ViewTools2.dox

/** @page ViewToolsEdit Command-line Tools For Editing HDF5 Files
Navigate back: \ref index "Main" / \ref GettingStarted / \ref ViewToolsCommand
<hr>

\section secViewToolsEditTOC Contents
<ul>
<li>\ref secViewToolsEditRemove</li>
<li>\ref secViewToolsEditChange</li>
<li>\ref secViewToolsEditApply</li>
<li>\ref secViewToolsEditCopy</li>
<li>\ref secViewToolsEditAdd</li>
</ul>

\section secViewToolsEditRemove Remove Inaccessible Objects and Unused Space in a File
HDF5 files may accumulate unused space when they are read and rewritten to or if objects are deleted within
them. With many edits and deletions this unused space can add up to a sizable amount.

The <code style="background-color:whitesmoke;">h5repack</code> tool can be used to remove unused space in an HDF5
file. If no options other than the input and output HDF5 files are specified on the
<code style="background-color:whitesmoke;">h5repack</code> command line, it will write the file to the new
file, getting rid of the unused space:
\code
h5repack <input file> <output file>
\endcode

\section secViewToolsEditChange Change a Dataset's Storage Layout
The <code style="background-color:whitesmoke;">h5repack</code> utility can be used to change a dataset's storage
layout. By default, the storage layout of a dataset is defined at creation time and it cannot be changed.
However, with h5repack you can write an HDF5 file to a new file and change the layout for objects in the new file.

The <code style="background-color:whitesmoke;">-l</code> option in <code style="background-color:whitesmoke;">h5repack</code>
is used to change the layout for an object. The string following the <code style="background-color:whitesmoke;">-l</code>
option defines the layout type and parameters for specified objects (or all objects):
\code
h5repack -l [list of objects:]<layout type>=<layout parameters> <input file> <output file>
\endcode

If no object is specified, then everything in the input file will be written to the output file with the specified
layout type and parameters. If objects are specified then everything in the input file will be written to the
output file as is, except for those specified objects. They will be written to the output file with the given
layout type and parameters.

Following is a description of the dataset layouts and the <code style="background-color:whitesmoke;">h5repack</code>
options to use to change a dataset:
<table>
<tr>
<th>Storage Layout</th><th>h5repack Option</th><th>Description</th>
</tr>
<tr>
<td>Contiguous  
</td>
<td>CONTI
</td>
<td>Data is stored physically together
</td>
</tr>
<tr>
<td>Chunked 
</td>
<td>CHUNK=DIM[xDIM...xDIM]
</td>
<td>Data is stored in DIM[xDIM...xDIM] chunks
</td>
</tr>
<tr>
<td>Compact 
</td>
<td>COMPA
</td>
<td>Data is stored in the header of the object (less I/O)
</td>
</tr>
</table>

If you type <code style="background-color:whitesmoke;">h5repack -h</code> on the command line, you will see
a detailed usage statement with examples of modifying the layout.

In the following example, the dataset <code style="background-color:whitesmoke;">/dset</code> in the file
dset.h5 is contiguous, as shown by the <code style="background-color:whitesmoke;">h5dump -pH</code> command.
The <code style="background-color:whitesmoke;">h5repack</code> utility writes dset.h5 to a new file, dsetrpk.h5,
where the dataset <code style="background-color:whitesmoke;">dset</code> is chunked. This can be seen by examining
the resulting dsetrpk.h5 file with <code style="background-color:whitesmoke;">h5dump</code>, as shown:
\code
$ h5dump -pH dset.h5
HDF5 "dset.h5" {
GROUP "/" {
   DATASET "dset" {
      DATATYPE  H5T_STD_I32BE
      DATASPACE  SIMPLE { ( 4, 6 ) / ( 4, 6 ) }
      STORAGE_LAYOUT {
         CONTIGUOUS
         SIZE 96
         OFFSET 1400
      }
      FILTERS {
         NONE
      }
      FILLVALUE {
         FILL_TIME H5D_FILL_TIME_IFSET
         VALUE  0
      }
      ALLOCATION_TIME {
         H5D_ALLOC_TIME_LATE
      }
   }
}
}

$ h5repack -l dset:CHUNK=4x6 dset.h5 dsetrpk.h5

$ h5dump -pH dsetrpk.h5
HDF5 "dsetrpk.h5" {
GROUP "/" {
   DATASET "dset" {
      DATATYPE  H5T_STD_I32BE
      DATASPACE  SIMPLE { ( 4, 6 ) / ( 4, 6 ) }
      STORAGE_LAYOUT {
         CHUNKED ( 4, 6 )
         SIZE 96
      }
      FILTERS {
         NONE
      }
      FILLVALUE {
         FILL_TIME H5D_FILL_TIME_IFSET
         VALUE  0
      }
      ALLOCATION_TIME {
         H5D_ALLOC_TIME_INCR
      }
   }
}
}
\endcode

There can be many reasons that the storage layout needs to be changed for a dataset. For example,
there may be a performance issue with a dataset due to a small chunk size.

\section secViewToolsEditApply Apply Compression Filter to a Dataset
The <code style="background-color:whitesmoke;">h5repack</code> utility can be used to compress or
remove compression from a dataset in a file. By default, compression cannot be added to or removed
from a dataset once it has been created. However, with <code style="background-color:whitesmoke;">h5repack</code>
you can write a file to a new file and specify a compression filter to apply to a dataset or datasets in the new file.

To apply a filter to an object in an HDF5 file, specify the <code style="background-color:whitesmoke;">-f</code> option,
where the string following the <code style="background-color:whitesmoke;">-f</code> option defines the filter and
its parameters (if there are any) to apply to a given object or objects:
\code
h5repack -f [list of objects:]<name of filter>=<filter parameters> <input file> <output file>
\endcode

If no objects are specified then everything in the input file will be written to the output file with
the filter and parameters specified. If objects are specified, then everything in the input file will
be written to the output file as is, except for the specified objects. They will be written to the
output file with the filter and parameters specified.

If you type <code style="background-color:whitesmoke;">h5repack --help</code> on the command line,
you will see a detailed usage statement with examples of modifying a filter. There are actually
numerous filters that you can apply to a dataset:
<table>
<tr>
<th>Filter<th></th>Options</th>
</tr>
<tr>
<td>GZIP compression (levels 1-9)
<td>GZIP=&lt;deflation level&gt;
</td>
</tr>
<tr>
<td>SZIP compression
<td>SZIP=<pixels per block,coding>
</td>
</tr>
<tr>
<td>Shuffle filter
<td>SHUF
</td>
</tr>
<tr>
<td>Checksum filter
<td>FLET
</td>
</tr>
<tr>
<td>NBIT compression
<td>NBIT
</td>
</tr>
<tr>
<td>HDF5 Scale/Offset filter
<td>SOFF=<scale_factor,scale_type>
</td>
</tr>
<tr>
<td>User defined filter
<td>UD=<filter_number,cd_value_count,value_1[,value_2,...,value_N]>
</td>
</tr>
<tr>
<td>Remove ALL filters
</td>
<td>NONE
</td>
</tr>
</table>

Be aware that a dataset must be chunked to apply compression to it. If the dataset is not already chunked,
then <code style="background-color:whitesmoke;">h5repack</code> will apply chunking to it. Both chunking
and compression cannot be applied to a dataset at the same time with <code style="background-color:whitesmoke;">h5repack</code>.

In the following example,
\li <em>h5dump</em> lists the properties for the objects in <em>dset.h5</em>. Note that the dataset <em>dset</em> is contiguous.
\li <em>h5repack</em> writes dset.h5 into a new file <em>dsetrpk.h5</em>, applying GZIP Level 5 compression to the dataset <em>/dset</em> in dsetrpk.h5.
\li <em>h5dump</em> lists the properties for the new <em>dsetrpk.h5</em> file. Note that <em>/dset</em> is both compressed and chunked.

<em>Example</em>
\code
$ h5dump -pH dset.h5
HDF5 "dset.h5" {
GROUP "/" {
   DATASET "dset" {
      DATATYPE  H5T_STD_I32BE
      DATASPACE  SIMPLE { ( 12, 18 ) / ( 12, 18 ) }
      STORAGE_LAYOUT {
         CONTIGUOUS
         SIZE 864
         OFFSET 1400
      }
      FILTERS {
         NONE
      }
      FILLVALUE {
         FILL_TIME H5D_FILL_TIME_IFSET
         VALUE  0
      }
      ALLOCATION_TIME {
         H5D_ALLOC_TIME_LATE
      }
   }
}
}

$ h5repack -f dset:GZIP=5 dset.h5 dsetrpk.h5

$ h5dump -pH dsetrpk.h5
HDF5 "dsetrpk.h5" {
GROUP "/" {
   DATASET "dset" {
      DATATYPE  H5T_STD_I32BE
      DATASPACE  SIMPLE { ( 12, 18 ) / ( 12, 18 ) }
      STORAGE_LAYOUT {
         CHUNKED ( 12, 18 )
         SIZE 160 (5.400:1 COMPRESSION)
      }
      FILTERS {
         COMPRESSION DEFLATE { LEVEL 5 }
      }
      FILLVALUE {
         FILL_TIME H5D_FILL_TIME_IFSET
         VALUE  0
      }
      ALLOCATION_TIME {
         H5D_ALLOC_TIME_INCR
      }
   }
}
}
\endcode

\section secViewToolsEditCopy Copy Objects to Another File
The <code style="background-color:whitesmoke;">h5copy</code> utility can be used to copy an object or
objects from one HDF5 file to another or to a different location in the same file. It uses the
#H5Ocopy and #H5Lcopy APIs in HDF5.

Following are some of the options that can be used with <code style="background-color:whitesmoke;">h5copy</code>.
<table>
<tr>
<th>h5copy Options</th><th>Description</th>
</tr>
<tr>
<td>-i, --input
</td>
<td>Input file name
</td>
</tr>
<tr>
<td>-o, --output
</td>
<td>Output file name
</td>
</tr>
<tr>
<td>-s, --source
</td>
<td>Source object name
</td>
</tr>
<tr>
<td>-d, --destination
</td>
<td>Destination object name
</td>
</tr>
<tr>
<td>-p, --parents
</td>
<td>Make parent groups as needed
</td>
</tr>
<tr>
<td>-v, --verbose
</td>
<td>Verbose mode
</td>
</tr>
<tr>
<td>-f, --flag
</td>
<td>Flag type
</td>
</tr>
</table>

For a complete list of options and information on using <code style="background-color:whitesmoke;">h5copy</code>, type:
\code
h5copy --help
\endcode

In the example below, the dataset <code style="background-color:whitesmoke;">/MyGroup/Group_A/dset2</code>
in <code style="background-color:whitesmoke;">groups.h5</code> gets copied to the root
("<code style="background-color:whitesmoke;">/</code>") group of a new file,
<code style="background-color:whitesmoke;">newgroup.h5</code>, with the name
<code style="background-color:whitesmoke;">dset3</code>:
\code
$h5dump -H groups.h5
HDF5 "groups.h5" {
GROUP "/" {
   GROUP "MyGroup" {
      GROUP "Group_A" {
         DATASET "dset2" {
            DATATYPE  H5T_STD_I32BE
            DATASPACE  SIMPLE { ( 2, 10 ) / ( 2, 10 ) }
         }
      }
      GROUP "Group_B" {
      }
      DATASET "dset1" {
         DATATYPE  H5T_STD_I32BE
         DATASPACE  SIMPLE { ( 3, 3 ) / ( 3, 3 ) }
      }
   }
}
}

$ h5copy -i groups.h5 -o newgroup.h5 -s /MyGroup/Group_A/dset2 -d /dset3

$ h5dump -H newgroup.h5
HDF5 "newgroup.h5" {
GROUP "/" {
   DATASET "dset3" {
      DATATYPE  H5T_STD_I32BE
      DATASPACE  SIMPLE { ( 2, 10 ) / ( 2, 10 ) }
   }
}
}
\endcode

There are also <code style="background-color:whitesmoke;">h5copy</code> flags that can be specified
with the <code style="background-color:whitesmoke;">-f</code> option. In the example below, the
<code style="background-color:whitesmoke;">-f shallow</code> option specifies to copy only the
immediate members of the group <code style="background-color:whitesmoke;">/MyGroup</code> from
the <code style="background-color:whitesmoke;">groups.h5</code> file mentioned above to a new
file <code style="background-color:whitesmoke;">mygrouponly.h5</code>:
\code
h5copy -v -i groups.h5 -o mygrouponly.h5 -s /MyGroup -d /MyGroup -f shallow
\endcode

The output of the above command is shown below. The verbose option <code style="background-color:whitesmoke;">-v</code>
describes the action that was taken, as shown in the highlighted text.
\code
Copying file <groups.h5> and object </MyGroup> to file <mygrouponly.h5> and object </MyGroup>
Using shallow flag

$ h5dump -H mygrouponly.h5
HDF5 "mygrouponly.h5" {
GROUP "/" {
   GROUP "MyGroup" {
      GROUP "Group_A" {
      }
      GROUP "Group_B" {
      }
      DATASET "dset1" {
         DATATYPE  H5T_STD_I32BE
         DATASPACE  SIMPLE { ( 3, 3 ) / ( 3, 3 ) }
      }
   }
}
}
\endcode

\section secViewToolsEditAdd Add or Remove User Block from File
The user block is a space in an HDF5 file that is not interpreted by the HDF5 library. It is a property
list that can be added when creating a file. See the #H5Pset_userblock API in the \ref RM for more
information regarding this property.

Once created in a file, the user block cannot be removed. However, you can use the
<code style="background-color:whitesmoke;">h5jam</code> and <code style="background-color:whitesmoke;">h5unjam</code>
utilities to add or remove a user block from a file into a new file.

These two utilities work similarly, except that <code style="background-color:whitesmoke;">h5jam</code>
adds a user block to a file and <code style="background-color:whitesmoke;">h5unjam</code> removes the user
block. You can also overwrite or delete a user block in a file.

Specify the <code style="background-color:whitesmoke;">-h</code> option to see a complete list of options
that can be used with <code style="background-color:whitesmoke;">h5jam</code> and
<code style="background-color:whitesmoke;">h5unjam</code>. For example:
\code
   h5jam -h
   h5unjam -h
\endcode

Below are the basic options for adding or removing a user block with <code style="background-color:whitesmoke;">h5jam</code>
and <code style="background-color:whitesmoke;">h5unjam</code>:

<table>
<tr>
<th>h5copy Options</th><th>Description</th>
</tr>
<tr>
<td>-i
</td>
<td>Input File
</td>
</tr>
<tr>
<td>-o
</td>
<td>Output File
</td>
</tr>
<tr>
<td>-u
</td>
<td>File to add or remove from user block
</td>
</tr>
</table>

Let's say you wanted to add the program that creates an HDF5 file to its user block. As an example, you
can take the <code style="background-color:whitesmoke;">h5_crtgrpar.c</code> program from the
\ref LBExamples
and add it to the file it creates, <code style="background-color:whitesmoke;">groups.h5</code>. This can
be done with <code style="background-color:whitesmoke;">h5jam</code>, as follows:
\code
h5jam -i groups.h5 -u h5_crtgrpar.c -o groupsub.h5
\endcode

You can actually view the file with more <code style="background-color:whitesmoke;">groupsub.h5</code>
to see that the <code style="background-color:whitesmoke;">h5_crtgrpar.c</code> file is indeed included.

To remove the user block that was just added, type:
\code
h5unjam -i groupsub.h5 -u h5_crtgrparNEW.c -o groups-noub.h5
\endcode

This writes the user block in the file <code style="background-color:whitesmoke;">groupsub.h5</code>
into <code style="background-color:whitesmoke;">h5_crtgrparNEW.c</code>. The new HDF5 file,
<code style="background-color:whitesmoke;">groups-noub.h5</code>, will not contain a user block.

<hr>
Navigate back: \ref index "Main" / \ref GettingStarted / \ref ViewToolsCommand

*/

/** @page ViewToolsConvert Command-line Tools For Converting HDF5 Files
Navigate back: \ref index "Main" / \ref GettingStarted / \ref ViewToolsCommand
<hr>

\section secViewToolsConvertTOC Contents
<ul>
<li>\ref secViewToolsConvertASCII</li>
<li>\ref secViewToolsConvertBinary</li>
<li>\ref secViewToolsConvertExport</li>
</ul>

\section secViewToolsConvertASCII Output HDF5 Dataset into an ASCII File (to Import into Excel and Other Applications)
The <code style="background-color:whitesmoke;">h5dump</code> utility can be used to convert an HDF5 dataset
into an ASCII file, which can then be imported into Excel and other applications. The following options are used:
<table>
<tr>
<th>Options</th><th>Description</th>
</tr>
<tr>
<td> -d D, --dataset=D
</td>
<td>Display dataset D
</td>
</tr>
<tr>
<td> -o F, --output=F 
</td>
<td>Output raw data into file F
</td>
</tr>
<tr>
<td> -y, --noindex
</td>
<td>Suppress printing of array indices with the data
</td>
</tr>
<tr>
<td> -w N, --width=N
</td>
<td>Set N number of columns of output. A value of 0
sets the number to 65535 (the maximum)
</td>
</tr>
</table>

As an example, <code style="background-color:whitesmoke;">h5_crtdat.c</code> from the \ref LBDsetCreate
HDF5 Tutorial topic, creates the file <code style="background-color:whitesmoke;">dset.h5</code> with
a dataset <code style="background-color:whitesmoke;">/dset</code> that is a 4 x 6 integer array. The
following is displayed when viewing <code style="background-color:whitesmoke;">dset.h5</code> with
<code style="background-color:whitesmoke;">h5dump</code>:
\code
$ h5dump dset.h5
HDF5 "dset.h5" {
GROUP "/" {
   DATASET "dset" {
      DATATYPE  H5T_STD_I32BE
      DATASPACE  SIMPLE { ( 4, 6 ) / ( 4, 6 ) }
      DATA {
      (0,0): 1, 2, 3, 4, 5, 6,
      (1,0): 7, 8, 9, 10, 11, 12,
      (2,0): 13, 14, 15, 16, 17, 18,
      (3,0): 19, 20, 21, 22, 23, 24
      }
   }
}
}
\endcode

The following command will output the values of the <code style="background-color:whitesmoke;">/dset</code>
dataset to the ASCII file <code style="background-color:whitesmoke;">dset.asci</code>:
\code
h5dump -d /dset -o dset.asci -y -w 50 dset.h5
\endcode

In particular, note that:
\li The default behavior of <code style="background-color:whitesmoke;">h5dump</code> is to print indices,
and the <code style="background-color:whitesmoke;">-y</code> option suppresses this.
\li The <code style="background-color:whitesmoke;">-w 50</code> option tells
<code style="background-color:whitesmoke;">h5dump</code> to allow 50 columns for outputting the data. The
value specified must be large enough to accommodate the dimension size of the dataset multiplied by the
number of positions and spaces needed to print each value. If the value is not large enough, the output
will wrap to the next line, and the data will not display as expected in Excel or other applications. To
ensure that the output does not wrap to the next line, you can also specify 0 (zero) for the
<code style="background-color:whitesmoke;">-w</code> option.

In addition to creating the ASCII file <code style="background-color:whitesmoke;">dset.asci</code>, the
above command outputs the metadata of the specified dataset:
\code
HDF5 "dset.h5" {
DATASET "/dset" {
   DATATYPE  H5T_STD_I32BE
   DATASPACE  SIMPLE { ( 4, 6 ) / ( 4, 6 ) }
   DATA {
   }
}
}
\endcode

The <code style="background-color:whitesmoke;">dset.asci</code> file will contain the values for the dataset:
\code
      1, 2, 3, 4, 5, 6,
      7, 8, 9, 10, 11, 12,
      13, 14, 15, 16, 17, 18,
      19, 20, 21, 22, 23, 24
\endcode

\section secViewToolsConvertBinary Output HDF5 Dataset into Binary File
The <code style="background-color:whitesmoke;">h5dump</code> utility can be used to convert an
HDF5 dataset to a binary file with the following options:
<table>
<tr>
<th>Options</th><th>Description</th>
</tr>
<tr>
<td>-d D, --dataset=D
</td>
<td>Display dataset D
</td>
</tr>
<tr>
<td>-o F, --output=F 
</td>
<td>Output raw data into file F
</td>
</tr>
<tr>
<td>-b B, --binary=B
</td>
<td>Binary file output of form B.
Valid values are: LE, BE, NATIVE, FILE
</td>
</tr>
</table>

As an example, <code style="background-color:whitesmoke;">h5_crtdat.c</code> from the
\ref LBDsetCreate HDF5 Tutorial topic, creates the file dset.h5 with a dataset
<code style="background-color:whitesmoke;">/dset</code> that is a 4 x 6 integer array. The
following is displayed when viewing <code style="background-color:whitesmoke;">dset.h5</code>
with <code style="background-color:whitesmoke;">h5dump</code>:
\code
$ h5dump -d /dset/ dset.h5
HDF5 "dset.h5" {
DATASET "/dset/" {
   DATATYPE  H5T_STD_I32BE
   DATASPACE  SIMPLE { ( 4, 6 ) / ( 4, 6 ) }
   DATA {
   (0,0): 1, 2, 3, 4, 5, 6,
   (1,0): 7, 8, 9, 10, 11, 12,
   (2,0): 13, 14, 15, 16, 17, 18,
   (3,0): 19, 20, 21, 22, 23, 24
   }
}
}
\endcode

As specified by the <code style="background-color:whitesmoke;">-d</code> and
<code style="background-color:whitesmoke;">-o</code> options, the following
<code style="background-color:whitesmoke;">h5dump</code> command will output the values of the dataset
<code style="background-color:whitesmoke;">/dset </code>to a file called
<code style="background-color:whitesmoke;">dset.bin</code>. The <code style="background-color:whitesmoke;">-b</code>
option specifies that the output will be binary in Little Endian format (LE).

\code
h5dump -d /dset -b LE -o dset.bin dset.h5
\endcode

This command outputs the metadata for the dataset, as well as creating the binary file
<code style="background-color:whitesmoke;">dset.bin</code>:
\code
HDF5 "dset.h5" {
DATASET "/dset" {
   DATATYPE  H5T_STD_I32BE
   DATASPACE  SIMPLE { ( 4, 6 ) / ( 4, 6 ) }
   DATA {
   }
}
}
\endcode

If you look at the resulting <code style="background-color:whitesmoke;">dset.bin</code> file with
a binary editor, you will see that it contains the dataset's values. For example (on Linux) you will see:
\code
$ od -t d dset.bin
0000000           1           2           3           4
0000020           5           6           7           8
0000040           9          10          11          12
0000060          13          14          15          16
0000100          17          18          19          20
0000120          21          22          23          24
0000140
\endcode

\section secViewToolsConvertExport Export from h5dump and Import into HDF5
The <code style="background-color:whitesmoke;">h5import</code> utility can use the output of
<code style="background-color:whitesmoke;">h5dump</code> as input to create a dataset or file.

The <code style="background-color:whitesmoke;">h5dump</code> utility must first create two files:
\li A DDL file, which will be used as an <code style="background-color:whitesmoke;">h5import</code> configuration file
\li A raw data file containing the data to be imported

The DDL file must be generated with the <code style="background-color:whitesmoke;">h5dump -p</code> option, to generate properties.

The raw data file that can be imported into HDF5 using this method may contain either numeric or string data with the following restrictions:
\li Numeric data requires the use of the <code style="background-color:whitesmoke;">h5dump -b</code> option to produce a binary data file.
\li String data must be written with the <code style="background-color:whitesmoke;">h5dump -y</code> and
<code style="background-color:whitesmoke;">--width=1</code> options, generating a single column of strings without indices.

Two examples follow: the first imports a dataset with a numeric datatype. Note that numeric data requires
the use of the <code style="background-color:whitesmoke;">h5dump -b</code> option to produce a binary data
file. The example program (<code style="background-color:whitesmoke;">h5_crtdat.c</code>) that creates this
file is included with the \ref IntroHDF5 tutorial and can be obtained from the \ref LBExamples page:
\code
h5dump -p -d "/dset" --ddl=dsetbin.dmp -o dset.bin -b dset.h5
h5import dset.bin -c dsetbin.dmp -o new-dset.h5
\endcode

The output before and after running these commands is shown below:
\code
$  h5dump dset.h5
HDF5 "dset.h5" {
GROUP "/" {
   DATASET "dset" {
      DATATYPE  H5T_STD_I32BE
      DATASPACE  SIMPLE { ( 4, 6 ) / ( 4, 6 ) }
      DATA {
      (0,0): 1, 2, 3, 4, 5, 6,
      (1,0): 7, 8, 9, 10, 11, 12,
      (2,0): 13, 14, 15, 16, 17, 18,
      (3,0): 19, 20, 21, 22, 23, 24
      }
   }
}
}
$ h5dump -p -d "/dset" --ddl=dsetbin.dmp -o dset.bin -b dset.h5

$ h5import dset.bin -c dsetbin.dmp -o new-dset.h5

$ h5dump new-dset.h5
HDF5 "new-dset.h5" {
GROUP "/" {
   DATASET "dset" {
      DATATYPE  H5T_STD_I32BE
      DATASPACE  SIMPLE { ( 4, 6 ) / ( 4, 6 ) }
      DATA {
      (0,0): 1, 2, 3, 4, 5, 6,
      (1,0): 7, 8, 9, 10, 11, 12,
      (2,0): 13, 14, 15, 16, 17, 18,
      (3,0): 19, 20, 21, 22, 23, 24
      }
   }
}
}
\endcode

The second example imports string data. The example program that creates this file can be downloaded
from the \ref ExAPI page.

Note that string data requires use of the <code style="background-color:whitesmoke;">h5dump -y</code>
option to exclude indexes and the <code style="background-color:whitesmoke;">h5dump --width=1</code>
option to generate a single column of strings. The <code style="background-color:whitesmoke;">-o</code>
option outputs the data into an ASCII file.
\code
h5dump -p -d "/DS1" -O vlstring.dmp -o vlstring.ascii -y --width=1 h5ex_t_vlstring.h5
h5import vlstring.ascii -c vlstring.dmp -o new-vlstring.h5
\endcode

The output before and after running these commands is shown below:
\code
$ h5dump h5ex_t_vlstring.h5
HDF5 "h5ex_t_vlstring.h5" {
GROUP "/" {
   DATASET "DS1" {
      DATATYPE  H5T_STRING {
         STRSIZE H5T_VARIABLE;
         STRPAD H5T_STR_SPACEPAD;
         CSET H5T_CSET_ASCII;
         CTYPE H5T_C_S1;
      }
      DATASPACE  SIMPLE { ( 4 ) / ( 4 ) }
      DATA {
      (0): "Parting", "is such", "sweet", "sorrow."
      }
   }
}
}

$ h5dump -p -d "/DS1" -O vlstring.dmp -o vlstring.ascii -y --width=1 h5ex_t_vlstring.h5

$ h5import vlstring.ascii -c vlstring.dmp -o new-vlstring.h5

$ h5dump new-vlstring.h5
HDF5 "new-vlstring.h5" {
GROUP "/" {
   DATASET "DS1" {
      DATATYPE  H5T_STRING {
         STRSIZE H5T_VARIABLE;
         STRPAD H5T_STR_NULLTERM;
         CSET H5T_CSET_ASCII;
         CTYPE H5T_C_S1;
      }
      DATASPACE  SIMPLE { ( 4 ) / ( 4 ) }
      DATA {
      (0): "Parting", "is such", "sweet", "sorrow."
      }
   }
}
\endcode

<hr>
Navigate back: \ref index "Main" / \ref GettingStarted / \ref ViewToolsCommand

*/