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 command 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 permissible 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.
One byte integer type data is displayed in decimal by default. When displayed in ASCII, a non-printable code is displayed in 3 octal digits preceeded by a back-slash unless there is a C language escape sequence for it. For example, CR and LF are printed as \r and \n. Though the NUL code is represented as \0 in C, it is printed as \000 to avoid ambiguity as illustrated in the following 1 byte char data (since this is not a string, embedded NUL is possible).
141 142 143 000 060 061 062 012 a b c \0 0 1 2 \nh5dump prints them as "abc\000012\n". But if h5dump prints NUL as \0, the output is "abc\0012\n" which is ambiguous.
--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://www.hdfgroup.org/DTDs/HDF5-File.dtd
.
The XML output is suitable for use with other tools, including the HDF5 Java Tools.
-h
or
--help
-n
or
--contents
-B
or
--bootblock
-H
or
--header
-A
-i
or
--object-ids
-r
or
--string
-e
-V
or
--version
-a P
or
--attribute=P
-d P
or
--dataset=P
-y
-p
or
--properties
-f D
or
--filedriver=D
-g P
or
--group=P
-l P
or
--soft-link=P
-o F
or
--output=F
-t P
or
--datatype=P
-w N
or
--width=N
-b B
or
--binary=B
B
.
B
must have one of the following values:
LE
Little-endian
BE
Big-endian
MEMORY
Memory datatype
FILE
File datatype
-d
and -o
options.
-x
or
--xml
-u
or
--use-dtd
-D U
or
--xml-dtd=U
-X S
or
--xml-dns=S
--
-
), which could
confuse the tool’s command-line parser.)
start
and count
parameters
are mandatory if subsetting is to be performed;
the stride
and block
parameters
are optional and will default to 1
(one).
-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
, which is 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
,
saving the listing in the file bobo.h5.xml
:
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
/GroupD/FreshData/
in the file quux.h5
, with data written in little-endian
form, to the output file FreshDataD.bin
:
h5dump -d "/GroupD/FreshData" -b LE -o "FreshDataD.bin"
quux.h5
h5dump
displays the
following information: