Example fortran code to create compressed dataset with compound data types.

H5Zszip.c_excerpt

/*-------------------------------------------------------------------------
 * Function:  H5Z_can_apply_szip
 *
 * Purpose:	Check the parameters for szip compression for validity and
 *              whether they fit a particular dataset.
 *
 * Note:        This function currently range-checks for datatypes with
 *              8-bit boundaries (8, 16, 24, etc.).  It appears that the szip
 *              library can actually handle 1-24, 32 & 64 bit samples.  If
 *              this becomes important, we should make the checks below more
 *              sophisticated and have them check for n-bit datatypes of the
 *              correct size, etc. - QAK
 *
 * Return:	Success: Non-negative
 *		Failure: Negative
 *
 * Programmer:	Quincey Koziol
 *              Monday, April  7, 2003
 *
 * Modifications:
 *
 *-------------------------------------------------------------------------
 */
static htri_t
H5Z_can_apply_szip(hid_t UNUSED dcpl_id, hid_t type_id, hid_t UNUSED space_id)
{
    const H5T_t	*type;                  /* Datatype */
    unsigned dtype_size;                /* Datatype's size (in bits) */
    H5T_order_t dtype_order;            /* Datatype's endianness order */
    htri_t ret_value = TRUE;            /* Return value */

    FUNC_ENTER_NOAPI(FAIL)

    /* Get datatype */
    if(NULL == (type = H5I_object_verify(type_id, H5I_DATATYPE)))
	HGOTO_ERROR(H5E_ARGS, H5E_BADTYPE, FAIL, "not a datatype")

    /* Get datatype's size, for checking the "bits-per-pixel" */
    if((dtype_size = (8 * H5T_get_size(type))) == 0)
	HGOTO_ERROR(H5E_PLINE, H5E_BADTYPE, FAIL, "bad datatype size")

    /* Range check datatype's size */
    if(dtype_size > 32 && dtype_size != 64)
	HGOTO_ERROR(H5E_ARGS, H5E_BADVALUE, FALSE, "invalid datatype size")

    /* Get datatype's endianness order */
    if((dtype_order = H5T_get_order(type)) == H5T_ORDER_ERROR)
	HGOTO_ERROR(H5E_PLINE, H5E_BADTYPE, FAIL, "can't retrieve datatype endianness order")

    /* Range check datatype's endianness order */
    /* (Note: this may not handle non-atomic datatypes well) */
    if(dtype_order != H5T_ORDER_LE && dtype_order != H5T_ORDER_BE)
	HGOTO_ERROR(H5E_ARGS, H5E_BADVALUE, FALSE, "invalid datatype endianness order")

done:
    FUNC_LEAVE_NOAPI(ret_value)
} /* end H5Z_can_apply_szip() */

hdfWriteParticleType.f90

!************************************************************
!
!  This example shows how to read and write compound
!  datatypes to a dataset.  
!
!  This file is intended for use with HDF5 Library version 1.8
!  with --enable-fortran2003
!
! Compile: gfortran -I/usr/local/Cellar/hdf5/1.8.11/include -L/usr/local/Cellar/hdf5/1.8.11/lib -lhdf5_fortran -lhdf5hl_fortran -lhdf5 -lhdf5_hl hdfWriteParticleType.f90 -o hdfWriteParticleType
!************************************************************
PROGRAM main

  USE ISO_C_BINDING
  USE HDF5

  IMPLICIT NONE
  ! This should map to REAL*8 on most modern processors
  INTEGER, PARAMETER :: real_kind_15 = SELECTED_REAL_KIND(Fortran_REAL_8)

  LOGICAL            :: avail
  INTEGER :: flags, filter_info, filter_info_both, filter_id


  CHARACTER(LEN=18), PARAMETER :: filename     = "hdfParticleType.h5"
  CHARACTER(LEN=3) , PARAMETER :: dataset      = "DS1"
  INTEGER          , PARAMETER :: ntsteps    = 100
  INTEGER          , PARAMETER :: nparticles = 100
  INTEGER          , PARAMETER :: chunk0     = 10
  INTEGER          , PARAMETER :: chunk1     = 10
  !INTEGER          , PARAMETER :: maxstringlen = 80
  INTEGER          , PARAMETER :: rank2        = 2
  INTEGER          , PARAMETER :: rank1        = 1
  
  INTEGER          , PARAMETER :: compression_level      = 9 ! http://www.hdfgroup.org/HDF5/doc/RM/RM_H5P.html#Property-SetDeflate
  INTEGER          , PARAMETER :: pixels_per_block      = 12 ! http://www.hdfgroup.org/HDF5/doc/RM/H5P/H5Pset_szip.htm
  
  
  TYPE sensor_t ! Compound data type
     INTEGER :: serial_no
     !CHARACTER(LEN=maxstringlen) :: location
     REAL(real_kind_15) :: temperature
     REAL(real_kind_15) :: pressure
  END TYPE sensor_t

  TYPE(sensor_t), DIMENSION(1:nparticles), TARGET ::  wdata ! Write buffer
  TYPE(sensor_t), DIMENSION(1:nparticles), TARGET ::  rdata ! Read buffer
  INTEGER(HID_T)  :: file, filetype, memtype, spaceParticles, spaceMemory, dset, strtype, dcplParticles ! Handles
  INTEGER :: hdferr
  INTEGER(HSIZE_T), DIMENSION(1:2)   :: dimParticles = (/nparticles, ntsteps /), &
                                        chunkParticles = (/chunk1, chunk0/)
                                        
  INTEGER(HSIZE_T), DIMENSION(1:2)   :: start2, stride2, count2, block2
  INTEGER(HSIZE_T), DIMENSION(1:1)   :: start1, stride1, count1, block1
  INTEGER(HSIZE_T), Dimension(1:2) :: memSize2
  INTEGER(HSIZE_T), Dimension(1:1) :: memSize1

  
  TYPE(C_PTR) :: f_ptr
  INTEGER :: i
  real*4 :: tic, toc
  !
  ! Initialize FORTRAN interface.
  !
  CALL h5open_f(hdferr)
  
  
  ! SZIP filter check  
  CALL h5zfilter_avail_f(H5Z_FILTER_SZIP_F, avail, hdferr)

  IF (.NOT.avail) THEN
     WRITE(*,'("szip filter not available.",/)')
     STOP
  ENDIF

  CALL h5zget_filter_info_f(H5Z_FILTER_SZIP_F, filter_info, hdferr)

  filter_info_both=IOR(H5Z_FILTER_ENCODE_ENABLED_F,H5Z_FILTER_DECODE_ENABLED_F)
  IF (filter_info .NE. filter_info_both) THEN
     WRITE(*,'("szip filter not available for encoding and decoding.",/)')
     STOP
  ENDIF

  ! GZIP filter check  
  CALL h5zfilter_avail_f(H5Z_FILTER_DEFLATE_F, avail, hdferr)

  IF (.NOT.avail) THEN
     WRITE(*,'("gzip filter not available.",/)')
     STOP
  ENDIF
  CALL h5zget_filter_info_f(H5Z_FILTER_DEFLATE_F, filter_info, hdferr)

  filter_info_both=IOR(H5Z_FILTER_ENCODE_ENABLED_F,H5Z_FILTER_DECODE_ENABLED_F)
  IF (filter_info .NE. filter_info_both) THEN
     WRITE(*,'("gzip filter not available for encoding and decoding.",/)')
     STOP
  ENDIF
  
  
  !
  ! Initialize data.
  !
  call random_seed()
  ! Initialize data arrays with a value
  call random_number(wdata%temperature)
  call random_number(wdata%pressure)
  wdata%serial_no = 0
  
  !
  ! Create a new file using the default properties.
  !
  CALL h5fcreate_f(filename, H5F_ACC_TRUNC_F, file, hdferr)
  !
  ! Create the compound datatype for memory.
  !
  CALL h5tcreate_f(H5T_COMPOUND_F, H5OFFSETOF(C_LOC(wdata(1)), C_LOC(wdata(2))), memtype, hdferr)
  CALL h5tinsert_f(memtype, "Serial number", &
       H5OFFSETOF(C_LOC(wdata(1)),C_LOC(wdata(1)%serial_no)), H5T_NATIVE_INTEGER, hdferr)
  !
  ! Create datatype for the String attribute.
  !
  !CALL h5tcopy_f(H5T_NATIVE_CHARACTER, strtype, hdferr)
  !CALL h5tset_size_f(strtype, INT(maxstringlen,size_t), hdferr)  
  !
  !CALL h5tinsert_f(memtype, "Location", &
  !   H5OFFSETOF(C_LOC(wdata(1)),C_LOC(wdata(1)%location)), strtype, hdferr)

  CALL h5tinsert_f(memtype, "Temperature (F)", &
       H5OFFSETOF(C_LOC(wdata(1)),C_LOC(wdata(1)%temperature)), &
       h5kind_to_type(real_kind_15,H5_REAL_KIND), hdferr)

  CALL h5tinsert_f(memtype, "Pressure (inHg)", &
       H5OFFSETOF(C_LOC(wdata(1)),C_LOC(wdata(1)%pressure)), &
       h5kind_to_type(real_kind_15,H5_REAL_KIND), hdferr)
  !
  ! Create the compound datatype for the file.  Because the standard
  ! types we are using for the file may have different sizes than
  ! the corresponding native types, we must manually calculate the
  ! offset of each member.
  !
  !CALL h5tcreate_f(H5T_COMPOUND_F, INT(8 + maxstringlen + 8 + 8 , size_t), filetype, hdferr)
  CALL h5tcreate_f(H5T_COMPOUND_F, INT(8 + 8 + 8 , size_t), filetype, hdferr)
  
  CALL h5tinsert_f(filetype, "Serial number", 0_size_t, H5T_STD_I64BE, hdferr)

  !CALL h5tinsert_f(filetype, "Location", 8_size_t, strtype, hdferr)

  CALL h5tinsert_f(filetype, "Temperature (F)", INT(8,size_t), &
       H5T_IEEE_F64BE, hdferr)

  CALL h5tinsert_f(filetype, "Pressure (inHg)", INT(8 + 8, size_t), &
       H5T_IEEE_F64BE, hdferr)
  !
  ! Create dataspace.  Set the size to be the current size.
  !
  CALL h5screate_simple_f(rank2, dimParticles, spaceParticles, hdferr)
  
  count1 = (/nparticles/)
  CALL h5screate_simple_f(rank1, count1, spaceMemory, hdferr)
  
  !!!!!  
  ! Create the dataset creation property list, and set the chunk size.
  CALL h5pcreate_f(H5P_DATASET_CREATE_F, dcplParticles, hdferr)
  
  !CALL h5pset_szip_f(dcplParticles, H5_SZIP_NN_OM_F, pixels_per_block, hdferr)
  CALL h5pset_deflate_f(dcplParticles, compression_level, hdferr)

  CALL h5pset_chunk_f(dcplParticles, rank2, chunkParticles, hdferr)
  !!!!
  
  
  !
  ! Create the dataset and write the compound data to it.
  !
  CALL h5dcreate_f(file, dataset, filetype, spaceParticles, dset, hdferr, dcplParticles)
  !CALL h5dcreate_f(file, dataset, filetype, spaceParticles, dset, hdferr)


  

  !
  ! Write the data to the dataset.
  call cpu_time(tic)
  DO i = 1,ntsteps

  start2(1:2) = (/0,i-1/)
    count2(1:2) = (/nParticles,1/)
    CALL h5sselect_hyperslab_f (spaceParticles, H5S_SELECT_SET_F, start2, count2, hdferr)

	wdata%serial_no = wdata%serial_no +1 
    call random_number(wdata%temperature)
    call random_number(wdata%pressure)

    f_ptr = C_LOC(wdata(1))
    CALL h5dwrite_f(dset, memtype, f_ptr, hdferr, mem_space_id=spaceMemory, file_space_id=spaceParticles)

  ENDDO

  call cpu_time(toc)
  print "('Completed dummy data output in ', f10.6,' Seconds')", toc - tic


  !
  ! Close and release resources.
  !
  CALL h5dclose_f(dset, hdferr)
  CALL h5sclose_f(spaceParticles, hdferr)
  CALL h5sclose_f(spaceMemory, hdferr)
  CALL h5tclose_f(filetype, hdferr)
  CALL h5fclose_f(file, hdferr)
  !
  ! Now we begin the read section of this example.
  !
  !
! Open file and dataset.
!
!  CALL h5fopen_f(filename, H5F_ACC_RDONLY_F, file, hdferr)
!  CALL h5dopen_f(file, dataset, dset, hdferr)
!
! Get dataspace.
!
!  CALL h5dget_space_f(dset, space, hdferr)
!  CALL h5sget_simple_extent_dims_f(space, dims, ndims, hdferr)
!
! Read the data.
!
!  f_ptr = C_LOC(rdata(1))
!  CALL h5dread_f(dset, memtype, f_ptr, hdferr)
!
! Output the data to the screen.
!
!  DO i = 1, ndims(1)
!     WRITE(*,'(A,I1,":")') dataset, i
!     WRITE(*,'("Serial number   : ", I6)') rdata(i)%serial_no
!     WRITE(*,'("Location        : ", A)' ) TRIM(rdata(i)%location)
!     WRITE(*,'("Temperature (F) : ", f8.2)') rdata(i)%temperature
!     WRITE(*,'("Pressure (inHg) : ", f8.2)') rdata(i)%pressure
!  END DO
!
! Close and release resources
!
!  CALL h5dclose_f(dset, hdferr)
!  CALL h5sclose_f(space, hdferr)
!  CALL h5tclose_f(strtype, hdferr)
!  CALL h5fclose_f(file, hdferr)

END PROGRAM main