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hdf5_utils.f90
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hdf5_utils.f90
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!> \brief A set of high level wrapper subroutines for HDF5
!>
!> \par \b Features:
!> - opening and closing files
!> - creating/opening/closing groups
!> - get rank and dimensions of dataset
!> - reading and writing dataset (integer, real, double)
!> - uses a generic interface to switch on rank and kind
!> - writing/reading attributes (integer, real, double, string)
!> - uses a generic interface to switch on rank and kind
!>
!> \todo
!> - reading and writing ( strings )
!> - hdf_exists (h5o_exist_by_name or h5l_exists)
!> - hdf_get_*
!> - hdf_get_obj_name (h5iget_name_f)
!> - hdf_get_obj_type (h5iget_type_f)
!> - hdf_get_dset_type (H5Dget_type)
!> - hdf_get_obj_id (not needed)
!> - error checking,
!> - check dims when reading
!> - check dataset/attribute name when reading
!> - check group name when reading/writing
!> - stop on error vs return error flag vs global error flag
!>
!> \note I might use H5T_STD_I32LE, H5T_IEEE_F32LE, H5T_IEEE_F64LE instead of H5T_NATIVE_DOUBLE when
!> creating a dataset. This would make the hdf5 file more portable?
!> \note should I support other integer types (ie 16 and 64)? I am not sure if hdf5 fortran supports these
!>
module HDF5_utils
use hdf5
implicit none
private
public :: hdf_open_file, hdf_close_file
public :: hdf_create_group, hdf_open_group, hdf_close_group
public :: hdf_exists, hdf_get_rank, hdf_get_dims
public :: hdf_write_dataset, hdf_read_dataset
public :: hdf_write_attribute, hdf_read_attribute
public :: hdf_create_dataset
public :: hdf_write_vector_to_dataset, hdf_read_vector_from_dataset
public :: HID_T, hdf_set_print_messages, hdf_set_default_filter
!> \brief Generic interface to write a dataset
!>
!> Supported types
!> - integers (scalar and 1d-6d arrays)
!> - doubles (scalar and 1d-6d arrays)
!> - reals (scalar and 1d-6d arrays)
! - string (scalar and 1d-6d arrays)
!>
!> \param[in] loc_id local id in file
!> \param[in] dset_name name of dataset
!> \param[in] array data array to be written
!> \param[in] chunks (optional) chunk size for dataset
!> \param[in] filter (optional) filter to use ('none', 'szip', 'gzip', 'gzip+shuffle')
interface hdf_write_dataset
module procedure hdf_write_dataset_integer_0
module procedure hdf_write_dataset_integer_1
module procedure hdf_write_dataset_integer_2
module procedure hdf_write_dataset_integer_3
module procedure hdf_write_dataset_integer_4
module procedure hdf_write_dataset_integer_5
module procedure hdf_write_dataset_integer_6
module procedure hdf_write_dataset_real_0
module procedure hdf_write_dataset_real_1
module procedure hdf_write_dataset_real_2
module procedure hdf_write_dataset_real_3
module procedure hdf_write_dataset_real_4
module procedure hdf_write_dataset_real_5
module procedure hdf_write_dataset_real_6
module procedure hdf_write_dataset_double_0
module procedure hdf_write_dataset_double_1
module procedure hdf_write_dataset_double_2
module procedure hdf_write_dataset_double_3
module procedure hdf_write_dataset_double_4
module procedure hdf_write_dataset_double_5
module procedure hdf_write_dataset_double_6
end interface hdf_write_dataset
!> \brief Generic interface to write a vector to dataset
!>
!> The vector is is written out in along the fast dimension
!> (column oriented in FORTRAN, row oriented in the HDF5 file).
!> So the vector should have the same length as the first dimension
!> of the dataset, and the offset should agree with dims(2:rank) of
!> of the dataset.
!>
!> Supported types
!> - integers (scalar and 1d-6d arrays)
!> - doubles (scalar and 1d-6d arrays)
!> - reals (scalar and 1d-6d arrays)
! - string (scalar and 1d-6d arrays)
!>
!> \param[in] loc_d local id in file
!> \param[in] dset_name name of dataset
!> \param[in] offset position within the dataset
!> \param[in] vector data array to be written
interface hdf_write_vector_to_dataset
module procedure hdf_write_vector_to_dataset_integer
module procedure hdf_write_vector_to_dataset_real
module procedure hdf_write_vector_to_dataset_double
end interface hdf_write_vector_to_dataset
!> \brief Generic interface to read a dataset of doubles
!>
!> Supported types
!> - integers (scalar and 1d-6d arrays)
!> - doubles (scalar and 1d-6d arrays)
!> - reals (scalar and 1d-6d arrays)
! - string (scalar and 1d-6d arrays)
!>
!> \param[in] loc_d local id in file
!> \param[in] dset_name name of dataset
!> \param[out] array data array to be read
interface hdf_read_dataset
module procedure hdf_read_dataset_integer_0
module procedure hdf_read_dataset_integer_1
module procedure hdf_read_dataset_integer_2
module procedure hdf_read_dataset_integer_3
module procedure hdf_read_dataset_integer_4
module procedure hdf_read_dataset_integer_5
module procedure hdf_read_dataset_integer_6
module procedure hdf_read_dataset_real_0
module procedure hdf_read_dataset_real_1
module procedure hdf_read_dataset_real_2
module procedure hdf_read_dataset_real_3
module procedure hdf_read_dataset_real_4
module procedure hdf_read_dataset_real_5
module procedure hdf_read_dataset_real_6
module procedure hdf_read_dataset_double_0
module procedure hdf_read_dataset_double_1
module procedure hdf_read_dataset_double_2
module procedure hdf_read_dataset_double_3
module procedure hdf_read_dataset_double_4
module procedure hdf_read_dataset_double_5
module procedure hdf_read_dataset_double_6
end interface hdf_read_dataset
!> \brief Generic interface to read a vector from a dataset
!>
!> The vector is is read in along the fast dimension
!> (column oriented in FORTRAN, row oriented in the HDF5 file).
!> So the vector should have the same length as the first dimension
!> of the dataset, and the offset should agree with dims(2:rank) of
!> of the dataset.
!>
!> Supported types
!> - integers (scalar and 1d-6d arrays)
!> - doubles (scalar and 1d-6d arrays)
!> - reals (scalar and 1d-6d arrays)
! - string (scalar and 1d-6d arrays)
!>
!> \param[in] loc_d local id in file
!> \param[in] dset_name name of dataset
!> \param[in] offset position within the dataset
!> \param[out] vector data array to be written
interface hdf_read_vector_from_dataset
module procedure hdf_read_vector_from_dataset_integer
module procedure hdf_read_vector_from_dataset_real
module procedure hdf_read_vector_from_dataset_double
end interface hdf_read_vector_from_dataset
!> \brief Generic interface to write attribute
!>
!> Supported types
!> - integers (scalar and 1d arrays)
!> - reals (scalar and 1d arrays)
!> - doubles (scalar and 1d arrays)
!> - string (1d array of characters)
!>
!> \param[in] loc_id local id in file
!> \param[in] obj_name name of object to be attached to (if left blank, just use loc_id)
!> \param[in] attr_name name of attribute to be added
!> \param[in] array attribute data to be written
interface hdf_write_attribute
module procedure hdf_write_attr_integer_0
module procedure hdf_write_attr_integer_1
module procedure hdf_write_attr_real_0
module procedure hdf_write_attr_real_1
module procedure hdf_write_attr_double_0
module procedure hdf_write_attr_double_1
module procedure hdf_write_attr_string
end interface hdf_write_attribute
!> \brief Generic interface to read attribute
!>
!> Supported types
!> - integers (scalar and 1d arrays)
!> - reals (scalar and 1d arrays)
!> - doubles (scalar and 1d arrays)
!> - string (1d array of characters)
!>
!> \param[in] loc_id local id in file
!> \param[in] obj_name name of object to be attached to (if left blank, just use loc_id)
!> \param[in] attr_name name of attribute to be added
!> \param[in] array attribute data to be written
interface hdf_read_attribute
module procedure hdf_read_attr_integer_0
module procedure hdf_read_attr_integer_1
module procedure hdf_read_attr_real_0
module procedure hdf_read_attr_real_1
module procedure hdf_read_attr_double_0
module procedure hdf_read_attr_double_1
module procedure hdf_read_attr_string
end interface hdf_read_attribute
! precision for this file
integer, parameter :: sp = kind(1.0) ! single precision
integer, parameter :: dp = kind(1.0d0) ! double precision
!
logical :: hdf_print_messages = .false.
!
character(len=32) :: hdf_default_filter = 'none'
integer :: hdf_gzip_level = 6 ! 0-9
integer :: hdf_szip_pixels_per_block = 8 ! should be even number less than 32 (https://portal.hdfgroup.org/display/HDF5/H5P_SET_SZIP)
character(len=2) :: hdf_szip_options = 'NN' ! H5_SZIP_NN_OM_F or H5_SZIP_EC_OM_F
contains
!> \brief Sets the value of hdf_print_messages
!>
!> By default, hdf_print_messages = .false. By setting it
!> to .true., some messages are printed detailing what hdf_utils
!> is doing.
subroutine hdf_set_print_messages(val_print_messages)
logical, intent(in) :: val_print_messages !< new value for hdf_print_messages
hdf_print_messages = val_print_messages
end subroutine hdf_set_print_messages
!> \brief Sets the value of hdf_print_messages
!>
!>
subroutine hdf_set_default_filter(filter, gzip_level, szip_pixels_per_block, szip_options)
character(len=*), intent(in) :: filter !< new value for hdf_print_messages
integer, optional, intent(in) :: gzip_level
integer, optional, intent(in) :: szip_pixels_per_block
character(len=2), optional, intent(in) :: szip_options
hdf_default_filter = filter
if (present(gzip_level)) then
hdf_gzip_level = gzip_level
endif
if(present(szip_pixels_per_block)) then
hdf_szip_pixels_per_block = szip_pixels_per_block
endif
if (present(szip_options)) then
!hdf_szip_options = szip_options
if (szip_options == 'NN') then
hdf_szip_options = 'NN'
elseif (szip_options == 'EC') then
hdf_szip_options = 'EC'
else
write(*,'(A)') "-->hdf_set_default_filter: warning szip_options "//trim(szip_options)//" not recognized"
stop
endif
endif
!write(*,'(A,I0,A,I0)') ' H5_SZIP_NN_OM_F=', H5_SZIP_NN_OM_F, ', H5_SZIP_EC_OM_F=', H5_SZIP_EC_OM_F
write(*,*) filter, gzip_level, szip_pixels_per_block, szip_options
end subroutine hdf_set_default_filter
!> \brief Check if location exists.
!>
!> Also checks is intemediate paths exists in a safe way.
function hdf_exists(loc_id, obj_name) result(exists)
integer(HID_T), intent(in) :: loc_id !< local id
character(len=*), intent(in) :: obj_name !< relative path to object
logical :: exists !< .TRUE. if everything exists, .FALSE. otherwise
integer :: hdferror, pos, cpos, str_len
if (hdf_print_messages) then
write(*,'(A,A)') "->hdf_exists: " // obj_name
end if
! check intermediate paths (subgroups)
str_len = len_trim(obj_name)
cpos = 0
do
!start = cpos + 1
!write(*,*) start, str_len, obj_name(start:str_len)
pos = index(obj_name(cpos+1:str_len), "/")
! no subgroup found
if (pos == 0) exit
! check subgroup
cpos = cpos + pos
call h5lexists_f(loc_id, obj_name(1:cpos-1), exists, hdferror)
!write(*,*) obj_name(1:cpos-1), exists
! return if intermediate path fails
if (exists .eqv. .false.) then
if (hdf_print_messages) then
write(*,'(A,A,A)') "--->hdf_exists: subpath '", obj_name(1:cpos-1), "' does not exist, return false"
end if
exists = .false.
return
end if
end do
! check object (unless obj_name ended with "/"
if (cpos /= str_len) then
call h5lexists_f(loc_id, obj_name, exists, hdferror)
!write(*,*) obj_name, exists
if (exists .eqv. .false.) then
if (hdf_print_messages) then
write(*,'(A,A,A)') "--->hdf_exists: object '", obj_name, "' does not exist, return false"
end if
exists = .false.
return
end if
end if
exists = .true.
return
end function hdf_exists
!> \brief Opens file and return identifier
!>
!> \todo
!> - case insentive STATUS and ACTION
!> - delete file for REPLACE case
!>
!> | STATUS | ACTION | Description |
!> | :-----: | :-------: | :----------------------------------- |
!> | NEW | na | calls h5fcreate with H5F_ACC_TRUNC_F |
!> | REPLACE | na | calls h5fcreate with H5F_ACC_EXCL_F |
!> | OLD | READ | calls h5fopen with H5F_ACC_RDONLY_F |
!> | OLD | WRITE | calls h5fopen with H5F_ACC_RDWR_F |
!> | OLD | READWRITE | calls h5fopen with H5F_ACC_RDWR_F |
!>
subroutine hdf_open_file(file_id, filename, STATUS, ACTION)
integer(HID_T), intent(out) :: file_id !< HDF5 id of the file
character(len=*), intent(in) :: filename !< the HDF5 filename
character(len=*), optional, intent(in) :: STATUS !< file status (OLD, NEW, REPLACE)
character(len=*), optional, intent(in) :: ACTION !< file action (READ, WRITE, READWRITE)
integer :: hdferror
character(len=16) :: status2, action2
if (hdf_print_messages) then
write(*,'(A)') "->hdf_open_file: " // trim(filename)
end if
! open hdf5 interface
call h5open_f(hdferror)
!write(*,'(A20,I0)') "h5open: ", hdferror
! set defaults
status2 = 'NEW'
if (present(STATUS)) status2 = STATUS
action2 = 'READWRITE'
if (present(STATUS)) action2 = ACTION
! open/create hdf5 file
if (status2 == 'OLD') then
if (action2 == 'READ') then
call h5fopen_f(filename, H5F_ACC_RDONLY_F, file_id, hdferror)
elseif ( (action2 == 'WRITE') .or. (action2 == 'READWRITE') ) then
call h5fopen_f(filename, H5F_ACC_RDWR_F, file_id, hdferror)
else
write(*,*) "hdf_open: action = ", action2, " not supported."
stop
end if
elseif (status2 == 'NEW') then
call h5fcreate_f(filename, H5F_ACC_TRUNC_F, file_id, hdferror)
elseif (status2 == 'REPLACE') then
call system("rm -f " // filename)
call h5fcreate_f(filename, H5F_ACC_EXCL_F, file_id, hdferror)
else
write(*,*) "hdf_open: status = ", status2, " not supported."
stop
end if
!write(*,'(A20,I0)') "h5fcreate: ", hdferror
end subroutine hdf_open_file
!> \brief Closes a hdf5 file
subroutine hdf_close_file(file_id)
integer(HID_T), intent(in) :: file_id !< file id to be closed
integer :: hdferror
if (hdf_print_messages) then
write(*,'(A)') "->hdf_close_file"
end if
call h5fclose_f(file_id, hdferror)
!write(*,'(A20,I0)') "h5fclose: ", hdferror
call h5close_f(hdferror)
end subroutine hdf_close_file
!> \brief Create a new group
subroutine hdf_create_group(loc_id, group_name)
integer(HID_T), intent(in) :: loc_id !< location id where to put the group
character(len=*), intent(in) :: group_name !< name of the group
integer(HID_T) :: grp_id
integer :: hdferror
if (hdf_print_messages) then
write(*,'(A)') "->hdf_create_group: " // trim(group_name)
end if
call h5gcreate_f(loc_id, group_name, grp_id, hdferror)
!write(*,'(A20,I0)') "h5gcreate: ", hdferror
call h5gclose_f(grp_id, hdferror)
!write(*,'(A20,I0)') "h5gclose: ", hdferror
end subroutine hdf_create_group
!> \brief Opens a group and returns the identifier
subroutine hdf_open_group(loc_id, group_name, group_id)
integer(HID_T), intent(in) :: loc_id !< location id where to put the group
character(len=*), intent(in) :: group_name !< name of the group
integer(HID_T), intent(out) :: group_id !< id for the group
integer :: hdferror
if (hdf_print_messages) then
write(*,'(A,A,A)') "->hdf_open_group: '" // trim(group_name) // "'"
end if
if (hdf_exists(loc_id, group_name)) then
if (hdf_print_messages) then
write(*,'(A,A,A)') "->hdf_open_group: opening group '" // trim(group_name) // "'"
end if
call h5gopen_f(loc_id, group_name, group_id, hdferror)
else
if (hdf_print_messages) then
write(*,'(A,A,A)') "->hdf_open_group: group '" // trim(group_name) // "' does not exist, return with error"
end if
hdferror = -1
end if
end subroutine hdf_open_group
!> \brief Close a group by identifier
subroutine hdf_close_group(group_id)
integer(HID_T), intent(in) :: group_id !< id for the group
integer :: hdferror
if (hdf_print_messages) then
write(*,'(A)') "->hdf_close_group"
end if
call h5gclose_f(group_id, hdferror)
!write(*,'(A20,I0)') "h5gclose: ", hdferror
end subroutine hdf_close_group
!> \brief Get the rank of a dataset
subroutine hdf_get_rank(loc_id, dset_name, rank)
integer(HID_T), intent(in) :: loc_id !< location id
character(len=*), intent(in) :: dset_name !< dataset name
integer, intent(out) :: rank !< rank of the dataset
integer(HID_T) :: dset_id, dspace_id
integer :: hdferror
if (hdf_print_messages) then
write(*,'(A)') "->hdf_get_rank"
end if
! open dataset
call h5dopen_f(loc_id, dset_name, dset_id, hdferror)
! get dataspace
call h5dget_space_f(dset_id, dspace_id, hdferror)
! get rank (ndims)
call h5sget_simple_extent_ndims_f(dspace_id, rank, hdferror)
! close id's
call h5sclose_f(dspace_id, hdferror)
call h5dclose_f(dset_id, hdferror)
end subroutine hdf_get_rank
!> \brief get the dimensions of a dataset
subroutine hdf_get_dims(loc_id, dset_name, dims)
integer(HID_T), intent(in) :: loc_id !< location id
character(len=*), intent(in) :: dset_name !< name of dataset
integer, intent(out) :: dims(:) !< dimensions of the dataset
integer(HID_T) :: dset_id, dspace_id
integer :: rank
integer(HSIZE_T) :: dset_dims(6), max_dims(6)
integer :: hdferror
if (hdf_print_messages) then
write(*,'(A)') "->hdf_get_dims"
end if
! open dataset
call h5dopen_f(loc_id, dset_name, dset_id, hdferror)
! get dataspace
call h5dget_space_f(dset_id, dspace_id, hdferror)
! get rank (ndims)
call h5sget_simple_extent_ndims_f(dspace_id, rank, hdferror)
! get dims
call h5sget_simple_extent_dims_f(dspace_id, dset_dims(1:rank), max_dims(1:rank), hdferror)
dims(1:rank) = int(dset_dims(1:rank))
! close id's
call h5sclose_f(dspace_id, hdferror)
call h5dclose_f(dset_id, hdferror)
end subroutine hdf_get_dims
! - hdf_get_kind (H5Dget_type)
!!----------------------------------------------------------------------------------------
!!--------------------------------hdf_write_vector_to_dataset-----------------------------
!!----------------------------------------------------------------------------------------
!> \brief create a dataset 'dset_name' with shape 'dset_dims' of type 'dset_type'
subroutine hdf_create_dataset(loc_id, dset_name, dset_dims, dset_type)
integer(HID_T), intent(in) :: loc_id !< local id in file
character(len=*), intent(in) :: dset_name !< name of dataset
integer, intent(in) :: dset_dims(:) !< dimensions of the dataset
character(len=*), intent(in) :: dset_type !< type of dataset (integer or double)
integer :: rank
integer(SIZE_T) :: dims(8)
integer(HID_T) :: dset_id, dspace_id
integer :: hdferror
if (hdf_print_messages) then
write(*,'(A)') "--->hdf_create_dataset: " // trim(dset_name)
end if
! set rank and dims
rank = size(dset_dims, 1)
dims(1:rank) = int(dset_dims, SIZE_T)
! create dataspace
call h5screate_simple_f(rank, dims, dspace_id, hdferror)
!write(*,'(A20,I0)') "h5screate_simple: ", hdferror
! create dataset
select case (dset_type)
case('integer')
call h5dcreate_f(loc_id, dset_name, H5T_NATIVE_INTEGER, dspace_id, dset_id, hdferror)
call h5dclose_f(dset_id, hdferror)
case('real')
call h5dcreate_f(loc_id, dset_name, H5T_NATIVE_DOUBLE, dspace_id, dset_id, hdferror)
call h5dclose_f(dset_id, hdferror)
case('double')
call h5dcreate_f(loc_id, dset_name, H5T_NATIVE_DOUBLE, dspace_id, dset_id, hdferror)
call h5dclose_f(dset_id, hdferror)
case default
write(*,'(A,A,A)') "---> ERROR: dset_type ", dset_type," not supported"
end select
! close all id's
call h5sclose_f(dspace_id, hdferror)
end subroutine hdf_create_dataset
!
subroutine hdf_write_vector_to_dataset_integer(loc_id, dset_name, offset, vector)
integer(HID_T), intent(in) :: loc_id ! local id in file
character(len=*), intent(in) :: dset_name ! name of dataset
integer, intent(in) :: offset(:) ! position within dataset
integer, intent(out) :: vector(:) ! data to be written
integer(HID_T) :: dset_id, dspace_id, mspace_id
integer :: rank
integer(HSIZE_T) :: dset_dims(6), max_dims(6), mdims(1)
integer(HSIZE_T) :: hs_count(6), hs_offset(6) ! Hyperslab offset
integer :: hdferror
integer :: i
character(len=32) :: format_string
if (hdf_print_messages) then
write(*,'(A)') "--->hdf_write_vector_to_dataset_integer: " // trim(dset_name)
end if
! open dataset
call h5dopen_f(loc_id, dset_name, dset_id, hdferror)
! get dataspace
call h5dget_space_f(dset_id, dspace_id, hdferror)
! get rank (ndims), and dims
call h5sget_simple_extent_ndims_f(dspace_id, rank, hdferror)
call h5sget_simple_extent_dims_f(dspace_id, dset_dims(1:rank), max_dims(1:rank), hdferror)
! check size and offset
if (size(vector,1) == dset_dims(1)) then
if (all(offset(1:rank-1) <= dset_dims(2:rank)) .and. all(offset(1:rank-1) > 0)) then
! select hyperslab in dataset (note: convert FORTRAN offset to C offset by subtracting 1)
hs_count(1) = dset_dims(1)
hs_count(2:rank) = 1
hs_offset(1) = 0
hs_offset(2:rank) = offset(1:rank-1) - 1
call h5sselect_hyperslab_f(dspace_id, H5S_SELECT_SET_F, hs_offset(1:rank), hs_count(1:rank), hdferror)
! set mspace to a vector
mdims(1) = size(vector,1)
call h5screate_simple_f(1, mdims, mspace_id, hdferror)
! write out vector
call h5dwrite_f(dset_id, H5T_NATIVE_INTEGER, vector, mdims, hdferror, mspace_id, dspace_id)
! close mspace_id
call h5sclose_f(mspace_id, hdferror)
else
write(format_string, '(A,I0,A,I0,A)') '(A,', rank-1, '(I0,A),A,', rank-1, '(I0,A),A)'
write(*,format_string) "--->ERROR: offset=(", (offset(i), ',', i=1,rank-1) , &
"), is not constent with dset_dims(2:rank)=(", (dset_dims(i), ',', i=2,rank),")"
end if
else
write(*,'(A,I0,A,I0)') "--->ERROR: size(vector)=", size(vector), &
", is not constent with dset_dims(1)=", dset_dims(1)
endif
! close id's
call h5sclose_f(dspace_id, hdferror)
call h5dclose_f(dset_id, hdferror)
end subroutine hdf_write_vector_to_dataset_integer
!
subroutine hdf_write_vector_to_dataset_real(loc_id, dset_name, offset, vector)
integer(HID_T), intent(in) :: loc_id ! local id in file
character(len=*), intent(in) :: dset_name ! name of dataset
integer, intent(in) :: offset(:) ! position within dataset
real(sp), intent(in) :: vector(:) ! data to be written
integer(HID_T) :: dset_id, dspace_id, mspace_id
integer :: rank
integer(HSIZE_T) :: dset_dims(6), max_dims(6), mdims(1)
integer(HSIZE_T) :: hs_count(6), hs_offset(6)
integer :: hdferror
integer :: i
character(len=32) :: format_string
if (hdf_print_messages) then
write(*,'(A)') "--->hdf_write_vector_to_dataset_real: " // trim(dset_name)
end if
! open dataset
call h5dopen_f(loc_id, dset_name, dset_id, hdferror)
! get dataspace
call h5dget_space_f(dset_id, dspace_id, hdferror)
! get rank (ndims), and dims
call h5sget_simple_extent_ndims_f(dspace_id, rank, hdferror)
call h5sget_simple_extent_dims_f(dspace_id, dset_dims(1:rank), max_dims(1:rank), hdferror)
! check size and offset
if (size(vector,1) == dset_dims(1)) then
if (all(offset(1:rank-1) <= dset_dims(2:rank)) .and. all(offset(1:rank-1) > 0)) then
! select hyperslab in dataset (note: convert FORTRAN offset to C offset by subtracting 1)
hs_count(1) = dset_dims(1)
hs_count(2:rank) = 1
hs_offset(1) = 0
hs_offset(2:rank) = offset(1:rank-1) - 1
call h5sselect_hyperslab_f(dspace_id, H5S_SELECT_SET_F, hs_offset(1:rank), hs_count(1:rank), hdferror)
! set mspace to a vector
mdims(1) = size(vector,1)
call h5screate_simple_f(1, mdims, mspace_id, hdferror)
! write out vector
call h5dwrite_f(dset_id, H5T_NATIVE_REAL, vector, mdims, hdferror, mspace_id, dspace_id)
! close mspace_id
call h5sclose_f(mspace_id, hdferror)
else
write(format_string, '(A,I0,A,I0,A)') '(A,', rank-1, '(I0,A),A,', rank-1, '(I0,A),A)'
write(*,format_string) "--->ERROR: offset=(", (offset(i), ',', i=1,rank-1) , &
"), is not constent with dset_dims(2:rank)=(", (dset_dims(i), ',', i=2,rank),")"
end if
else
write(*,'(A,I0,A,I0)') "--->ERROR: size(vector)=", size(vector), &
", is not constent with dset_dims(1)=", dset_dims(1)
endif
! close id's
call h5sclose_f(dspace_id, hdferror)
call h5dclose_f(dset_id, hdferror)
end subroutine hdf_write_vector_to_dataset_real
!
subroutine hdf_write_vector_to_dataset_double(loc_id, dset_name, offset, vector)
integer(HID_T), intent(in) :: loc_id ! local id in file
character(len=*), intent(in) :: dset_name ! name of dataset
integer, intent(in) :: offset(:) ! position within dataset
real(dp), intent(in) :: vector(:) ! data to be written
integer(HID_T) :: dset_id, dspace_id, mspace_id
integer :: rank
integer(HSIZE_T) :: dset_dims(6), max_dims(6), mdims(1)
integer(HSIZE_T) :: hs_count(6), hs_offset(6)
integer :: hdferror
integer :: i
character(len=32) :: format_string
if (hdf_print_messages) then
write(*,'(A)') "--->hdf_write_vector_to_dataset_double: " // trim(dset_name)
end if
! open dataset
call h5dopen_f(loc_id, dset_name, dset_id, hdferror)
! get dataspace
call h5dget_space_f(dset_id, dspace_id, hdferror)
! get rank (ndims), and dims
call h5sget_simple_extent_ndims_f(dspace_id, rank, hdferror)
call h5sget_simple_extent_dims_f(dspace_id, dset_dims(1:rank), max_dims(1:rank), hdferror)
! check size and offset
if (size(vector,1) == dset_dims(1)) then
if (all(offset(1:rank-1) <= dset_dims(2:rank)) .and. all(offset(1:rank-1) > 0)) then
! select hyperslab in dataset (note: convert FORTRAN offset to C offset by subtracting 1)
hs_count(1) = dset_dims(1)
hs_count(2:rank) = 1
hs_offset(1) = 0
hs_offset(2:rank) = offset(1:rank-1) - 1
call h5sselect_hyperslab_f(dspace_id, H5S_SELECT_SET_F, hs_offset(1:rank), hs_count(1:rank), hdferror)
! set mspace to a vector
mdims(1) = size(vector,1)
call h5screate_simple_f(1, mdims, mspace_id, hdferror)
! write out vector
call h5dwrite_f(dset_id, H5T_NATIVE_DOUBLE, vector, mdims, hdferror, mspace_id, dspace_id)
! close mspace_id
call h5sclose_f(mspace_id, hdferror)
else
write(format_string, '(A,I0,A,I0,A)') '(A,', rank-1, '(I0,A),A,', rank-1, '(I0,A),A)'
write(*,format_string) "--->ERROR: offset=(", (offset(i), ',', i=1,rank-1) , &
"), is not constent with dset_dims(2:rank)=(", (dset_dims(i), ',', i=2,rank),")"
end if
else
write(*,'(A,I0,A,I0)') "--->ERROR: size(vector)=", size(vector), &
", is not constent with dset_dims(1)=", dset_dims(1)
endif
! close id's
call h5sclose_f(dspace_id, hdferror)
call h5dclose_f(dset_id, hdferror)
end subroutine hdf_write_vector_to_dataset_double
!
subroutine hdf_read_vector_from_dataset_integer(loc_id, dset_name, offset, vector)
integer(HID_T), intent(in) :: loc_id ! local id in file
character(len=*), intent(in) :: dset_name ! name of dataset
integer, intent(in) :: offset(:) ! position within dataset
integer, intent(out) :: vector(:) ! data to be written
integer(HID_T) :: dset_id, dspace_id, mspace_id
integer :: rank
integer(HSIZE_T) :: dset_dims(6), max_dims(6), mdims(1)
integer(HSIZE_T) :: hs_count(6), hs_offset(6) ! Hyperslab offset
integer :: hdferror
integer :: i
character(len=32) :: format_string
if (hdf_print_messages) then
write(*,'(A)') "--->hdf_read_vector_from_dataset_integer: " // trim(dset_name)
end if
! open dataset
call h5dopen_f(loc_id, dset_name, dset_id, hdferror)
! get dataspace
call h5dget_space_f(dset_id, dspace_id, hdferror)
! get rank (ndims), and dims
call h5sget_simple_extent_ndims_f(dspace_id, rank, hdferror)
call h5sget_simple_extent_dims_f(dspace_id, dset_dims(1:rank), max_dims(1:rank), hdferror)
! check size and offset
if (size(vector,1) == dset_dims(1)) then
if (all(offset(1:rank-1) <= dset_dims(2:rank)) .and. all(offset(1:rank-1) > 0)) then
! select hyperslab in dataset (note: convert FORTRAN offset to C offset by subtracting 1)
hs_count(1) = dset_dims(1)
hs_count(2:rank) = 1
hs_offset(1) = 0
hs_offset(2:rank) = offset(1:rank-1) - 1
call h5sselect_hyperslab_f(dspace_id, H5S_SELECT_SET_F, hs_offset(1:rank), hs_count(1:rank), hdferror)
! set mspace to a vector
mdims(1) = size(vector,1)
call h5screate_simple_f(1, mdims, mspace_id, hdferror)
! write out vector
call h5dread_f(dset_id, H5T_NATIVE_INTEGER, vector, mdims, hdferror, mspace_id, dspace_id)
! close mspace_id
call h5sclose_f(mspace_id, hdferror)
else
write(format_string, '(A,I0,A,I0,A)') '(A,', rank-1, '(I0,A),A,', rank-1, '(I0,A),A)'
write(*,format_string) "--->ERROR: offset=(", (offset(i), ',', i=1,rank-1) , &
"), is not constent with dset_dims(2:rank)=(", (dset_dims(i), ',', i=2,rank),")"
end if
else
write(*,'(A,I0,A,I0)') "--->ERROR: size(vector)=", size(vector), &
", is not constent with dset_dims(1)=", dset_dims(1)
endif
! close id's
call h5sclose_f(dspace_id, hdferror)
call h5dclose_f(dset_id, hdferror)
end subroutine hdf_read_vector_from_dataset_integer
!
subroutine hdf_read_vector_from_dataset_real(loc_id, dset_name, offset, vector)
integer(HID_T), intent(in) :: loc_id ! local id in file
character(len=*), intent(in) :: dset_name ! name of dataset
integer, intent(in) :: offset(:) ! position within dataset
real(sp), intent(out) :: vector(:) ! data to be written
integer(HID_T) :: dset_id, dspace_id, mspace_id
integer :: rank
integer(HSIZE_T) :: dset_dims(6), max_dims(6), mdims(1)
integer(HSIZE_T) :: hs_count(6), hs_offset(6)
integer :: hdferror
integer :: i
character(len=32) :: format_string
if (hdf_print_messages) then
write(*,'(A)') "--->hdf_read_vector_from_dataset_real: " // trim(dset_name)
end if
! open dataset
call h5dopen_f(loc_id, dset_name, dset_id, hdferror)
! get dataspace
call h5dget_space_f(dset_id, dspace_id, hdferror)
! get rank (ndims), and dims
call h5sget_simple_extent_ndims_f(dspace_id, rank, hdferror)
call h5sget_simple_extent_dims_f(dspace_id, dset_dims(1:rank), max_dims(1:rank), hdferror)
! check size and offset
if (size(vector,1) == dset_dims(1)) then
if (all(offset(1:rank-1) <= dset_dims(2:rank)) .and. all(offset(1:rank-1) > 0)) then
! select hyperslab in dataset (note: convert FORTRAN offset to C offset by subtracting 1)
hs_count(1) = dset_dims(1)
hs_count(2:rank) = 1
hs_offset(1) = 0
hs_offset(2:rank) = offset(1:rank-1) - 1
call h5sselect_hyperslab_f(dspace_id, H5S_SELECT_SET_F, hs_offset(1:rank), hs_count(1:rank), hdferror)
! set mspace to a vector
mdims(1) = size(vector,1)
call h5screate_simple_f(1, mdims, mspace_id, hdferror)
! write out vector
call h5dwrite_f(dset_id, H5T_NATIVE_REAL, vector, mdims, hdferror, mspace_id, dspace_id)
! close mspace_id
call h5sclose_f(mspace_id, hdferror)
else
write(format_string, '(A,I0,A,I0,A)') '(A,', rank-1, '(I0,A),A,', rank-1, '(I0,A),A)'
write(*,format_string) "--->ERROR: offset=(", (offset(i), ',', i=1,rank-1) , &
"), is not constent with dset_dims(2:rank)=(", (dset_dims(i), ',', i=2,rank),")"
end if
else
write(*,'(A,I0,A,I0)') "--->ERROR: size(vector)=", size(vector), &
", is not constent with dset_dims(1)=", dset_dims(1)
endif
! close id's
call h5sclose_f(dspace_id, hdferror)
call h5dclose_f(dset_id, hdferror)
end subroutine hdf_read_vector_from_dataset_real
!
subroutine hdf_read_vector_from_dataset_double(loc_id, dset_name, offset, vector)
integer(HID_T), intent(in) :: loc_id ! local id in file
character(len=*), intent(in) :: dset_name ! name of dataset
integer, intent(in) :: offset(:) ! position within dataset
real(dp), intent(out) :: vector(:) ! data to be written
integer(HID_T) :: dset_id, dspace_id, mspace_id
integer :: rank
integer(HSIZE_T) :: dset_dims(6), max_dims(6), mdims(1)
integer(HSIZE_T) :: hs_count(6), hs_offset(6)
integer :: hdferror
integer :: i
character(len=32) :: format_string
if (hdf_print_messages) then
write(*,'(A)') "--->hdf_read_vector_from_dataset_double: " // trim(dset_name)
end if
! open dataset
call h5dopen_f(loc_id, dset_name, dset_id, hdferror)
! get dataspace
call h5dget_space_f(dset_id, dspace_id, hdferror)
! get rank (ndims), and dims
call h5sget_simple_extent_ndims_f(dspace_id, rank, hdferror)
call h5sget_simple_extent_dims_f(dspace_id, dset_dims(1:rank), max_dims(1:rank), hdferror)
! check size and offset
if (size(vector,1) == dset_dims(1)) then
if (all(offset(1:rank-1) <= dset_dims(2:rank)) .and. all(offset(1:rank-1) > 0)) then
! select hyperslab in dataset (note: convert FORTRAN offset to C offset by subtracting 1)
hs_count(1) = dset_dims(1)
hs_count(2:rank) = 1
hs_offset(1) = 0
hs_offset(2:rank) = offset(1:rank-1) - 1
call h5sselect_hyperslab_f(dspace_id, H5S_SELECT_SET_F, hs_offset(1:rank), hs_count(1:rank), hdferror)