Hi Steve,
boost::multi_array provides a clean interface for multi dimensional arrays
in C++.
You can also do something like this:
auto data = new double[rows*cols]; // allocate all data in one block
auto md_data = new double*[rows]; // allocate pointers for each row
for (int r = 0; r != rows; ++r) // set row pointers
md_data[r] = data + r*cols;
md_data[2][5] = 1.0; // row pointer array can be used as a pseudo md array
On Fri, May 6, 2016 at 1:29 PM, Steven Walton <[email protected]>
wrote:
> So I am noticing some interesting behavior and is wondering if there is a
> way around this.
> I am able so assign a rank 1 array dynamically and write this to an hdf5
> filetype but I do not seem to be able to do with with higher order arrays.
> I would like to be able to write a PPx array to h5 and retain the data
> integrity. More specifically I am trying to create a easy to use vector to
> array library <https://github.com/stevenwalton/H5Easy> that can handle
> multidimensional data (works with rank 1).
>
> Let me give some examples. I will also show the typenames of the arrays.
>
> Works:
> double *a = new double[numPts]; // typename: Pd
> double a[numPts]; // typename A#pts_d
> double a[num1][num2]; typename:Anum1_Anum2_d
>
> What doesn't work:
> double **a = new double*[num1];
> for ( size_t i = 0; i < num1; ++i )
> a[i] = new double[num2];
> // typename PPd
>
> Testing the saved arrays with h5dump (and loading and reading directly) I
> find that if I have typename PPx (not necessarily double) I get garbage
> stored. Here is an example code and output from h5dump showing the
> behavior.
> ------------------------------------------------------------
> compiled with h5c++ -std=c++11
> ------------------------------------------------------------
> #include "H5Cpp.h"
> using namespace H5;
>
> #define FILE "multi.h5"
>
> int main()
> {
> hsize_t dims[2];
> herr_t status;
> H5File file(FILE, H5F_ACC_TRUNC);
> dims[0] = 4;
> dims[1] = 6;
>
> double **data = new double*[dims[0]];
> for ( size_t i = 0; i < dims[0]; ++i )
> data[i] = new double[dims[1]];
>
> for ( size_t i = 0; i < dims[0]; ++i )
> for ( size_t j = 0; j < dims[1]; ++j )
> data[i][j] = i + j;
>
> DataSpace dataspace = DataSpace(2,dims);
> DataSet dataset( file.createDataSet( "test", PredType::IEEE_F64LE,
> dataspace ) );
> dataset.write(data, PredType::IEEE_F64LE);
> dataset.close();
> dataspace.close();
> file.close();
>
> return 0;
> }
> ------------------------------------------------------------
> h5dump
> ------------------------------------------------------------
> HDF5 "multi.h5" {
> GROUP "/" {
> DATASET "test" {
> DATATYPE H5T_IEEE_F64LE
> DATASPACE SIMPLE { ( 4, 6 ) / ( 4, 6 ) }
> DATA {
> (0,0): 1.86018e-316, 1.86018e-316, 1.86018e-316, 1.86019e-316, 0,
> (0,5): 3.21143e-322,
> (1,0): 0, 1, 2, 3, 4, 5,
> (2,0): 0, 3.21143e-322, 1, 2, 3, 4,
> (3,0): 5, 6, 0, 3.21143e-322, 2, 3
> }
> }
> }
> }
> ------------------------------------------------------------------
> As can be seen the (0,0) set is absolute garbage (except the last
> character which is the first number of the actual array), (0,5) is out of
> bounds, and has garbage data. (1,0) has always contained real data (though
> it should be located at (0,0)). So this seems like some addressing problem.
>
> Is this a bug in the h5 libraries that allows me to read and write Pd data
> as well as Ax0_...Axn_t data but not P...Pt data? Or is this for some
> reason intentional? As using new is a fairly standard way to assign arrays,
> making P...Pt type data common, I have a hard time seeing this as
> intentional. In the mean time is anyone aware of a workaround to this? The
> data I am taking in will be dynamically allocated so I do not see a way to
> get Ax_... type data.
>
> Thank you,
> Steven
>
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>
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