使用Fortran读取HDF5数据

使用Fortran读取HDF5数据

下面我将介绍如何在Fortran中读取HDF5文件中的各种类型数组数据，包括一维数组、二维数组、元数组和变长数组。

准备工作

首先需要确保系统安装了HDF5库，并且在编译时链接了HDF5库。例如使用gfortran编译时：

gfortran -o hdf5_example hdf5_example.f90 -I/path/to/hdf5/include -L/path/to/hdf5/lib -lhdf5_fortran -lhdf5

基本代码框架

program hdf5_read_exampleuse hdf5implicit none! 声明变量integer :: hdferrinteger(hid_t) :: file_id, dataset_id, dataspace_idinteger(hsize_t), dimension(2) :: dims, maxdimsinteger :: rank! 初始化HDF5库call h5open_f(hdferr)if (hdferr /= 0) thenwrite(*,*) "Error initializing HDF5 library"stopend if! 打开HDF5文件call h5fopen_f("example.h5", H5F_ACC_RDONLY_F, file_id, hdferr)if (hdferr /= 0) thenwrite(*,*) "Error opening HDF5 file"stopend if! 在这里添加读取不同数据集的代码! 关闭文件call h5fclose_f(file_id, hdferr)! 关闭HDF5库call h5close_f(hdferr)
end program hdf5_read_example

1. 读取一维数组

subroutine read_1d_array(file_id)use hdf5implicit noneinteger(hid_t), intent(in) :: file_idinteger :: hdferrinteger(hid_t) :: dataset_idinteger(hsize_t), dimension(1) :: dimsreal, allocatable :: data_1d(:)! 打开数据集call h5dopen_f(file_id, "/1d_array", dataset_id, hdferr)! 获取数据集维度call h5dget_space_f(dataset_id, dataspace_id, hdferr)call h5sget_simple_extent_dims_f(dataspace_id, dims, maxdims, hdferr)! 分配内存allocate(data_1d(dims(1)))! 读取数据call h5dread_f(dataset_id, H5T_NATIVE_REAL, data_1d, dims, hdferr)! 输出数据write(*,*) "1D Array:"write(*,*) data_1d! 清理deallocate(data_1d)call h5dclose_f(dataset_id, hdferr)
end subroutine read_1d_array

2. 读取二维数组

subroutine read_2d_array(file_id)use hdf5implicit noneinteger(hid_t), intent(in) :: file_idinteger :: hdferrinteger(hid_t) :: dataset_id, dataspace_idinteger(hsize_t), dimension(2) :: dimsreal, allocatable :: data_2d(:,:)! 打开数据集call h5dopen_f(file_id, "/2d_array", dataset_id, hdferr)! 获取数据集维度call h5dget_space_f(dataset_id, dataspace_id, hdferr)call h5sget_simple_extent_dims_f(dataspace_id, dims, maxdims, hdferr)! 分配内存allocate(data_2d(dims(1), dims(2)))! 读取数据call h5dread_f(dataset_id, H5T_NATIVE_REAL, data_2d, dims, hdferr)! 输出数据write(*,*) "2D Array:"do i = 1, dims(1)write(*,*) data_2d(i,:)end do! 清理deallocate(data_2d)call h5dclose_f(dataset_id, hdferr)
end subroutine read_2d_array

3. 读取元数组（复合数据类型）

subroutine read_compound_array(file_id)use hdf5implicit noneinteger(hid_t), intent(in) :: file_idinteger :: hdferrinteger(hid_t) :: dataset_id, datatype_idinteger(hsize_t), dimension(1) :: dimsinteger :: i! 定义复合数据类型type compound_typereal :: temperatureinteger :: pressurecharacter(len=10) :: nameend type compound_typetype(compound_type), allocatable :: compound_data(:)! 打开数据集call h5dopen_f(file_id, "/compound_data", dataset_id, hdferr)! 获取数据集维度call h5dget_space_f(dataset_id, dataspace_id, hdferr)call h5sget_simple_extent_dims_f(dataspace_id, dims, maxdims, hdferr)! 分配内存allocate(compound_data(dims(1)))! 创建内存中的复合数据类型call h5tcreate_f(H5T_COMPOUND_F, sizeof(compound_data(1)), datatype_id, hdferr)call h5tinsert_f(datatype_id, "temperature", 0, H5T_NATIVE_REAL, hdferr)call h5tinsert_f(datatype_id, "pressure", sizeof(real), H5T_NATIVE_INTEGER, hdferr)call h5tinsert_f(datatype_id, "name", sizeof(real)+sizeof(integer), H5T_C_S1, hdferr)! 读取数据call h5dread_f(dataset_id, datatype_id, compound_data, dims, hdferr)! 输出数据write(*,*) "Compound Data:"do i = 1, dims(1)write(*,*) compound_data(i)%temperature, compound_data(i)%pressure, trim(compound_data(i)%name)end do! 清理deallocate(compound_data)call h5tclose_f(datatype_id, hdferr)call h5dclose_f(dataset_id, hdferr)
end subroutine read_compound_array

4. 读取变长数组

subroutine read_vlen_array(file_id)use hdf5implicit noneinteger(hid_t), intent(in) :: file_idinteger :: hdferrinteger(hid_t) :: dataset_id, datatype_id, space_id, base_type_idinteger(hsize_t), dimension(1) :: dimsinteger(hsize_t) :: num_elementsinteger :: i, j! 定义变长数组类型type h5_vlen_tinteger(hsize_t) :: lenreal, pointer :: data(:)end type h5_vlen_ttype(h5_vlen_t), allocatable :: vlen_data(:)! 打开数据集call h5dopen_f(file_id, "/vlen_array", dataset_id, hdferr)! 获取数据集维度call h5dget_space_f(dataset_id, space_id, hdferr)call h5sget_simple_extent_dims_f(space_id, dims, maxdims, hdferr)! 分配内存allocate(vlen_data(dims(1)))! 创建变长数据类型call h5tcopy_f(H5T_NATIVE_REAL, base_type_id, hdferr)call h5tvlen_create_f(base_type_id, datatype_id, hdferr)! 读取数据call h5dread_f(dataset_id, datatype_id, vlen_data, dims, hdferr)! 输出数据write(*,*) "Variable-length Array:"do i = 1, dims(1)write(*,'(A,I0,A)', advance='no') "Element ", i, ": "do j = 1, vlen_data(i)%lenwrite(*,'(F8.2)', advance='no') vlen_data(i)%data(j)end dowrite(*,*)end do! 释放变长数组内存do i = 1, dims(1)deallocate(vlen_data(i)%data)end do! 清理deallocate(vlen_data)call h5tclose_f(datatype_id, hdferr)call h5tclose_f(base_type_id, hdferr)call h5dclose_f(dataset_id, hdferr)
end subroutine read_vlen_array

完整示例

program hdf5_read_exampleuse hdf5implicit noneinteger :: hdferrinteger(hid_t) :: file_id! 初始化HDF5库call h5open_f(hdferr)! 打开HDF5文件call h5fopen_f("example.h5", H5F_ACC_RDONLY_F, file_id, hdferr)! 读取各种类型的数据call read_1d_array(file_id)call read_2d_array(file_id)call read_compound_array(file_id)call read_vlen_array(file_id)! 关闭文件call h5fclose_f(file_id, hdferr)! 关闭HDF5库call h5close_f(hdferr)contains! 在这里包含上面所有的子程序! ...end program hdf5_read_example

注意事项

1. 错误处理：在实际应用中，应该对每个HDF5调用进行错误检查
2. 内存管理：特别是对于变长数组，需要正确释放内存
3. 数据类型匹配：确保HDF5文件中的数据类型与程序中读取的数据类型匹配
4. 路径处理：数据集路径需要与HDF5文件中的实际路径一致

以上代码提供了Fortran读取HDF5中各种类型数组的基本框架，可以根据实际需求进行修改和扩展。