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H5Z: Filter and Compression Interface

Filter and Compression API Functions


The C Interface:
These functions enable the user to configure new filters for the local environment.
             

The Fortran Interface:
In general, each Fortran subroutine performs exactly the same task as the corresponding C function.
             

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

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_DEFLATEThe gzip compression, or deflation, filter
H5Z_FILTER_SZIPThe SZIP compression filter
H5Z_FILTER_NBITThe N-bit compression filter
H5Z_FILTER_SCALEOFFSET  The scale-offset compression filter
H5Z_FILTER_SHUFFLEThe shuffle algorithm filter
H5Z_FILTER_FLETCHER32The Fletcher32 checksum, or error checking, filter

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

See HDF5 Dynamically Loaded Filters for more information on how an HDF5 application can apply a filter that is not registered with the HDF5 Library.


Name: H5Zfilter_avail
Signature:
htri_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:
Returns:
Returns a Boolean value (TRUE/FALSE) 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
	
History:

Name: H5Zget_filter_info
Signature:
herr_t H5Zget_filter_info( H5Z_filter_t filter, unsigned int *filter_config )
Purpose:
Retrieves information about a filter.
Description:
H5Zget_filter_info retrieves information about a filter. At present, this means that the function retrieves a filter's configuration flags, indicating whether the filter is configured to decode data, to encode data, neither, or both.

If filter_config is not set to NULL prior to the function call, the returned parameter contains a bit field specifying the available filter configuration. The configuration flag values can then be determined through a series of bitwise AND operations, as described below.

Valid filter configuration flags include the following:
     H5Z_FILTER_CONFIG_ENCODE_ENABLED  Encoding is enabled for this filter.
In Fortran, H5Z_FILTER_ENCODE_ENABLED_F.
  H5Z_FILTER_CONFIG_DECODE_ENABLED     Decoding is enabled for this filter.
In Fortran, H5Z_FILTER_DECODE_ENABLED_F.
  (These flags are defined for C in the HDF5 Library source code file H5Zpublic.h.)
A bitwise AND of the returned filter_config and a valid filter configuration flag will reveal whether the related configuration option is available. For example, if the value of
     H5Z_FILTER_CONFIG_ENCODE_ENABLED & filter_config
is true, i.e., greater than 0 (zero), the queried filter is configured to encode data; if the value is FALSE, i.e., equal to 0 (zero), the filter is not so configured.

If a filter is not encode-enabled, the corresponding H5Pset_* function will return an error if the filter is added to a dataset creation property list (which is required if the filter is to be used to encode that dataset). For example, if the H5Z_FILTER_CONFIG_ENCODE_ENABLED flag is not returned for the SZIP filter, H5Z_FILTER_SZIP, a call to H5Pset_szip will fail.

If a filter is not decode-enabled, the application will not be able to read an existing file encoded with that filter.

This function should be called, and the returned filter_config analyzed, before calling any other function, such as H5Pset_szip, that might require a particular filter configuration.

Parameters:
H5Z_filter_t filter
IN: Identifier of the filter to query. See the introduction to this section of the reference manual for a list of valid filter identifiers.
unsigned int *filter_config
OUT: A bit field encoding the returned filter information
Returns:
Returns a non-negative value on success, a negative value on failure.
Fortran90 Interface:
SUBROUTINE h5zget_filter_info_f(filter, config_flags, hdferr)

  IMPLICIT NONE
  INTEGER, INTENT(IN)  :: filter        ! Filter, may be one of the
                                        ! following:
                                        !     H5Z_FILTER_DEFLATE_F
                                        !     H5Z_FILTER_SHUFFLE_F
                                        !     H5Z_FILTER_FLETCHER32_F
                                        !     H5Z_FILTER_SZIP_F
  INTEGER, INTENT(OUT) :: config_flags  ! Bit field indicating whether
                                        ! a filter's encoder and/or
                                        ! decoder are available
  INTEGER, INTENT(OUT) :: hdferr        ! Error code

END SUBROUTINE h5zfilter_avail_f
    
History:

Last modified: 23 August 2012
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, set_local, and filter. This call to H5Zregister, registering the filter with the library, is the second step. The can_apply and set_local fields can be set to NULL if they are not required for the filter being registered.

H5Zregister accepts a single parameter, a pointer to a buffer for the filter_class data structure. That data structure must conform to one of the following definitions:

        typedef struct H5Z_class1_t {
            H5Z_filter_t id;
            const char  *name;
            H5Z_can_apply_func_t can_apply;
            H5Z_set_local_func_t set_local;
            H5Z_func_t filter;
        } H5Z_class1_t;

        typedef struct H5Z_class2_t {
            int version;
            H5Z_filter_t id;
            unsigned encoder_present;
            unsigned decoder_present;
            const char  *name;
            H5Z_can_apply_func_t can_apply;
            H5Z_set_local_func_t set_local;
            H5Z_func_t filter;
        } H5Z_class2_t;
      

version is a libray-defined value reporting the version number of the H5Z_class_t struct. This currently must be set to H5Z_CLASS_T_VERS.

id is the identifier for the new filter. This is a user-defined value between H5Z_FILTER_RESERVED and H5Z_FILTER_MAX. These values are defined in the HDF5 source file H5Zpublic.h, but the symbols H5Z_FILTER_RESERVED and H5Z_FILTER_MAX should always be used instead of the literal values.

encoder_present is a library-defined value indicating whether the filter’s encoding capability is available to the application.

decoder_present is a library-defined value indicating whether the filter’s encoding capability is available to the application.

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

can_apply, 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, 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, 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.

H5Z_class_t is a macro which maps to either H5Z_class1_t or H5Z_class2_t, depending on the needs of the application. To affect only this macro, H5Z_class_t_vers may be defined to either 1 or 2. Otherwise, it will behave in the same manner as other API compatibility macros. See “API Compatibility Macros in HDF5” for more information. H5Z_class1_t matches the H5Z_class_t structure that is used in the 1.6.x versions of the HDF5 library.

H5Zregister will automatically detect which structure type has been passed in, regardless of the mapping of the H5Z_class_t macro. However, the application must make sure that the fields are filled in according to the correct structure definition if the macro is used to declare the structure.

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.

When a filter is applied to the fractal heap for a group (e.g., when compressing group metadata) and if the can apply and set local callback functions have been defined for that filter, HDF5 passes the value -1 for all parameters for those callback functions. This is done to ensure that the filter will not be applied to groups if it relies on these parameters, as they are not applicable to group fractal heaps; to operate on group fractal heaps, a filter must be capable of operating on an opaque block of binary data.

The can apply callback function is defined as follows:

typedef htri_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. If this filter is enabled through H5Pset_filter as optional and the can apply function returns FALSE, the library will skip the filter in the filter pipeline.

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.

Programming Note for C++ Developers Using C Functions:

If a C routine that takes a function pointer as an argument is called from within C++ code, the C routine should be returned from normally.

Examples of this kind of routine include callbacks such as H5Pset_elink_cb and H5Pset_type_conv_cb and functions such as H5Tconvert and H5Ewalk2.

Exiting the routine in its normal fashion allows the HDF5 C Library to clean up its work properly. In other words, if the C++ application jumps out of the routine back to the C++ “catch” statement, the library is not given the opportunity to close any temporary data structures that were set up when the routine was called. The C++ application should save some state as the routine is started so that any problem that occurs might be diagnosed.

Parameters:
const H5Z_class_t *filter_class     IN: A pointer to a buffer for the struct containing filter-definition information.

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

Fortran90 Interface:
None.

History:

Last modified: 2 July 2013
Name: H5Zunregister
Signature:
herr_t H5Zunregister(H5Z_filter_t filter)

Purpose:
Unregisters a filter.

Description:
H5Zunregister unregisters the filter specified in filter.

This function first iterates through all opened datasets and groups. If an open object that uses this filter is found, the function will fail with a message indicating that an object using the filter is still open. All open files are then flushed to make sure that all cached data that may use this filter are written out.

If the application is a parallel program, all processes that participate in collective data write should call this function to ensure that all data is flushed.

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 identifiers for standard filters distributed with the HDF5 Library.

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
    

History:

HDF5 documents and links 
Introduction to HDF5 
HDF5 User’s Guide 
In the HDF5 Reference Manual 
H5DS   H5IM   H5LT   H5PT   H5TB  Optimized 
H5   H5A   H5D   H5E   H5F   H5G   H5I   H5L 
H5O   H5P   H5PL   H5R   H5S   H5T   H5Z 
Tools   Datatypes   Fortran   Compatibility Macros 
Collective Calls in Parallel 

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