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POHDF5 C++ interface: writing dynamic 2D arrays
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  1. POHDF5 C++ interface: writing dynamic 2D arrays
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    copied!<p>I am using the <a href="http://www.hdfgroup.org/HDF5/doc/cpplus_RM/index.html" rel="nofollow noreferrer">HDF5 C++ API</a> to write 2D array dataset files. The HDF Group has <a href="ftp://ftp.hdfgroup.org/HDF5/current/src/unpacked/c++/examples/create.cpp" rel="nofollow noreferrer">an example to create</a> a HDF5 file from a statically defined array size, which I've modified to suite my needs below. However, I require a dynamic array, where both <code>NX</code> and <code>NY</code> are determined at runtime. I've found <a href="https://stackoverflow.com/questions/936687/how-do-i-declare-a-2d-array-using-new">another solution to create 2D arrays using the "new" keyword</a> to help create a dynamic array. Here is what I have:</p> <pre><code>#include "StdAfx.h" #include "H5Cpp.h" using namespace H5; const H5std_string FILE_NAME("C:\\SDS.h5"); const H5std_string DATASET_NAME("FloatArray"); const int NX = 5; // dataset dimensions const int NY = 6; int main (void) { // Create a 2D array using "new" method double **data = new double*[NX]; for (int j = 0; j &lt; NX; j++) // 0 1 2 3 4 5 { // 1 2 3 4 5 6 data[j] = new double[NY]; // 2 3 4 5 6 7 for (int i = 0; i &lt; NY; i++) // 3 4 5 6 7 8 data[j][i] = (float)(i + j); // 4 5 6 7 8 9 } // Create HDF5 file and dataset H5File file(FILE_NAME, H5F_ACC_TRUNC); hsize_t dimsf[2] = {NX, NY}; DataSpace dataspace(2, dimsf); DataSet dataset = file.createDataSet(DATASET_NAME, PredType::NATIVE_DOUBLE, dataspace); // Attempt to write data to HDF5 file dataset.write(data, PredType::NATIVE_DOUBLE); // Clean up for(int j = 0; j &lt; NX; j++) delete [] data[j]; delete [] data; return 0; } </code></pre> <p>The resulting file, however, is not as expected (output from <a href="http://www.hdfgroup.org/HDF5/doc/RM/Tools.html#Tools-Dump" rel="nofollow noreferrer"><code>hdf5dump</code></a>):</p> <pre><code>HDF5 "SDS.h5" { GROUP "/" { DATASET "FloatArray" { DATATYPE H5T_IEEE_F64LE DATASPACE SIMPLE { ( 5, 6 ) / ( 5, 6 ) } DATA { (0,0): 4.76465e-307, 4.76541e-307, -7.84591e+298, -2.53017e-098, 0, (0,5): 3.8981e-308, (1,0): 4.76454e-307, 0, 2.122e-314, -7.84591e+298, 0, 1, (2,0): 2, 3, 4, 5, -2.53017e-098, -2.65698e+303, (3,0): 0, 3.89814e-308, 4.76492e-307, 0, 2.122e-314, -7.84591e+298, (4,0): 1, 2, 3, 4, 5, 6 } } } } </code></pre> <p>The problem stems back to how the 2D array was created (since this example works fine with a static array method). As I understand from <a href="http://mail.hdfgroup.org/pipermail/hdf-forum_hdfgroup.org/2008-June/001118.html" rel="nofollow noreferrer">this email thread</a>:</p> <blockquote> <p>The HDF5 library expects to a contiguous array of elements, not pointers to elements in lower dimensions</p> </blockquote> <p>As I am rather new to C++/HDF5, I'm not sure how to create a dynamically sized array at runtime that is a contiguous array of elements. I do not want to do the more complicated "hyperslab" method described in the email thread, as this looks overly complicated. Any help is appreciated.</p>
 

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