如何将浮点数的2D std向量写入HDF5文件，然后在python中读取它(How to write 2D std vector of floats to HDF5 file and then read it in python)

 我想写一个浮动的2D矢量到HDF5文件。 我使用了以下代码（writeh5.cpp）： 
 
#include <cstdlib> 
#include <ctime> 
#include <iostream>
#include <string>
#include <vector>
#include <iterator>
#include <H5Cpp.h>

using namespace H5;
using namespace std;

int main(void) {
  int nrow = 5;
  int ncol = 4;

  vector<vector< double > > vec2d;
  vec2d.resize(nrow, vector<double>(ncol, 0.0));

  srand((unsigned)time(0));

  typename vector< vector< double > >::iterator row;
  typename vector< double >::iterator col;
  for (row = vec2d.begin(); row != vec2d.end(); row++) {
    cout << endl;
    for (col = row->begin(); col != row->end(); col++) {

      *col = (rand()/(RAND_MAX+1.0));
      cout << *col << '\t';
    }
  }
  cout << endl;

  H5File file("test.h5", H5F_ACC_TRUNC);

  // dataset dimensions
  hsize_t dimsf[2];
  dimsf[0] = nrow;
  dimsf[1] = ncol;
  DataSpace dataspace(2, dimsf);

  DataType datatype(H5::PredType::NATIVE_DOUBLE);
  DataSet dataset = file.createDataSet("data", datatype, dataspace);

  // dataset.write(vec2d.data(), H5::PredType::NATIVE_DOUBLE);
  dataset.write(&vec2d[0][0], H5::PredType::NATIVE_DOUBLE);

  cout << endl << " vec2d has " << endl;
  for (row = vec2d.begin(); row != vec2d.end(); row++) {
      cout << endl;
      for (col = row->begin(); col != row->end(); col++) {            

        cout << *col << '\t';
      }
  }
  cout << endl;

  dataset.close();
  dataspace.close();
  file.close();

  return 0;
}
 
 我使用g++ writeh5.cpp -I/usr/include/hdf5/ -lhdf5_cpp -lhdf5 -Wall编译它 
 
 一段代码产生了以下输出： 
 
0.325553        0.598941        0.364489        0.0125061
0.374205        0.0319419       0.380329        0.815621
0.863754        0.386279        0.0173515       0.15448
0.703936        0.372486        0.728436        0.991631
0.666207        0.568983        0.807475        0.964276
 
 和文件test.h5 
 
 然后，当我从python中读取此文件时（使用以下内容） 
 
import h5py
import numpy as np

file = h5py.File("test.h5", 'r')
dataset = np.array(file["data"])

print dataset

file.close()
 
 我有 
 
 [[  3.25553381e-001   5.98941262e-001   3.64488814e-001   1.25061036e-002]
 [  0.00000000e+000   2.42092166e-322   3.74204732e-001   3.19418786e-002]
 [  3.80329057e-001   8.15620518e-001   0.00000000e+000   2.42092166e-322]
 [  8.63753530e-001   3.86278684e-001   1.73514970e-002   1.54479635e-001]
 [  0.00000000e+000   2.42092166e-322   7.03935940e-001   3.72486182e-001]]
 
 第一行是好的，其他行是垃圾。 
 
 我尝试使用dataset.write(&vec2d[0]...和dataset.write(vec2d[0].data()... ，我遇到了类似的问题。 
 
 我要 
 
 
 
 写一个HDF5文件，其内容为2D std :: vector of double， 
 
 
 在python中读取文件并将内容存储在numpy数组中 
 
 
 我做错了什么？ 

I want to write a 2D vector of floats to a HDF5 file. I used the following code (writeh5.cpp):
 
#include <cstdlib> 
#include <ctime> 
#include <iostream>
#include <string>
#include <vector>
#include <iterator>
#include <H5Cpp.h>

using namespace H5;
using namespace std;

int main(void) {
  int nrow = 5;
  int ncol = 4;

  vector<vector< double > > vec2d;
  vec2d.resize(nrow, vector<double>(ncol, 0.0));

  srand((unsigned)time(0));

  typename vector< vector< double > >::iterator row;
  typename vector< double >::iterator col;
  for (row = vec2d.begin(); row != vec2d.end(); row++) {
    cout << endl;
    for (col = row->begin(); col != row->end(); col++) {

      *col = (rand()/(RAND_MAX+1.0));
      cout << *col << '\t';
    }
  }
  cout << endl;

  H5File file("test.h5", H5F_ACC_TRUNC);

  // dataset dimensions
  hsize_t dimsf[2];
  dimsf[0] = nrow;
  dimsf[1] = ncol;
  DataSpace dataspace(2, dimsf);

  DataType datatype(H5::PredType::NATIVE_DOUBLE);
  DataSet dataset = file.createDataSet("data", datatype, dataspace);

  // dataset.write(vec2d.data(), H5::PredType::NATIVE_DOUBLE);
  dataset.write(&vec2d[0][0], H5::PredType::NATIVE_DOUBLE);

  cout << endl << " vec2d has " << endl;
  for (row = vec2d.begin(); row != vec2d.end(); row++) {
      cout << endl;
      for (col = row->begin(); col != row->end(); col++) {            

        cout << *col << '\t';
      }
  }
  cout << endl;

  dataset.close();
  dataspace.close();
  file.close();

  return 0;
}
 
I compiled it using g++ writeh5.cpp -I/usr/include/hdf5/ -lhdf5_cpp -lhdf5 -Wall
 
A run of the code produced the following output:
 
0.325553        0.598941        0.364489        0.0125061
0.374205        0.0319419       0.380329        0.815621
0.863754        0.386279        0.0173515       0.15448
0.703936        0.372486        0.728436        0.991631
0.666207        0.568983        0.807475        0.964276
 
And the file test.h5
 
Then when i read this file from python (using the following)
 
import h5py
import numpy as np

file = h5py.File("test.h5", 'r')
dataset = np.array(file["data"])

print dataset

file.close()
 
I got
 
 [[  3.25553381e-001   5.98941262e-001   3.64488814e-001   1.25061036e-002]
 [  0.00000000e+000   2.42092166e-322   3.74204732e-001   3.19418786e-002]
 [  3.80329057e-001   8.15620518e-001   0.00000000e+000   2.42092166e-322]
 [  8.63753530e-001   3.86278684e-001   1.73514970e-002   1.54479635e-001]
 [  0.00000000e+000   2.42092166e-322   7.03935940e-001   3.72486182e-001]]
 
the first row is good, the other rows are garbage.
 
I tried with dataset.write(&vec2d[0]... and dataset.write(vec2d[0].data()..., i got similar problems.
 
I want to
 
 
 
Write a HDF5 file with the contents of a 2D std::vector of doubles,
 
 
Read the file in python and store the contents in a numpy array
 
 
What i am doing wrong?

原文：https://stackoverflow.com/questions/32447628