file with the name of the intended HDF4 file already exists, h5toh4 exits with an error without changing the contents of any file.
The -m option allows multiple HDF5 file arguments. Each file name is treated the same as the single file name case above.
The -h option causes the following syntax summary to be displayed:
h5toh4 file.h5 file.hdf h5toh4 file.h5 h5toh4 -m file1.h5 file2.h5 ...

The following HDF5 objects occurring in an HDF5 file are converted to HDF4 objects in the HDF4 file:

HDF5 group objects are converted into HDF4 Vgroup objects. HDF5 hardlinks and softlinks pointing to objects are converted to HDF4 Vgroup references.
HDF5 dataset objects of integer datatype are converted into HDF4 SDS objects. These datasets may have up to 32 fixed dimensions. The slowest varying dimension may be extendable. 8-bit, 16-bit, and 32-bit integer datatypes are supported.
HDF5 dataset objects of floating point datatype are converted into HDF4 SDS objects. These datasets may have up to 32 fixed dimensions. The slowest varying dimension may be extendable. 32-bit and 64-bit floating point datatypes are supported.
HDF5 dataset objects of single dimension and compound datatype are converted into HDF4 Vdata objects. The length of that single dimension may be fixed or extendable. The members of the compound datatype are constrained to be no more than rank 4.
HDF5 dataset objects of single dimension and fixed length string datatype are converted into HDF4 Vdata objects. The HDF4 Vdata is a single field whose order is the length of the HDF5 string type. The number of records of the Vdata is the length of the single dimension which may be fixed or extendable.
Other objects are not converted and are not recorded in the resulting h4file.
Attributes associated with any of the supported HDF5 objects are carried over to the HDF4 objects. Attributes may be of integer, floating point, or fixed length string datatype and they may have up to 32 fixed dimensions.
All datatypes are converted to big-endian. Floating point datatypes are converted to IEEE format.
Options and Parameters:

-h
Displays a syntax summary.
-m
Converts multiple HDF5 files to multiple HDF4 files.
h5file
The HDF5 file to be converted.
h4file
The HDF4 file to be created.

Tool Name: h4toh5
Syntax:
h4toh5 -h
h4toh5 h4file h5file
h4toh5 h4file

Purpose:
Converts an HDF4 file to an HDF5 file.
Description:
h4toh5 is a file conversion utility that reads an HDF4 file, h4file (input.hdf for example), and writes an HDF5 file, h5file (output.h5 for example), containing the same data.
If no output file h5file is specified, h4toh5 uses the input filename to designate the output file, replacing the extension .hdf with .h5. For example, if the input file scheme3.hdf is specified with no output filename, h4toh5 will name the output file scheme3.h5.
The -h option causes a syntax summary similar to the following to be displayed:
h4toh5 inputfile.hdf outputfile.h5 h5toh4 inputfile.hdf

Each object in the HDF4 file is converted to an equivalent HDF5 object, according to the mapping described in Mapping HDF4 Objects to HDF5 Objects. (If this mapping changes between HDF5 Library releases, a more up-to-date version may be available at Mapping HDF4 Objects to HDF5 Objects on the HDF FTP server.)
In this inital version, h4toh5 converts the following HDF4 objects:

HDF4 Object Resulting HDF5 Object

SDS Dataset

GR, RI8, and RI24 image Dataset

Vdata Dataset

Vgroup Group

Annotation Attribute

Palette Dataset

Options and Parameters:

-h
Displays a syntax summary.
h4file
The HDF4 file to be converted.
h5file
The HDF5 file to be created.

Introduction to HDF5
HDF5 User Guide
Other HDF5 documents and links
And in this document, the HDF5 Reference Manual
H5   H5A   H5D   H5E   H5F   H5G   H5I   H5P
H5R   H5RA   H5S   H5T   H5Z   Tools   Datatypes

HDF Help Desk
Last modified: 15 December 2000
Describes HDF5 Release 1.4 Beta, December 2000

HDF4 Object	Resulting HDF5 Object
SDS	Dataset
GR, RI8, and RI24 image	Dataset
Vdata	Dataset
Vgroup	Group
Annotation	Attribute
Palette	Dataset