H5Z: Filter and Compression Interface

Filter and Compression API Functions

HDF5 supports a filter pipeline that provides the capability for standard and customized raw data processing during I/O operations. HDF5 is distributed with a small set of standard filters such as compression (gzip, SZIP, and a shuffling algorithm) and error checking (Fletcher32 checksum). For further flexibility, the library allows a user application to extend the pipeline through the creation and registration of customized filters.

The flexibility of the filter pipeline implementation enables the definition of additional filters by a user application. A filter

• is associated with a dataset when the dataset is created,
  
• can be used only with chunked data
  (i.e., datasets stored in the H5D_CHUNKED storage layout), and
• is applied independently to each chunk of the dataset.

The HDF5 library does not support filters for contiguous datasets because of the difficulty of implementing random access for partial I/O. Compact dataset filters are not supported because it would not produce significant results.

Filter identifiers for the filters distributed with the HDF5 Library are as follows:

H5Z_FILTER_DEFLATE	The gzip compression, or deflation, filter
H5Z_FILTER_SZIP	The SZIP compression filter
H5Z_FILTER_SHUFFLE	The shuffle algorithm filter
H5Z_FILTER_FLETCHER32	The Fletcher32 checksum, or error checking, filter

Custom filters that have been registered with the library will have additional unique identifiers.

See The Dataset Interface (H5D) in the HDF5 User's Guide for further information regarding data compression.

Name: H5Zfilter_avail

Signature:

herr_t H5Zfilter_avail(H5Z_filter_t filter)

Purpose:

Determines whether a filter is available.

Description:

H5Zfilter_avail determines whether the filter specified in filter is available to the application.

Parameters:

H5Z_filter_t filter

IN: Filter identifier. See the introduction to this section of the reference manual for a list of filter identifiers

Returns:

Returns a non-negative value if successful; otherwise returns a negative value.

Fortran90 Interface: h5zfilter_avail_f

SUBROUTINE h5zfilter_avail_f(filter, status, hdferr)
  IMPLICIT NONE
  INTEGER, INTENT(IN)  :: filter     ! Filter
                                     ! Valid values are:
                                     !    H5Z_FILTER_DEFLATE_F
                                     !    H5Z_FILTER_SHUFFLE_F
                                     !    H5Z_FILTER_FLETCHER32_F
                                     !    H5Z_FILTER_SZIP_F
  LOGICAL, INTENT(OUT) :: status     ! Flag indicating whether 
                                     ! filter is available: 
                                     !    .TRUE.
                                     !    .FALSE.
END SUBROUTINE h5zfilter_avail_f
	

Name: H5Zregister

Signature:

herr_t H5Zregister(const H5Z_class_t filter_class) )

Purpose:

Registers new filter.

Description:

H5Zregister registers a new filter with the HDF5 library.

Making a new filter available to an application is a two-step process. The first step is to write the three filter callback functions described below: can_apply_func, set_local_func, and filter_func. This call to H5Zregister, registering the filter with the library, is the second step. The can_apply_func and set_local_func fields can be set to NULL if they are not required for the filter being registered.

H5Zregister accepts a single parameter, the filter_class data structure, which is defined as follows:

       typedef struct H5Z_class_t {
           H5Z_filter_t filter_id;
           const char  *comment;
           H5Z_can_apply_func_t can_apply_func;
           H5Z_set_local_func_t set_local_func;
           H5Z_func_t filter_func;            
       } H5Z_class_t;
      

filter_id is the identifier for the new filter. This is a user-defined value between H5Z_FILTER_RESERVED and H5Z_FILTER_MAX, both of which are defined in the HDF5 source file H5Zpublic.h.

comment is used for debugging, may contain a descriptive name for the filter, and may be the null pointer.

can_apply_func, described in detail below, is a user-defined callback function which determines whether the combination of the dataset creation property list values, the datatype, and the dataspace represent a valid combination to apply this filter to.

set_local_func, described in detail below, is a user-defined callback function which sets any parameters that are specific to this dataset, based on the combination of the dataset creation property list values, the datatype, and the dataspace.

filter_func, described in detail below, is a user-defined callback function which performs the action of the filter.

The statistics associated with a filter are not reset by this function; they accumulate over the life of the library.

The callback functions
Before H5Zregister can link a filter into an application, three callback functions must be defined as described in the HDF5 Library header file H5Zpublic.h.

The can apply callback function is defined as follows:

typedef herr_t (*H5Z_can_apply_func_t) (hid_t dcpl_id, hid_t type_id, hid_t space_id)

Before a dataset is created, the can apply callbacks for any filters used in the dataset creation property list are called with the dataset's dataset creation property list, dcpl_id, the dataset's datatype, type_id, and a dataspace describing a chunk, space_id, (for chunked dataset storage).

This callback must determine whether the combination of the dataset creation property list settings, the datatype, and the dataspace represent a valid combination to which to apply this filter. For example, an invalid combination may involve the filter not operating correctly on certain datatypes, on certain datatype sizes, or on certain sizes of the chunk dataspace.

This callback can be the NULL pointer, in which case the library will assume that the filter can be applied to a dataset with any combination of dataset creation property list values, datatypes, and dataspaces.

The can apply callback function must return a positive value for a valid combination, zero for an invalid combination, and a negative value for an error.

The set local callback function is defined as follows:

typedef herr_t (*H5Z_set_local_func_t) (hid_t dcpl_id, hid_t type_id, hid_t space_id)

After the can apply callbacks are checked for a new dataset, the set local callback functions for any filters used in the dataset creation property list are called. These callbacks receive dcpl_id, the dataset's private copy of the dataset creation property list passed in to H5Dcreate (i.e. not the actual property list passed in to H5Dcreate); type_id, the datatype identifier passed in to H5Dcreate, which is not copied and should not be modified; and space_id, a dataspace describing the chunk (for chunked dataset storage), which should also not be modified.

The set local callback must set any filter parameters that are specific to this dataset, based on the combination of the dataset creation property list values, the datatype, and the dataspace. For example, some filters perform different actions based on different datatypes, datatype sizes, numbers of dimensions, or dataspace sizes.

The set local callback may be the NULL pointer, in which case, the library will assume that there are no dataset-specific settings for this filter.

The set local callback function must return a non-negative value on success and a negative value for an error.

The filter operation callback function, defining the filter's operation on the data, is defined as follows:

typedef size_t (*H5Z_func_t) (unsigned int flags, size_t cd_nelmts, const unsigned int cd_values[], size_t nbytes, size_t *buf_size, void **buf)

The parameters flags, cd_nelmts, and cd_values are the same as for the function H5Pset_filter. The one exception is that an additional flag, H5Z_FLAG_REVERSE, is set when the filter is called as part of the input pipeline.

The parameter *buf points to the input buffer which has a size of *buf_size bytes, nbytes of which are valid data.

The filter should perform the transformation in place if possible. If the transformation cannot be done in place, then the filter should allocate a new buffer with malloc() and assign it to *buf, assigning the allocated size of that buffer to *buf_size. The old buffer should be freed by calling free().

If successful, the filter operation callback function returns the number of valid bytes of data contained in *buf. In the case of failure, the return value is 0 (zero) and all pointer arguments are left unchanged.

Note:

The H5Zregister interface is substantially revised from the HDF5 Release 1.4.x series. The H5Z_class_t struct and the set local and can apply callback functions first appeared in HDF5 Release 1.6.

Parameters:

const H5Z_class_t filter_class

IN: Struct containing filter-definition information.

Returns:

Returns a non-negative value if successful; otherwise returns a negative value.

Fortran90 Interface:

None.

Name: H5Zunregister

Signature:

herr_t H5Zunregister(H5Z_filter_t filter)

Purpose:

Unregisters a filter.

Description:

H5Zunregister unregisters the filter specified in filter.  

After a call to H5Zunregister, the filter specified in filter will no longer be available to the application.

Parameters:

H5Z_filter_t filter

IN: Identifier of the filter to be unregistered. See the introduction to this section of the reference manual for a list of filter identifiers

Returns:

Returns a non-negative value if successful; otherwise returns a negative value.

Fortran90 Interface: h5zunregister_f

SUBROUTINE h5zunregister_f(filter, hdferr) 
  IMPLICIT NONE
  INTEGER, INTENT(IN)  :: filter  ! Filter; one of the possible values:
                                  !    H5Z_FILTER_DEFLATE_F
                                  !    H5Z_FILTER_SHUFFLE_F
                                  !    H5Z_FILTER_FLETCHER32_F
                                  !    H5Z_FILTER_SZIP_F
  INTEGER, INTENT(OUT) :: hdferr  ! Error code
                                  ! 0 on success, and -1 on failure
END SUBROUTINE h5zunregister_f