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9 changes: 6 additions & 3 deletions src/H5Dmodule.h
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* </tr>
* <tr>
* <td>szip compression</td>
* <td>Data compression using the szip library. The HDF Group now uses the libaec library for the szip filter.</td>
* <td>Data compression using the szip library. The HDF Group now uses the libaec library for the szip
filter.</td>
* </tr>
* </table>
*
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*
* It is clear that the internal HDF5 filter mechanism, while extensible, does not work well with third-party
* filters. It would be a maintenance nightmare to keep adding and supporting new compression methods
* in HDF5. For any set of HDF5 “internal” filters, there always will be data with which the “internal” filters
* in HDF5. For any set of HDF5 “internal” filters, there always will be data with which the “internal”
filters
* will not achieve the optimal performance needed to address data I/O and storage problems. Thus the
* internal HDF5 filter mechanism is enhanced to address the issues discussed above.
*
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* and the filter will be applied when data is written to the file.
*
* When an application reads data compressed with a third-party HDF5 filter, the HDF5 Library will search
* for the required filter plugin, register the filter with the library (if the filter function is not registered) and
* for the required filter plugin, register the filter with the library (if the filter function is not
registered) and
* apply it to the data on the read operation.
*
* For more information,
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58 changes: 27 additions & 31 deletions src/H5PLmodule.h
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* available on the system in a default location. The HDF5 filter plugin is discussed in detail in the
* \ref subsec_filter_plugins_prog section.
*
* \subsubsection subsubsec_filter_plugins_model_apply Applying a Third-party Filter When Creating and Writing a Dataset
* A third-party filter can be added to the HDF5 filter pipeline by using the H5Pset_filter function, as a
* user would do in the past. The identification number and the filter parameters should be available to the
* application. For example, if the application intends to apply the HDF5 bzip2 compression filter that was
* registered with The HDF Group and has an identification number 307
* (<a href="https://portal.hdfgroup.org/documentation/hdf5-docs/registered_filter_plugins.html">Registered Filters</a>)
* then the application would follow the steps as outlined below:
* \code
* dcpl = H5Pcreate (H5P_DATASET_CREATE);
* status = H5Pset_filter (dcpl, (H5Z_filter_t)307, H5Z_FLAG_MANDATORY, (size_t)6, cd_values);
* dset = H5Dcreate (file, DATASET, H5T_STD_I32LE, space, H5P_DEFAULT, dcpl,
* status = H5Dwrite (dset, H5T_NATIVE_INT, H5S_ALL, H5S_ALL, H5P_DEFAULT, wdata[0]);
* \endcode
* \subsubsection subsubsec_filter_plugins_model_apply Applying a Third-party Filter When Creating and Writing
* a Dataset A third-party filter can be added to the HDF5 filter pipeline by using the H5Pset_filter
* function, as a user would do in the past. The identification number and the filter parameters should be
* available to the application. For example, if the application intends to apply the HDF5 bzip2 compression
* filter that was registered with The HDF Group and has an identification number 307
* (<a href="https://portal.hdfgroup.org/documentation/hdf5-docs/registered_filter_plugins.html">Registered
* Filters</a>) then the application would follow the steps as outlined below: \code dcpl = H5Pcreate
* (H5P_DATASET_CREATE); status = H5Pset_filter (dcpl, (H5Z_filter_t)307, H5Z_FLAG_MANDATORY, (size_t)6,
* cd_values); dset = H5Dcreate (file, DATASET, H5T_STD_I32LE, space, H5P_DEFAULT, dcpl, status = H5Dwrite
* (dset, H5T_NATIVE_INT, H5S_ALL, H5S_ALL, H5P_DEFAULT, wdata[0]); \endcode
*
* \subsubsection subsubsec_filter_plugins_model_read Reading Data with an Applied Third-party Filter
* An application does not need to do anything special to read the data with a third-party filter applied. For
* example, if one wants to read data written in the previous example, the following regular steps should be taken:
* \code
* file = H5Fopen (FILE, H5F_ACC_RDONLY, H5P_DEFAULT);
* dset = H5Dopen (file, DATASET, H5P_DEFAULT);
* H5Dread (dset, H5T_NATIVE_INT, H5S_ALL, H5S_ALL, H5P_DEFAULT, rdata[0]);
* \endcode
* example, if one wants to read data written in the previous example, the following regular steps should be
* taken: \code file = H5Fopen (FILE, H5F_ACC_RDONLY, H5P_DEFAULT); dset = H5Dopen (file, DATASET,
* H5P_DEFAULT); H5Dread (dset, H5T_NATIVE_INT, H5S_ALL, H5S_ALL, H5P_DEFAULT, rdata[0]); \endcode
*
* The command-line utility h5dump, for example, will read and display the data as shown:
* \code
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* Data goes through the HDF5 filter pipeline only when it is written to the file or read into application
* memory space from the file. For example, the I/O operation is triggered with a call to #H5Fflush, or when
* a data item (HDF5 metadata or a raw data chunk) is evicted from the cache or brought into the cache.
* Please notice that #H5Dread/#H5Dwrite calls on the chunked datasets do not necessarily trigger I/O since the
* HDF5 Library uses a separate chunk cache.
* Please notice that #H5Dread/#H5Dwrite calls on the chunked datasets do not necessarily trigger I/O since
* the HDF5 Library uses a separate chunk cache.
*
* A data item may remain in the cache until the HDF5 Library is closed. If the HDF5 plugin that has to be
* applied to the data item becomes unavailable before the file and all objects in the file are closed, an
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*
* \subsubsection subsubsec_filter_plugins_prog_write Writing a Filter Function
* The HDF5 filter function for the dynamically loaded filter feature should be written as any custom filter
* described in <a href="http://www.hdfgroup.org/HDF5/doc/H5.user/Filters.html">Custom Filters</a>. See the “Example” section,
* section 5, of that document to get an idea of the simple filter function, and see the example of the more
* sophisticated HDF5 bzip2 filter function in the “Building an HDF5 bzip2 Plugin Example” section.
* The HDF5 bzip2 filter function is also available for download from
* <a href="https://github.com/HDFGroup/hdf5_plugins">Filter Plugin Repository</a>.
* described in <a href="http://www.hdfgroup.org/HDF5/doc/H5.user/Filters.html">Custom Filters</a>. See the
* “Example” section, section 5, of that document to get an idea of the simple filter function, and see the
* example of the more sophisticated HDF5 bzip2 filter function in the “Building an HDF5 bzip2 Plugin Example”
* section. The HDF5 bzip2 filter function is also available for download from <a
* href="https://github.com/HDFGroup/hdf5_plugins">Filter Plugin Repository</a>.
*
* The user has to remember a few things when writing an HDF5 filter function.
* <ul><li>1. An HDF5 filter is bidirectional.
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* \subsubsection subsubsec_filter_plugins_prog_reg Registering a Filter with The HDF Group
* If you are writing a filter that will be used by others, it would be a good idea to request a filter
* identification number and register it with The HDF Group. Please follow the procedure described at
* <a href="https://portal.hdfgroup.org/documentation/hdf5-docs/registered_filter_plugins.html">Registered Filters</a>.
* <a href="https://portal.hdfgroup.org/documentation/hdf5-docs/registered_filter_plugins.html">Registered
* Filters</a>.
*
* The HDF Group anticipates that developers of HDF5 filter plugins will not only register new filters, but
* will also provide links to the source code and/or binaries for the corresponding HDF5 filter plugins.
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* use the H5Pget_filter<*> functions to retrieve information about the filters.
*
* Using the example of the structure above, the h5dump tool will print the string “HDF5 bzip2
* filter found at …” pointing users to the applied filter (see the example in the \ref subsubsec_filter_plugins_model_read
* section) thus solving the problem of the filter’s origin.
* filter found at …” pointing users to the applied filter (see the example in the \ref
* subsubsec_filter_plugins_model_read section) thus solving the problem of the filter’s origin.
*
* \subsubsection subsubsec_filter_plugins_prog_create Creating an HDF5 Filter Plugin
* The HDF5 filter plugin source should include:
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* GIT_BRANCH: "master"
* \endcode
*
* See the documentation at <aref="https://github.com/HDFGroup/hdf5_plugins/tree/master/docs">hdf5_plugins/docs</a> folder
* In particular:
* See the documentation at
* <aref="https://github.com/HDFGroup/hdf5_plugins/tree/master/docs">hdf5_plugins/docs</a> folder In
* particular:
* <aref="https://github.com/HDFGroup/hdf5_plugins/blob/master/docs/INSTALL_With_CMake.txt">INSTALL_With_CMake</a>
* <aref="https://github.com/HDFGroup/hdf5_plugins/blob/master/docs/USING_HDF5_AND_CMake.txt">USING_HDF5_AND_CMake</a>
*/
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