C++：从 hdf5 文件中读取复数的 numpy 数组

Question

正如标题所说，我想从 c++ 中的 hdf5 文件中读取数据集。数据集是用 h5py 编写的。它包含一个 numpy 复数数组。

我可以正确检测出数组的总维数

using namespace H5;
std::string file_name = "/path/to/my/file.hdf5";
std::string dataset_name = "dataset_name";
H5File file(file_name, H5F_ACC_RDONLY);
DataSet dset = file.openDataSet(dataset_name);
DataSpace dspace = dset.getSpace();
int size = dspace.getSimpleExtentNpoints();

我可以准备一个vector

std::vector<std::complex<double>> out_vector(size);

如何读取数据集？

dset.read(out_vector.data(), ???);

Answer 1

HDF5 API 没有复合物 DataType。 python API 也没有。但是，h5py 会自动创建一个包含双打对的复合类型。 h5dump /path/to/my/file.hdf5 显示它：

DATATYPE  H5T_COMPOUND {
   H5T_IEEE_F64LE "r";
   H5T_IEEE_F64LE "i"  
}

在 c++ 中，必须手动创建兼容的复合数据类型。例如：

CompType complex_data_type(sizeof(out_vector[0]));
complex_data_type.insertMember( "r", 0, PredType::NATIVE_DOUBLE);
complex_data_type.insertMember( "i", sizeof(double), PredType::NATIVE_DOUBLE);

现在可以读取 DataSet

dset.read(out_vector.data(), complex_data_type);

Answer 2

https://support.hdfgroup.org/ 上有一个示例解释了如何处理 HDF5 C++ 的复合数据类型（不仅是复杂的）API 1.10.1:

https://support.hdfgroup.org/HDF5/doc/cpplus_RM/compound_8cpp-example.html

复杂的需要定义为复合类型:

typedef struct complex_type{
                double r;
                double i;
            } complex_type;

H5::CompType complex_compound( sizeof(complex_type) );
complex_compound.insertMember("r", HOFFSET(complex_type, r), H5::PredType::NATIVE_DOUBLE);
complex_compound.insertMember("i", HOFFSET(complex_type, i), H5::PredType::NATIVE_DOUBLE);

完整代码如下：

/* * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * *
 * Copyright by The HDF Group.                                               *
 * Copyright by the Board of Trustees of the University of Illinois.         *
 * All rights reserved.                                                      *
 *                                                                           *
 * This file is part of HDF5.  The full HDF5 copyright notice, including     *
 * terms governing use, modification, and redistribution, is contained in    *
 * the COPYING file, which can be found at the root of the source code       *
 * distribution tree, or in https://support.hdfgroup.org/ftp/HDF5/releases.  *
 * If you do not have access to either file, you may request a copy from     *
 * help@hdfgroup.org.                                                        *
 * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * */
/*
 * This example shows how to create a compound datatype,
 * write an array which has the compound datatype to the file,
 * and read back fields' subsets.
 */
#ifdef OLD_HEADER_FILENAME
#include <iostream.h>
#else
#include <iostream>
#endif
using std::cout;
using std::endl;
#include <string>
#include "H5Cpp.h"
using namespace H5;
const H5std_string FILE_NAME( "SDScompound.h5" );
const H5std_string DATASET_NAME( "ArrayOfStructures" );
const H5std_string MEMBER1( "a_name" );
const H5std_string MEMBER2( "b_name" );
const H5std_string MEMBER3( "c_name" );
const int   LENGTH = 10;
const int   RANK = 1;
int main(void)
{
   /* First structure  and dataset*/
   typedef struct s1_t {
    int    a;
    float  b;
    double c;
   } s1_t;
   /* Second structure (subset of s1_t)  and dataset*/
   typedef struct s2_t {
    double c;
    int    a;
   } s2_t;
   // Try block to detect exceptions raised by any of the calls inside it
   try
   {
      /*
       * Initialize the data
       */
      int  i;
      s1_t s1[LENGTH];
      for (i = 0; i< LENGTH; i++)
      {
         s1[i].a = i;
         s1[i].b = i*i;
         s1[i].c = 1./(i+1);
      }
      /*
       * Turn off the auto-printing when failure occurs so that we can
       * handle the errors appropriately
       */
      Exception::dontPrint();
      /*
       * Create the data space.
       */
      hsize_t dim[] = {LENGTH};   /* Dataspace dimensions */
      DataSpace space( RANK, dim );
      /*
       * Create the file.
       */
      H5File* file = new H5File( FILE_NAME, H5F_ACC_TRUNC );
      /*
       * Create the memory datatype.
       */
      CompType mtype1( sizeof(s1_t) );
      mtype1.insertMember( MEMBER1, HOFFSET(s1_t, a), PredType::NATIVE_INT);
      mtype1.insertMember( MEMBER3, HOFFSET(s1_t, c), PredType::NATIVE_DOUBLE);
      mtype1.insertMember( MEMBER2, HOFFSET(s1_t, b), PredType::NATIVE_FLOAT);
      /*
       * Create the dataset.
       */
      DataSet* dataset;
      dataset = new DataSet(file->createDataSet(DATASET_NAME, mtype1, space));
      /*
       * Write data to the dataset;
       */
      dataset->write( s1, mtype1 );
      /*
       * Release resources
       */
      delete dataset;
      delete file;
      /*
       * Open the file and the dataset.
       */
      file = new H5File( FILE_NAME, H5F_ACC_RDONLY );
      dataset = new DataSet (file->openDataSet( DATASET_NAME ));
      /*
       * Create a datatype for s2
       */
      CompType mtype2( sizeof(s2_t) );
      mtype2.insertMember( MEMBER3, HOFFSET(s2_t, c), PredType::NATIVE_DOUBLE);
      mtype2.insertMember( MEMBER1, HOFFSET(s2_t, a), PredType::NATIVE_INT);
      /*
       * Read two fields c and a from s1 dataset. Fields in the file
       * are found by their names "c_name" and "a_name".
       */
      s2_t s2[LENGTH];
      dataset->read( s2, mtype2 );
      /*
       * Display the fields
       */
      cout << endl << "Field c : " << endl;
      for( i = 0; i < LENGTH; i++)
     cout << s2[i].c << " ";
      cout << endl;
      cout << endl << "Field a : " << endl;
      for( i = 0; i < LENGTH; i++)
     cout << s2[i].a << " ";
      cout << endl;
      /*
       * Create a datatype for s3.
       */
      CompType mtype3( sizeof(float) );
      mtype3.insertMember( MEMBER2, 0, PredType::NATIVE_FLOAT);
      /*
       * Read field b from s1 dataset. Field in the file is found by its name.
       */
      float s3[LENGTH];  // Third "structure" - used to read float field of s1
      dataset->read( s3, mtype3 );
      /*
       * Display the field
       */
      cout << endl << "Field b : " << endl;
      for( i = 0; i < LENGTH; i++)
     cout << s3[i] << " ";
      cout << endl;
      /*
       * Release resources
       */
      delete dataset;
      delete file;
   }  // end of try block
   // catch failure caused by the H5File operations
   catch( FileIException error )
   {
      error.printError();
      return -1;
   }
   // catch failure caused by the DataSet operations
   catch( DataSetIException error )
   {
      error.printError();
      return -1;
   }
   // catch failure caused by the DataSpace operations
   catch( DataSpaceIException error )
   {
      error.printError();
      return -1;
   }
   // catch failure caused by the DataSpace operations
   catch( DataTypeIException error )
   {
      error.printError();
      return -1;
   }
   return 0;
}

C++：从 hdf5 文件中读取复数的 numpy 数组

C++: reading a numpy array of complex numbers from an hdf5 file

c++

hdf5

h5py