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HDF5 documents and links Introduction to HDF5 HDF5 User Guide |
And in this document, the
HDF5 Reference Manual
H5 H5A H5D H5E H5F H5G H5I H5P H5R H5S H5T H5Z Tools Datatypes |
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.
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h5dump
[OPTIONS] file
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
It's possible to select the file driver with which to open the HDF5 file by using the --filedriver (-f) command-line option. Acceptable values for the --filedriver option are: "sec2", "family", "split", "multi", and "stream". If the file driver flag isn't specified, then the file will be opened with each driver in turn and in the order specified above until one driver succeeds in opening the file.
--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.
-h or
--help-B or
--bootblock-H or
--header-i or
--object-ids-r or
--string-V or
--version-a P or
--attribute=P-d P or
--dataset=P-f D or
--filedriver=D-g P or
--group=P-l P or
--soft-link=P-o F or
--output=F-t T or
--datatype=T-w N or
--width=N-x U or
--xml-D U or
--xml-dtd=U-s L or
--start=L-S L or
--stride=L-c L or
--count=L-k L or
--block=L----dataset="/foo/mydataset[START;STRIDE;COUNT;BLOCK]"
;) are required, even when
a parameter value is not specified.
When not specified, default parameter values are used.
/GroupFoo/GroupBar in the file
quux.h5:
h5dump -g /GroupFoo/GroupBar quux.h5
Fnord in the group
/GroupFoo/GroupBar in the file quux.h5:
h5dump -d /GroupFoo/GroupBar/Fnord quux.h5
metadata of the dataset
Fnord which is in group
/GroupFoo/GroupBar in the file quux.h5:
h5dump -a /GroupFoo/GroupBar/Fnord/metadata quux.h5
metadata which is an
attribute of the root group in the file quux.h5:
h5dump -a /metadata quux.h5
bobo.h5:
h5dump --xml bobo.h5 > bobo.h5.xml
/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
h5dump -d "/GroupFoo/databar[1,1;2,3;3,19;1,1]" quux.h5
h5dump displays the
following information:
h5ls
[OPTIONS]
file
[OBJECTS...]
h5ls prints selected information about file objects
in the specified format.
-h or
-? or
--help
-a or
--address
-d or --data
-e or
--errors
-f or
--full
-g or
--group
-l or
--label
-r or
--recursive
-s or
--string
-S or
--simple
-wN or
--width=N
-v or
--verbose
-V or
--version
-x or
--hexdump
%%05d to open a file family.
printf(3C) integer format such
as "%05d" to open a file family.
h5repart
[-v]
[-V]
[-[b|m]N[g|m|k]]
source_file
dest_file
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.
-v
-V
-bN
-mN
gif2h5
gif_file h5_file
gif2h5 accepts as input the GIF file gif_file
and produces the HDF5 file h5_file as output.
h52gif
h5_file gif_file
-i h5_image
[-p h5_palette]
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.
-i h5_image
-p h5_palette
h5toh4 -hh5toh4
h5file
h4fileh5toh4
h5fileh5toh4 -m
h5file1
h5file2
h5file3 ...
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:
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.
-h
-m
h4toh5 -hh4toh5
h4file
h5fileh4toh5
h4fileh4toh5 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 |
-h
h5cc
[OPTIONS] <compile line>
h5cc can be used in much the same way MPIch is used
to compile an 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 example, 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 h5cc to compile the program
hdf_prog, which consists of modules
prog1.c and prog2.c and uses the HDF5
shared library, would be as follows:
# h5cc -c prog1.c
# h5cc -c prog2.c
# h5cc -shlib -o hdf_prog prog1.o prog2.o
-help
-echo
-prefix=DIR
DIR to find the HDF5
lib/ and include/ subdirectories.
-show
-shlib
-noshlib
h5cc uses the same compiler you used to compile HDF5.
Check your compiler's manual for more information on which
options are needed.
h5cc.
HDF5_CC
HDF5_CLINKER
HDF5_USE_SHLIB=[yes|no]
h5fc
[OPTIONS] <compile line>
h5fc can be used in much the same way MPIch is used
to compile an HDF5 program. It takes care of specifying where the
HDF5 header files and libraries are on the commandline.
h5fc supercedes all other compiler scripts in that
if you've used them to compile the HDF5 Fortran library, then
h5fc also uses those scripts. For example, when
compiling an MPIch program, you use the mpif90
script. If you've built HDF5 using MPIch, then h5fc
uses the MPIch program for compilation.
Some programs use HDF5 in only a few modules. It isn't necessary
to use h5fc to compile those modules which don't use
HDF5. In fact, since h5fc is only a convenience
script, you are still able to compile HDF5 Fortran 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 h5fc to compile the program
hdf_prog, which consists of modules
prog1.f90 and prog2.f90
and uses the HDF5 Fortran library, would be as follows:
# h5fc -c prog1.f90
# h5fc -c prog2.f90
# h5fc -o hdf_prog prog1.o prog2.o
-help
-echo
-prefix=DIR
DIR to find HDF5
lib/ and include/ subdirectories
-show
h5fc uses the same compiler you used
to compile HDF5. Check your compiler's manual for
more information on which options are needed.
h5cc.
HDF5_FC
HDF5_FLINKER
|
HDF5 documents and links Introduction to HDF5 HDF5 User Guide |
And in this document, the
HDF5 Reference Manual
H5 H5A H5D H5E H5F H5G H5I H5P H5R H5S H5T H5Z Tools Datatypes |