HDF5 Tools

HDF5 Tool Interfaces

These tools enable the user to examine HDF5 file contents, to modify HDF5 file contents in a carefully prescribed manner, and to convert files from HDF4 format to HDF5 format and vice versa.

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 gif2h5 -- A tool for converting a GIF file to an HDF5 file h52gif -- A tool for converting images in an HDF5 file to a GIF file h5toh4 -- A tool for converting an HDF5 file to an HDF4 file h4toh5 -- A tool for converting an HDF4 file to an HDF5 file h5cc -- A tool for compiling HDF5 programs Java-based tools for HDF5 -- (at http://hdf.ncsa.uiuc.edu/java-hdf5-html/) Java-based tools for viewing, manipulating, and generating HDF5 files (distributed separately) Includes H5view, H5gen, Java HDF5 Interface (JHI5), and HDF5 VisAD Data Adapter

Tool Name: h5dump

Syntax:

h5dump [OPTIONS] file

Purpose:

Displays HDF5 file contents.

Description:

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

h5dump dumps HDF5 file content to standard output. It can display the contents of the entire HDF5 file or selected objects, which can be groups, datasets, a subset of a dataset, links, attributes, or datatypes.

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 datatype 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.

Datatypes are displayed with standard type names. For example, if a dataset 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 dataset.

h5dump can also dump a subset of a dataset. This feature operates in much the same way as hyperslabs in HDF5; the parameters specified on the commnd line are passed to the function H5Sselect_hyperslab and the resulting selection is displayed.

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

Note: It is not permissable to specify multiple attributes, datasets, datatypes, groups, or soft links with one flag. For example, one may not issue the command
         WRONG:   h5dump -a /attr1 /attr2 foo.h5
to display both /attr1 and /attr2. One must issue the following command:
         CORRECT:   h5dump -a /attr1 -a /attr2 foo.h5

XML Output:

With the --xml option, h5dump generates XML output. This output contains a complete description of the file, marked up in XML. The XML conforms to the HDF5 Document Type Definition (DTD) available at http://hdf.ncsa.uiuc.edu/DTDs/HDF5-File.dtd.

The XML output is suitable for use with other tools, including the HDF5 Java Tools.

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.

-f D   or   --filedriver=D

Specify which driver to open the file with.

-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 F   or   --output=F

Output raw data into file F.

-t T   or   --datatype=T

Print the specified named datatype.

-w N   or   --width=N

Set the number of columns of output.

-x U   or   --xml

Output XML instead of DDL.

-D U   or   --xml-dtd=U

In XML output, refer to the DTD at U instead of the default DTD.

-s L   or   --start=L

Offset of start of subsetting selection.
Default: the beginning of the dataset.

-S L   or   --stride=L

Hyperslab stride.
Default: 1 in all dimensions.

-c L   or   --count=L

Number of blocks to include in the selection.

-k L   or   --block=L

Size of block in hyperslab.
Default: 1 in all dimensions.

file

The file to be examined.

The option parameters listed above are defined as follows:

D -- which file driver to use in opening the file. Acceptable values are "sec2", "family", "split", "multi", and "stream". Without the file driver flag the file will be opened with each driver in turn and in the order specified above until one driver succeeds in opening the file.

P -- The full path from the root group to the object

T -- The name of the datatype

F -- A filename

N -- An integer greater than 1

L -- A list of integers, the number of which is equal to the number of dimensions in the dataspace being queried

U -- A URI (as defined in [IETF RFC 2396], updated by [IETF RFC 2732]) that refers to the DTD to be used to validate the XML

Subsetting paramaters can also be expressed in a convenient compact form, as follows:
         --dataset="/foo/mydataset[START;STRIDE;COUNT;BLOCK]"
All of the semicolons (;) are required, even when a parameter value is not specified. When not specified, default parameter values are used.

Examples:

1. Dumping the group /GroupFoo/GroupBar in the file quux.h5:

   h5dump -g /GroupFoo/GroupBar quux.h5

2. Dumping the dataset Fnord in the group /GroupFoo/GroupBar in the file quux.h5:

   h5dump -d /GroupFoo/GroupBar/Fnord quux.h5

3. 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

4. Dumping the attribute metadata which is an attribute of the root group in the file quux.h5:

   h5dump -a /metadata quux.h5

5. Producing an XML listing of the file bobo.h5:

   h5dump --xml bobo.h5 > bobo.h5.xml

6. Dumping a subset of the dataset /GroupFoo/databar/ in the file quux.h5

   h5dump -d /GroupFoo/databar --start="1,1" --stride="2,3"
         --count="3,19" --block="1,1" quux.h5

7. The same example using the short form to specify the subsetting parameters:

   h5dump -d "/GroupFoo/databar[1,1;2,3;3,19;1,1]" 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 Datatype)
  • dataset space (see Dataspace)
  • dataset data
• Attribute
  • attribute type (see Datatype)
  • attribute space (see Dataspace)
  • attribute data
• Datatype
  • 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
• Dataspace
  • scalar and simple space
• Soft link
• Hard link
• Loop detection

See Also:

• HDF5 Data Description Language syntax at DDL for HDF5
• HDF5 XML DTD at http://hdf.ncsa.uiuc.edu/DTDs/HDF5-File.dtd
• HDF5 XML information at http://hdf.ncsa.uiuc.edu/HDF5/XML/

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: gif2h5

Syntax:

gif2h5 gif_file h5_file

Purpose:

Converts a GIF file to an HDF5 file.

Description:

gif2h5 accepts as input the GIF file gif_file and produces the HDF5 file h5_file as output.

Options and Parameters:

gif_file

The name of the input GIF file

h5_file

The name of the output HDF5 file

Tool Name: h52gif

Syntax:

h52gif h5_file gif_file -i h5_image [-p h5_palette]

Purpose:

Converts an HDF5 file to a GIF file.

Description:

h52gif accepts as input the HDF5 file h5_file and the names of images and associated palettes within that file as input and produces the GIF file gif_file, containing those images, as output.

h52gif expects at least one h5_image. You may repeat
     -i h5_image [-p h5_palette]
up to 50 times, for a maximum of 50 images.

Options and Parameters:

h5_file

The name of the input HDF5 file

gif_file

The name of the output GIF file

-i h5_image

Image option, specifying the name of an HDF5 image or dataset containing an image to be converted

-p h5_palette

Palette option, specifying the name of an HDF5 dataset containing a palette to be used in an image conversion

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.

Tool Name: h5cc

Syntax:

h5cc [OPTIONS] <compile line>

Purpose:

Helper script to compile HDF5 applications.

Description:

h5cc can be used in much the same way MPIch is used to compile HDF5 program. It takes care of specifying where the HDF5 header files and libraries are on the commandline.

h5cc supercedes all other compiler scripts in that if you've used them to compile the HDF5 library, then h5cc also uses those scripts. For examples, when compiling an MPIch program, you use the mpicc script. If you've built HDF5 using MPIch, then h5cc uses the MPIch program for compilation.

Some programs use HDF5 in only a few modules. It isn't necessary to use h5cc to compile those modules which don't use HDF5. In fact, since h5cc is only a convenience script, you are still able to compile HDF5 modules in the normal way. In that case, you will have to specify the HDF5 libraries and include paths yourself.

An example of how to use HDF5 to compile the program hdf_prog which consists of modules prog1.c and prog2.c and uses the HDF5 shared library:

        # h5cc -c prog1.c
        # h5cc -c prog2.c
        # h5cc -shlib -o hdf_prog prog1.o prog2.o
        

Options and Parameters:

-help

Prints a help message.

-echo

Show all the shell commands executed.

-prefix=DIR

Use the directory DIR to find HDF5 lib/ and include/ subdirectories [default: prefix specified when configuring HDF5].

-show

Show the commands without executing them.

-shlib

Compile using shared HDF5 libraries.

-noshlib

Compile using static HDF5 libraries [default].

<compile line>

The normal compile line options for your compiler. h5cc uses the same compiler you used to compile HDF5. Check with your compiler's manual for more information on which options are needed.

Environment Variables:
When set, these environment variables override some of the built-in defaults of h5cc.

HDF5_CC

Use a different C compiler.

HDF5_CLINKER

Use a different linker.

HDF5_USE_SHLIB=[yes|no]

Use shared version of the HDF5 library [default: no].