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Convert HDF5 write_attribute to C++
This commit is contained in:
Paul Romano
parent
cc5e99eac4
commit
342d207fc4
3 changed files with 121 additions and 114 deletions
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@ -132,6 +132,34 @@ module hdf5_interface
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logical(C_BOOL), intent(in) :: indep
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end subroutine read_llong_c
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subroutine write_attr_double_c(obj_id, ndim, dims, name, buffer) &
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bind(C, name='write_attr_double')
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import HID_T, HSIZE_T, C_INT, C_DOUBLE, C_CHAR
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integer(HID_T), value :: obj_id
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integer(C_INT), value :: ndim
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integer(HSIZE_T), intent(in) :: dims(*)
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character(kind=C_CHAR), intent(in) :: name(*)
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real(C_DOUBLE), intent(in) :: buffer(*)
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end subroutine write_attr_double_c
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subroutine write_attr_int_c(obj_id, ndim, dims, name, buffer) &
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bind(C, name='write_attr_int')
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import HID_T, HSIZE_T, C_INT, C_CHAR
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integer(HID_T), value :: obj_id
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integer(C_INT), value :: ndim
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integer(HSIZE_T), intent(in) :: dims(*)
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character(kind=C_CHAR), intent(in) :: name(*)
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integer(C_INT), intent(in) :: buffer(*)
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end subroutine write_attr_int_c
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subroutine write_attr_string_c(obj_id, name, buffer) &
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bind(C, name='write_attr_string')
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import HID_T, C_CHAR
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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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character(kind=C_CHAR), intent(in) :: buffer(*)
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end subroutine write_attr_string_c
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subroutine write_double_c(group_id, ndim, dims, name, buffer, indep) &
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bind(C, name='write_double')
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import HID_T, HSIZE_T, C_INT, C_DOUBLE, C_CHAR, C_BOOL
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@ -1141,41 +1169,8 @@ contains
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character(*), intent(in) :: name ! name of attribute
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character(*), intent(in), target :: buffer ! string to write
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integer :: hdf5_err
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integer(HID_T) :: dspace_id
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integer(HID_T) :: attr_id
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integer(HID_T) :: filetype
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integer(SIZE_T) :: i
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integer(SIZE_T) :: n
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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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! Create datatype for HDF5 file based on C char
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n = len_trim(buffer)
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if (n > 0) then
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call h5tcopy_f(H5T_C_S1, filetype, hdf5_err)
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call h5tset_size_f(filetype, n, hdf5_err)
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! Create memory space and attribute
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call h5screate_f(H5S_SCALAR_F, dspace_id, hdf5_err)
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call h5acreate_f(obj_id, trim(name), filetype, dspace_id, &
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attr_id, hdf5_err)
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! Copy string to temporary buffer
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allocate(temp_buffer(n))
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do i = 1, n
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temp_buffer(i) = buffer(i:i)
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end do
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! Write attribute
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f_ptr = c_loc(buffer(1:1))
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call h5awrite_f(attr_id, filetype, f_ptr, hdf5_err)
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! Close attribute
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call h5aclose_f(attr_id, hdf5_err)
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call h5sclose_f(dspace_id, hdf5_err)
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call h5tclose_f(filetype, hdf5_err)
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end if
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call write_attr_string_c(obj_id, to_c_string(name), to_c_string(buffer))
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end subroutine write_attribute_string
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subroutine read_attribute_double(buffer, obj_id, name)
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@ -1198,18 +1193,11 @@ contains
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character(*), intent(in) :: name
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real(8), intent(in), target :: buffer
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integer :: hdf5_err
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integer(HID_T) :: dspace_id
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integer(HID_T) :: attr_id
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type(C_PTR) :: f_ptr
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integer(HSIZE_T) :: dims(0)
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real(C_DOUBLE) :: buffer_(1)
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call h5screate_f(H5S_SCALAR_F, dspace_id, hdf5_err)
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call h5acreate_f(obj_id, trim(name), H5T_NATIVE_DOUBLE, dspace_id, &
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attr_id, hdf5_err)
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f_ptr = c_loc(buffer)
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call h5awrite_f(attr_id, H5T_NATIVE_DOUBLE, f_ptr, hdf5_err)
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call h5aclose_f(attr_id, hdf5_err)
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call h5sclose_f(dspace_id, hdf5_err)
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buffer_(1) = buffer
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call write_attr_double_c(obj_id, 0, dims, to_c_string(name), buffer_)
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end subroutine write_attribute_double
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subroutine read_attribute_double_1D(buffer, obj_id, name)
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@ -1257,30 +1245,10 @@ contains
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integer(HSIZE_T) :: dims(1)
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dims(:) = shape(buffer)
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call write_attribute_double_1D_explicit(obj_id, dims, name, buffer)
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dims(1) = size(buffer)
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call write_attr_double_c(obj_id, 1, dims, to_c_string(name), buffer)
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end subroutine write_attribute_double_1D
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subroutine write_attribute_double_1D_explicit(obj_id, dims, name, buffer)
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integer(HID_T), intent(in) :: obj_id
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integer(HSIZE_T), intent(in) :: dims(1)
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character(*), intent(in) :: name
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real(8), target, intent(in) :: buffer(dims(1))
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integer :: hdf5_err
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integer(HID_T) :: dspace_id
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integer(HID_T) :: attr_id
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type(C_PTR) :: f_ptr
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call h5screate_simple_f(1, dims, dspace_id, hdf5_err)
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call h5acreate_f(obj_id, trim(name), H5T_NATIVE_DOUBLE, dspace_id, &
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attr_id, hdf5_err)
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f_ptr = c_loc(buffer)
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call h5awrite_f(attr_id, H5T_NATIVE_DOUBLE, f_ptr, hdf5_err)
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call h5aclose_f(attr_id, hdf5_err)
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call h5sclose_f(dspace_id, hdf5_err)
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end subroutine write_attribute_double_1D_explicit
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subroutine read_attribute_double_2D(buffer, obj_id, name)
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real(8), target, allocatable, intent(inout) :: buffer(:,:)
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integer(HID_T), intent(in) :: obj_id
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@ -1339,18 +1307,11 @@ contains
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character(*), intent(in) :: name
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integer, intent(in), target :: buffer
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integer :: hdf5_err
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integer(HID_T) :: dspace_id
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integer(HID_T) :: attr_id
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type(C_PTR) :: f_ptr
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integer(HSIZE_T) :: dims(0)
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integer(C_INT) :: buffer_(1)
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call h5screate_f(H5S_SCALAR_F, dspace_id, hdf5_err)
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call h5acreate_f(obj_id, trim(name), H5T_NATIVE_INTEGER, dspace_id, &
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attr_id, hdf5_err)
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f_ptr = c_loc(buffer)
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call h5awrite_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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call h5sclose_f(dspace_id, hdf5_err)
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buffer_(1) = buffer
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call write_attr_int_c(obj_id, 0, dims, to_c_string(name), buffer_)
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end subroutine write_attribute_integer
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subroutine read_attribute_integer_1D(buffer, obj_id, name)
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@ -1398,30 +1359,10 @@ contains
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integer(HSIZE_T) :: dims(1)
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dims(:) = shape(buffer)
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call write_attribute_integer_1D_explicit(obj_id, dims, name, buffer)
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dims(1) = size(buffer)
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call write_attr_int_c(obj_id, 1, dims, to_c_string(name), buffer)
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end subroutine write_attribute_integer_1D
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subroutine write_attribute_integer_1D_explicit(obj_id, dims, name, buffer)
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integer(HID_T), intent(in) :: obj_id
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integer(HSIZE_T), intent(in) :: dims(1)
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character(*), intent(in) :: name
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integer, target, intent(in) :: buffer(dims(1))
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integer :: hdf5_err
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integer(HID_T) :: dspace_id
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integer(HID_T) :: attr_id
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type(C_PTR) :: f_ptr
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call h5screate_simple_f(1, dims, dspace_id, hdf5_err)
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call h5acreate_f(obj_id, trim(name), H5T_NATIVE_INTEGER, dspace_id, &
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attr_id, hdf5_err)
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f_ptr = c_loc(buffer)
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call h5awrite_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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call h5sclose_f(dspace_id, hdf5_err)
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end subroutine write_attribute_integer_1D_explicit
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subroutine read_attribute_integer_2D(buffer, obj_id, name)
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integer, target, allocatable, intent(inout) :: buffer(:,:)
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integer(HID_T), intent(in) :: obj_id
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@ -161,7 +161,7 @@ open_group(hid_t group_id, const char* name)
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void
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read_data(hid_t obj_id, const char* name, hid_t mem_type_id,
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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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{
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hid_t dset = obj_id;
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@ -191,27 +191,84 @@ read_data(hid_t obj_id, const char* name, hid_t mem_type_id,
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void
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read_double(hid_t obj_id, const char* name, double* buffer, bool indep)
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{
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read_data(obj_id, name, H5T_NATIVE_DOUBLE, buffer, indep);
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read_dataset(obj_id, name, H5T_NATIVE_DOUBLE, buffer, indep);
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}
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void
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read_int(hid_t obj_id, const char* name, int* buffer, bool indep)
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{
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read_data(obj_id, name, H5T_NATIVE_INT, buffer, indep);
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read_dataset(obj_id, name, H5T_NATIVE_INT, buffer, indep);
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}
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void
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read_llong(hid_t obj_id, const char* name, long long* buffer, bool indep)
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{
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read_data(obj_id, name, H5T_NATIVE_LLONG, buffer, indep);
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read_dataset(obj_id, name, H5T_NATIVE_LLONG, buffer, indep);
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}
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void
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write_data(hid_t group_id, int ndim, const hsize_t* dims, const char* name,
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hid_t mem_type_id, const void* buffer, bool indep)
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write_attr(hid_t obj_id, int ndim, const hsize_t* dims, const char* name,
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hid_t mem_type_id, const void* buffer)
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{
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// If array is given, create a simple dataspace. Otherwise, create a scalar
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// datascape.
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hid_t dspace;
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if (ndim > 0) {
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dspace = H5Screate_simple(ndim, dims, nullptr);
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} else {
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dspace = H5Screate(H5S_SCALAR);
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}
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// Create attribute and Write data
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hid_t attr = H5Acreate(obj_id, name, mem_type_id, dspace,
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H5P_DEFAULT, H5P_DEFAULT);
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H5Awrite(attr, mem_type_id, buffer);
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// Free resources
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H5Aclose(attr);
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H5Sclose(dspace);
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}
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void
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write_attr_double(hid_t obj_id, int ndim, const hsize_t* dims, const char* name,
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const double* buffer)
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{
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write_attr(obj_id, ndim, dims, name, H5T_NATIVE_DOUBLE, buffer);
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}
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void
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write_attr_int(hid_t obj_id, int ndim, const hsize_t* dims, const char* name,
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const int* buffer)
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{
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write_attr(obj_id, ndim, dims, name, H5T_NATIVE_INT, buffer);
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}
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void
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write_attr_string(hid_t obj_id, const char* name, const char* buffer)
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{
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size_t n = strlen(buffer);
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if (n > 0) {
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// Set up appropriate datatype for a fixed-length string
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hid_t datatype = H5Tcopy(H5T_C_S1);
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H5Tset_size(datatype, n);
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write_attr(obj_id, 0, nullptr, name, datatype, buffer);
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// Free resources
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H5Tclose(datatype);
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}
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}
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void
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write_dataset(hid_t group_id, int ndim, const hsize_t* dims, const char* name,
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hid_t mem_type_id, const void* buffer, bool indep)
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{
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// If array is given, create a simple dataspace. Otherwise, create a scalar
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// datascape.
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@ -252,7 +309,7 @@ void
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write_double(hid_t group_id, int ndim, const hsize_t* dims, const char* name,
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const double* buffer, bool indep)
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{
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write_data(group_id, ndim, dims, name, H5T_NATIVE_DOUBLE, buffer, indep);
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write_dataset(group_id, ndim, dims, name, H5T_NATIVE_DOUBLE, buffer, indep);
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}
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@ -260,7 +317,7 @@ void
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write_int(hid_t group_id, int ndim, const hsize_t* dims, const char* name,
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const int* buffer, bool indep)
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{
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write_data(group_id, ndim, dims, name, H5T_NATIVE_INT, buffer, indep);
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write_dataset(group_id, ndim, dims, name, H5T_NATIVE_INT, buffer, indep);
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}
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@ -268,7 +325,7 @@ void
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write_llong(hid_t group_id, int ndim, const hsize_t* dims, const char* name,
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const long long* buffer, bool indep)
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{
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write_data(group_id, ndim, dims, name, H5T_NATIVE_LLONG, buffer, indep);
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write_dataset(group_id, ndim, dims, name, H5T_NATIVE_LLONG, buffer, indep);
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}
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@ -281,7 +338,7 @@ write_string(hid_t group_id, int ndim, const hsize_t* dims, size_t slen,
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hid_t datatype = H5Tcopy(H5T_C_S1);
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H5Tset_size(datatype, slen);
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write_data(group_id, ndim, dims, name, datatype, buffer, indep);
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write_dataset(group_id, ndim, dims, name, datatype, buffer, indep);
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// Free resources
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H5Tclose(datatype);
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@ -41,8 +41,8 @@ write_double_1D(hid_t group_id, char const *name,
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H5Dclose(dataset);
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}
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void read_data(hid_t obj_id, const char* name, double* buffer,
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hid_t mem_type_id, bool indep);
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void read_dataset(hid_t obj_id, const char* name, double* buffer,
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hid_t mem_type_id, bool indep);
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extern "C" void read_double(hid_t obj_id, const char* name, double* buffer,
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bool indep);
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extern "C" void read_int(hid_t obj_id, const char* name, int* buffer,
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@ -50,8 +50,17 @@ extern "C" void read_int(hid_t obj_id, const char* name, int* buffer,
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extern "C" void read_llong(hid_t obj_id, const char* name, long long* buffer,
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bool indep);
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void write_data(hid_t group_id, int ndim, const hsize_t* dims, const char* name,
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hid_t mem_type_id, const void* buffer, bool indep);
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void write_attr(hid_t obj_id, int ndim, const hsize_t* dims, const char* name,
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hid_t mem_type_id, const void* buffer);
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extern "C" void write_attr_double(hid_t obj_id, int ndim, const hsize_t* dims,
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const char* name, const double* buffer);
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extern "C" void write_attr_int(hid_t obj_id, int ndim, const hsize_t* dims,
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const char* name, const int* buffer);
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extern "C" void write_attr_string(hid_t obj_id, const char* name, const char* buffer);
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void write_dataset(hid_t group_id, int ndim, const hsize_t* dims, const char* name,
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hid_t mem_type_id, const void* buffer, bool indep);
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extern "C" void write_double(hid_t group_id, int ndim, const hsize_t* dims,
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const char* name, const double* buffer, bool indep);
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extern "C" void write_int(hid_t group_id, int ndim, const hsize_t* dims,
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