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Convert HDF5 read_attribute_string/logical to C++
This commit is contained in:
Paul Romano
parent
95b05ef02d
commit
c50c6f0700
3 changed files with 81 additions and 96 deletions
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@ -100,6 +100,13 @@ module hdf5_interface
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public :: get_name
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interface
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function attribute_typesize(obj_id, name) result(sz) bind(C)
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import HID_T, C_CHAR, SIZE_T
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integer(HID_T), value :: obj_id
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character(kind=C_CHAR), intent(in) :: name(*)
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integer(SIZE_T) :: sz
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end function attribute_typesize
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function dataset_typesize(dset) result(sz) bind(C)
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import HID_T, SIZE_T
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integer(HID_T), value :: dset
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@ -149,6 +156,15 @@ module hdf5_interface
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real(C_DOUBLE), intent(out) :: buffer(*)
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end subroutine read_attr_double_c
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subroutine read_attr_string_c(obj_id, name, slen, buffer) &
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bind(C, name='read_attr_string')
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import HID_T, C_CHAR, C_SIZE_T
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integer(HID_T), value :: obj_id
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character(kind=C_CHAR), intent(in) :: name(*)
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integer(C_SIZE_T), value :: slen
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character(kind=C_CHAR), intent(out) :: buffer(*)
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end subroutine read_attr_string_c
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subroutine read_int_c(obj_id, name, buffer, indep) &
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bind(C, name='read_int')
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import HID_T, C_INT, C_BOOL, C_PTR
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@ -1290,44 +1306,22 @@ contains
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integer(HID_T), intent(in) :: obj_id
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character(*), intent(in) :: name ! name for data
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integer :: hdf5_err
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integer(HID_T) :: attr_id ! data set handle
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integer(HID_T) :: filetype
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integer(HID_T) :: memtype
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integer(SIZE_T) :: i
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integer(SIZE_T) :: size
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character(kind=C_CHAR), allocatable, target :: temp_buffer(:)
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type(c_ptr) :: f_ptr
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integer(C_SIZE_T) :: i, n
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character(kind=C_CHAR), allocatable, target :: buffer_(:)
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! Get dataset and dataspace
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call h5aopen_f(obj_id, trim(name), attr_id, hdf5_err)
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! Allocate a C char array to get string
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n = attribute_typesize(obj_id, to_c_string(name))
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allocate(buffer_(n))
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! Make sure buffer is large enough
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call h5aget_type_f(attr_id, filetype, hdf5_err)
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call h5tget_size_f(filetype, size, hdf5_err)
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allocate(temp_buffer(size))
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if (size > len(buffer)) then
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call fatal_error("Character buffer is not long enough to &
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&read HDF5 string.")
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end if
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! Read attribute
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call read_attr_string_c(obj_id, to_c_string(name), n, buffer_)
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! Get datatype in memory based on Fortran character
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call h5tcopy_f(H5T_C_S1, memtype, hdf5_err)
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call h5tset_size_f(memtype, size + 1, hdf5_err)
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! Get pointer to start of string
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f_ptr = c_loc(temp_buffer(1))
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call h5aread_f(attr_id, memtype, f_ptr, hdf5_err)
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! Copy back to Fortran string
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buffer = ''
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do i = 1, size
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if (temp_buffer(i) == C_NULL_CHAR) cycle
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buffer(i:i) = temp_buffer(i)
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do i = 1, n
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if (buffer_(i) == C_NULL_CHAR) cycle
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buffer(i:i) = buffer_(i)
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end do
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call h5aclose_f(attr_id, hdf5_err)
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call h5tclose_f(filetype, hdf5_err)
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call h5tclose_f(memtype, hdf5_err)
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end subroutine read_attribute_string
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subroutine read_attribute_string_1D(buffer, obj_id, name)
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@ -1335,82 +1329,43 @@ contains
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integer(HID_T), intent(in) :: obj_id
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character(*), intent(in) :: name
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integer :: hdf5_err
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integer(HID_T) :: space_id
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integer(HID_T) :: attr_id
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integer(C_SIZE_T) :: i, j, k, n, m
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integer(HSIZE_T) :: dims(1)
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integer(HSIZE_T) :: maxdims(1)
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character(kind=C_CHAR), allocatable, target :: buffer_(:)
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call h5aopen_f(obj_id, trim(name), attr_id, hdf5_err)
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if (allocated(buffer)) then
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dims(:) = shape(buffer)
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else
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call h5aget_space_f(attr_id, space_id, hdf5_err)
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call h5sget_simple_extent_dims_f(space_id, dims, maxdims, hdf5_err)
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if (.not. allocated(buffer)) then
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call get_shape_attr(obj_id, to_c_string(name), dims)
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allocate(buffer(dims(1)))
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call h5sclose_f(space_id, hdf5_err)
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end if
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call read_attribute_string_1D_explicit(attr_id, dims, buffer)
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call h5aclose_f(attr_id, hdf5_err)
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! Allocate a C char array to get strings
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n = attribute_typesize(obj_id, to_c_string(name))
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m = size(buffer)
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allocate(buffer_(n*m))
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! Read attribute
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call read_attr_string_c(obj_id, to_c_string(name), n, buffer_)
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! Convert null-terminated C strings into Fortran strings
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do i = 1, m
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buffer(i) = ''
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do j = 1, n
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k = (i-1)*n + j
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if (buffer_(k) == C_NULL_CHAR) exit
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buffer(i)(j:j) = buffer_(k)
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end do
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end do
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end subroutine read_attribute_string_1D
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subroutine read_attribute_string_1D_explicit(attr_id, dims, buffer)
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integer(HID_T), intent(in) :: attr_id
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integer(HSIZE_T), intent(in) :: dims(1)
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character(*), target, intent(inout) :: buffer(dims(1))
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integer :: hdf5_err
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integer(HID_T) :: filetype
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integer(HID_T) :: memtype
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integer(SIZE_T) :: size
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integer(SIZE_T) :: n
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type(c_ptr) :: f_ptr
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! Make sure buffer is large enough
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call h5aget_type_f(attr_id, filetype, hdf5_err)
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call h5tget_size_f(filetype, size, hdf5_err)
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if (size > len(buffer(1)) + 1) then
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call fatal_error("Character buffer is not long enough to &
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&read HDF5 string array.")
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end if
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! Get datatype in memory based on Fortran character
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n = len(buffer(1))
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call h5tcopy_f(H5T_FORTRAN_S1, memtype, hdf5_err)
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call h5tset_size_f(memtype, n, hdf5_err)
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! Get pointer to start of string
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f_ptr = c_loc(buffer(1)(1:1))
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call h5aread_f(attr_id, memtype, f_ptr, hdf5_err)
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call h5tclose_f(filetype, hdf5_err)
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call h5tclose_f(memtype, hdf5_err)
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end subroutine read_attribute_string_1D_explicit
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subroutine read_attribute_logical(buffer, obj_id, name)
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logical, intent(inout), target :: buffer
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integer(HID_T), intent(in) :: obj_id
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character(*), intent(in) :: name
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integer, target :: int_buffer
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integer :: hdf5_err
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integer(HID_T) :: attr_id
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type(c_ptr) :: f_ptr
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integer :: tmp
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call h5aopen_f(obj_id, trim(name), attr_id, hdf5_err)
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f_ptr = c_loc(int_buffer)
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call h5aread_f(attr_id, H5T_NATIVE_INTEGER, f_ptr, hdf5_err)
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call h5aclose_f(attr_id, hdf5_err)
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! Convert to Fortran logical
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if (int_buffer == 0) then
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buffer = .false.
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else
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buffer = .true.
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end if
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call read_attribute_integer(tmp, obj_id, name)
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buffer = (tmp /= 0)
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end subroutine read_attribute_logical
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subroutine get_shape(obj_id, dims)
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@ -19,6 +19,18 @@ attribute_exists(hid_t obj_id, const char* name)
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}
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size_t
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attribute_typesize(hid_t obj_id, const char* name)
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{
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hid_t attr = H5Aopen(obj_id, name, H5P_DEFAULT);
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hid_t filetype = H5Aget_type(attr);
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size_t n = H5Tget_size(filetype);
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H5Tclose(filetype);
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H5Aclose(attr);
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return n;
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}
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bool
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using_mpio_device(hid_t obj_id)
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{
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@ -238,6 +250,21 @@ read_attr_int(hid_t obj_id, const char* name, int* buffer)
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}
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void
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read_attr_string(hid_t obj_id, const char* name, size_t slen, char* buffer)
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{
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// Create datatype for a string
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hid_t datatype = H5Tcopy(H5T_C_S1);
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H5Tset_size(datatype, slen + 1);
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// Read data into buffer
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read_attr(obj_id, name, datatype, buffer);
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// Free resources
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H5Tclose(datatype);
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}
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void
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read_dataset(hid_t obj_id, const char* name, hid_t mem_type_id,
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void* buffer, bool indep)
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@ -13,6 +13,7 @@
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namespace openmc {
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extern "C" bool attribute_exists(hid_t obj_id, const char* name);
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extern "C" size_t attribute_typesize(hid_t obj_id, const char* name);
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extern "C" hid_t create_group(hid_t parent_id, const char* name);
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hid_t create_group(hid_t parent_id, const std::string& name);
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extern "C" void close_dataset(hid_t dataset_id);
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@ -51,6 +52,8 @@ void read_attr(hid_t obj_id, const char* name, hid_t mem_type_id,
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const void* buffer);
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extern "C" void read_attr_double(hid_t obj_id, const char* name, double* buffer);
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extern "C" void read_attr_int(hid_t obj_id, const char* name, int* buffer);
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extern "C" void read_attr_string(hid_t obj_id, const char* name, size_t slen,
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char* buffer);
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void read_dataset(hid_t obj_id, const char* name, hid_t mem_type_id,
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void* buffer, bool indep);
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