1h5dump(1) General Commands Manual h5dump(1)
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6 h5dump - Displays HDF5 file contents.
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9 h5dump [OPTIONS] file
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12 h5dump enables the user to examine the contents of an HDF5 file and
13 dump those contents, in human readable form, to an ASCII file.
14 h5dump dumps HDF5 file content to standard output. It can display the
16 contents of the entire HDF5 file or selected objects, which can be
17 groups, datasets, a subset of a dataset, links, attributes, or
18 datatypes.
19 The --header option displays object header information only.
21 Names are the absolute names of the objects. h5dump displays objects in
23 the order same as the command order. If a name does not start with a
24 slash, h5dump begins searching for the specified object starting at the
25 root group.
26 If an object is hard linked with multiple names, h5dump displays the
28 content of the object in the first occurrence. Only the link informa‐
29 tion is displayed in later occurrences.
30 h5dump assigns a name for any unnamed datatype in the form of
32 #oid1:oid2, where oid1 and oid2 are the object identifiers assigned by
33 the library. The unnamed types are displayed within the root group.
34 Datatypes are displayed with standard type names. For example, if a
36 dataset is created with H5T_NATIVE_INT type and the standard type name
37 for integer on that machine is H5T_STD_I32BE, h5dump displays
38 H5T_STD_I32BE as the type of the dataset.
39 h5dump can also dump a subset of a dataset. This feature operates in
41 much the same way as hyperslabs in HDF5; the parameters specified on
42 the commnd line are passed to the function H5Sselect_hyperslab and the
43 resulting selection is displayed.
44 The h5dump output is described in detail in the DDL for HDF5, the Data
46 Description Language document.
47 Note: It is not permissable to specify multiple attributes, datasets,
49 datatypes, groups, or soft links with one flag. For example, one may
50 not issue the command
51 WRONG: h5dump -a /attr1 /attr2 foo.h5
52 to display both /attr1 and /attr2. One must issue the following com‐
53 mand:
54 CORRECT: h5dump -a /attr1 -a /attr2 foo.h5
55 It's possible to select the file driver with which to open the HDF5
57 file by using the --filedriver (-f) command-line option. Acceptable
58 values for the --filedriver option are: "sec2", "family", "split",
59 "multi", and "stream". If the file driver flag isn't specified, then
60 the file will be opened with each driver in turn and in the order spec‐
61 ified above until one driver succeeds in opening the file.
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64 With the --xml option, h5dump generates XML output. This output con‐
65 tains a complete description of the file, marked up in XML. The XML
66 conforms to the HDF5 Document Type Definition (DTD) available at
67 http://hdf.ncsa.uiuc.edu/DTDs/HDF5-File.dtd.
68 The XML output is suitable for use with other tools, including the HDF5
70 Java Tools.
71
73 -h or --help Print a usage message and exit.
74 -B or --bootblock Print the content of the boot block. (This option
76 is not yet implemented.)
77 -H or --header Print the header only; no data is displayed.
79 -A Print the header and value of attributes; data of datasets is
81 not displayed.
82 -i or --object-ids Print the object ids.
84 -r or --string Print 1-bytes integer datasets as ASCII.
86 -V or --version Print version number and exit.
88 -a P or --attribute=P Print the specified attribute.
90 -d P or --dataset=P Print the specified dataset.
92 -f D or --filedriver=D Specify which driver to open the file with.
94 -g P or --group=P Print the specified group and all members.
96 -l P or --soft-link=P Print the value(s) of the specified soft link.
98 -o F or --output=F Output raw data into file F.
100 -t T or --datatype=T Print the specified named datatype.
102 -w N or --width=N Set the number of columns of output.
104 -x or --xml Output XML using XML schema (default) instead of DDL.
106 -u or --use-dtd Output XML using XML DTD instead of DDL.
108 -D U or --xml-dtd=U In XML output, refer to the DTD or schema at U
110 instead of the default schema/DTD.
111 -X S or --xml-dns=S In XML output, (XML Schema) use qualified names
113 in the XML: ":": no namespace, default: "hdf5:"
114 -s L or --start=L Offset of start of subsetting selection. Default:
116 the beginning of the dataset.
117 -S L or --stride=L Hyperslab stride. Default: 1 in all dimensions.
119 -c L or --count=L Number of blocks to include in the selection.
121 -k L or --block=L Size of block in hyperslab. Default: 1 in all
123 dimensions.
124 -- Indicate that all following arguments are non-options. E.g., to
126 dump a file called `-f', use h5dump -- -f.
127 file The file to be examined.
129 The option parameters listed above are defined as follows:
131 D which file driver to use in opening the file. Acceptable values
133 are "sec2", "family", "split", "multi", and "stream". Without
134 the file driver flag the file will be opened with each driver in
135 turn and in the order specified above until one driver succeeds
136 in opening the file.
137 P The full path from the root group to the object
139 T The name of the datatype
141 F A filename
143 N An integer greater than 1
145 L A list of integers, the number of which is equal to the number
147 of dimensions in the dataspace being queried
148 U A URI (as defined in [IETF RFC 2396], updated by [IETF RFC
150 2732]) that refers to the DTD to be used to validate the XML
151 Subsetting paramaters can also be expressed in a convenient compact
153 form, as follows:
154 --dataset="/foo/mydataset[START;STRIDE;COUNT;BLOCK]"
155 All of the semicolons (;) are required, even when a parameter value is
157 not specified. When not specified, default parameter values are used.
158
161 1. Dumping the group /GroupFoo/GroupBar in the file quux.h5:
162 h5dump -g /GroupFoo/GroupBar quux.h5
163 2. Dumping the dataset Fnord in the group /GroupFoo/GroupBar in the
165 file quux.h5:
166 h5dump -d /GroupFoo/GroupBar/Fnord quux.h5
167 3. Dumping the attribute metadata of the dataset Fnord which is in
169 group /GroupFoo/GroupBar in the file quux.h5:
170 h5dump -a /GroupFoo/GroupBar/Fnord/metadata quux.h5
171 4. Dumping the attribute metadata which is an attribute of the root
173 group in the file quux.h5:
174 h5dump -a /metadata quux.h5
175 5. Producing an XML listing of the file bobo.h5:
177 h5dump --xml bobo.h5 > bobo.h5.xml
178 6. Dumping a subset of the dataset /GroupFoo/databar/ in the file
180 quux.h5
181 h5dump -d /GroupFoo/databar --start="1,1" --stride="2,3"
182 --count="3,19" --block="1,1" quux.h5
183 7. The same example using the short form to specify the subsetting
185 parameters:
186 h5dump -d "/GroupFoo/databar[1,1;2,3;3,19;1,1]" quux.h5
187
189 The current version of h5dump displays the following information:
190 * Group
191 o group attribute (see Attribute)
192 o group member
193 * Dataset
194 o dataset attribute (see Attribute)
195 o dataset type (see Datatype)
196 o dataset space (see Dataspace)
197 o dataset data
198 * Attribute
199 o attribute type (see Datatype)
200 o attribute space (see Dataspace)
201 o attribute data
202 * Datatype
203 o integer type
204 - H5T_STD_I8BE, H5T_STD_I8LE, H5T_STD_I16BE, ...
205 o floating point type
206 - H5T_IEEE_F32BE, H5T_IEEE_F32LE, H5T_IEEE_F64BE,
207 ...
208 o string type
209 o compound type
210 - named, unnamed and transient compound type -
211 integer, floating or string type member
212 o opaque types
213 o reference type
214 - object references
215 - data regions
216 o enum type
217 o variable-length datatypes
218 - atomic types only
219 - scalar or single dimensional array of variable-
220 length types supported
221 * Dataspace
222 o scalar and simple space
223 * Soft link
224 * Hard link
225 * Loop detection
226
229 h5ls(1), h5diff(1), h5repart(1), h5import(1), gif2h5(1), h52gif(1),
230 h5perf(1)
231 * HDF5 Data Description Language syntax at
233 file:///usr/share/doc/libhdf5-doc/html/ddl.html
234 * HDF5 XML Schema at http://hdf.ncsa.uiuc.edu/DTDs/HDF5-File.xsd
235 * HDF5 XML information at http://hdf.ncsa.uiuc.edu/HDF5/XML/
236 h5dump(1)