[c++][hdf5]HDF5格式dataset在c++中的读取

HDF5格式在存储数据集，使用很广泛。下述内容，主要集中于HDF5格式在c++中的使用。其中记录了源码安装、apt-get安装、c、c++读取等。推荐apt-get安装、c++接口。

参考

1. HDF5 C++ API：https://support.hdfgroup.org/HDF5/doc/cpplus_RM/index.html

2. https://support.hdfgroup.org/HDF5/

3. https://portal.hdfgroup.org/display/support

4. 下载：https://portal.hdfgroup.org/display/support/Downloads

5. 用户指南：https://portal.hdfgroup.org/display/HDF5/HDF5+User+Guides

6. 样例：https://portal.hdfgroup.org/display/HDF5/Examples+in+the+Source+Code

HDF5安装

源码安装

cmake -G "Unix Makefiles" -DBUILD_SHARED_LIBS:BOOL=ON ~/hdf5-1.12.1
cmake --build . --config Release
make
sudo make install

或者也可以采用如下：https://blog.csdn.net/weixin_40255337/article/details/84256604

sudo ./configure --prefix=/usr/local/hdf5
sudo make
sudo make check   
sudo make install

安装后的关键路径：

~/hdf5/HDF_Group/HDF5/1.12.1/
/usr/local/HDF_Group/HDF5/1.12.1/lib/
/usr/local/HDF_Group/HDF5/1.12.1/share/cmake/hdf5
/usr/local/HDF_Group/HDF5/1.12.1/include/

apt-get 安装：https://github.com/ros-industrial-consortium/reuleaux/issues/41

sudo apt-get install libhdf5-dev
# 查找头文件和库地址
sudo find /usr -name H5Cpp.h
sudo find /usr -name libhdf5.so
whereis hdf5

安装后的关键路径：

/usr/include/hdf5/serial
/usr/lib/x86_64-linux-gnu/hdf5/serial

cmake配置

下述cmake文件编写调试通过，其中动态链接库参考

/usr/local/HDF_Group/HDF5/1.12.1/lib目录下的/pkgconfig目录中的参考信息。

cmake_minimum_required(VERSION 3.5)
project(test1)
set(CMAKE_CXX_STANDARD 14)
include_directories(
        SYSTEM
        /usr/local/HDF_Group/HDF5/1.12.1/include
        /usr/include/hdf5/serial
)
link_directories(
        /usr/local/HDF_Group/HDF5/1.12.1/lib
        /usr/lib/x86_64-linux-gnu/hdf5/serial
)
add_executable(test1 main.cpp)
target_link_libraries(test1 -lm -ldl -lhdf5 -lhdf5_hl)

c/c++ 读写

c++读取矩阵

//! 头文件
#include "H5Cpp.h"
//! 名称空间
using namespace H5;
//! 关闭打印
Exception::dontPrint();
//! 打开文件和数据集
const H5std_string FILE_NAME("SDSextendible.h5");
const H5std_string DATASET_NAME("ExtendibleArray");
H5File file(FILE_NAME, H5F_ACC_RDONLY);
DataSet dataset = file.openDataSet(DATASET_NAME);
//! Get filespace for rank and dimension
DataSpace filespace = dataset.getSpace();
//! Get number of dimensions in the file dataspace
int rank = filespace.getSimpleExtentNdims();
//! Get and print the dimension sizes of the file dataspace
hsize_t dims[2]; // dataset dimensions
rank = filespace.getSimpleExtentDims(dims);
DataSpace mspace1(RANK, dims);
//! 读取数据集矩阵
int data_out[NX][NY]; // buffer for dataset to be read
dataset.read(data_out, PredType::NATIVE_INT, mspace1, filespace);

或者采用这种比较简单的形式

hid_t   file_id;
int     data[6];
hsize_t dims[2];
size_t  i, j, nrow, n_values;
/* open file from ex_lite1.c */
file_id = H5Fopen("ex_lite1.h5", H5F_ACC_RDONLY, H5P_DEFAULT);
/* read dataset */
H5LTread_dataset_int(file_id, "/dset", data);
/* get the dimensions of the dataset */
H5LTget_dataset_info(file_id, "/dset", dims, NULL, NULL);

c读取属性

读取数据集的属性

#include "hdf5.h"
#include "hdf5_hl.h"
#include <stdlib.h>
#define ATTR_SIZE 5
/* get the attribute "attr1" from the dataset "dset" */
int data[ATTR_SIZE] = {1, 2, 3, 4, 5};
H5LTset_attribute_int(file_id, "dset", "attr1", data, ATTR_SIZE);
H5LTget_attribute_int(file_id, "dset", "attr1", data);

读取数据根层属性

#include <hdf5.h>
#include <hdf5_hl.h>

void hdf5_write_example() {
    auto file_id = H5Fcreate("tmp.h5", H5F_ACC_TRUNC, H5P_DEFAULT, H5P_DEFAULT);
    auto aid3 = H5Screate(H5S_SCALAR);
    auto atype = H5Tcopy(H5T_C_S1);
    std::string str_value = "HDF5_TEST_STR";
    H5Tset_size(atype, str_value.length() + 1);
    H5Tset_strpad(atype, H5T_STR_NULLTERM);
    auto attr3 = H5Acreate2(file_id, "test_attr_str", atype, aid3, H5P_DEFAULT, H5P_DEFAULT);
    H5Awrite(attr3, atype, str_value.c_str());
    H5Aclose(attr3);
    H5Sclose(aid3);
    H5Tclose(atype);
    H5Fclose(file_id);
}

void hdf5_read_example() {
    char res[100] = "____________";
    auto file_id = H5Fopen("tmp.h5", H5F_ACC_RDONLY, H5P_DEFAULT);
    auto atype = H5Tcopy(H5T_C_S1);
    H5Tset_size(atype, 100);
    H5Tset_strpad(atype, H5T_STR_NULLTERM);
    auto attr = H5Aopen(file_id, "test_attr_str", H5P_DEFAULT);
    H5Aread(attr, atype, res);
    H5Aclose(attr);
    H5Tclose(atype);
    std::cout << "value of attribute test_attr_str: " << res << std::endl;
    H5Fclose(file_id);
}

int main() {
    hdf5_write_example();
    hdf5_read_example();
    return 0;
}

输出：

value of attribute test_attr_str: HDF5_TEST_STR

c++ 读取属性

void test_read_attribute_cpp() {
    H5File file("tmp.h5", H5F_ACC_RDONLY);
    Group what = file.openGroup("/");
    Attribute attr = what.openAttribute("test_attr_str");
    H5std_string test;
    DataType type = attr.getDataType();
    attr.read(type, test);
    std::cout << "value of attribute test_attr_str (c++ api): " << test << std::endl;
}

int main() {
    hdf5_write_example();
    test_read_attribute_cpp();
    return 0;
}

输出：

value of attribute test_attr_str (c++ api): HDF5_TEST_STR

参考

https://raw.githubusercontent.com/HDFGroup/hdf5/develop/c++/examples/chunks.cpp

https://raw.githubusercontent.com/HDFGroup/hdf5/develop/c++/examples/readdata.cpp

https://raw.githubusercontent.com/HDFGroup/hdf5/develop/hl/examples/ex_lite2.c

c的属性信息读取：google search: hdf5 read attribute c++

https://raw.githubusercontent.com/HDFGroup/hdf5/develop/hl/examples/ex_lite3.c

https://raw.githubusercontent.com/HDFGroup/hdf5/develop/examples/h5_attribute.c

https://fossies.org/linux/hdf5/examples/h5_attribute.c

https://support.hdfgroup.org/HDF5/doc1.6/UG/13_Attributes.html

c++接口

https://support.hdfgroup.org/HDF5/doc/cpplus_RM/index.html

https://stackoverflow.com/questions/22842541/hdf5-c-read-the-contents-of-an-attribute/22847313

https://portal.hdfgroup.org/pages/viewpage.action?pageId=50073884