I guess I am just surprised that hdf5 does not accept the standard c++ "array" creation. New allocates to the heap. It may be pointer, but this is pretty standard and they teach it in all c++ classes. New has existed for quite some time. I just thought the hdf5 group would follow these standard types.
I understand that vector is a 1D array. My original example was about new and allocating to the heap, with standard c++. On Mon, May 16, 2016 at 9:30 PM, David <[email protected]> wrote: > The limitation you ran into in your original example was that std::vector > is only for 1 dimensional arrays and you wanted to use multi dimensional > indexing. C++ does not have a built in class for heap allocated multi dim > arrays. However you can simply use boost::multi_array. The standards > committee wisely has been using boost as a testing ground for new library > features, allowing them to mature and prove themselves before being > canonized. I will not be surprised if boost::multi_array is adopted into a > future standard. > > David > > > On Mon, May 16, 2016 at 7:01 PM, Steven Walton <[email protected]> > wrote: > >> I actually just created a buffer array and then passed back to a vector. >> But what I'm saying is that this is an extremely common way to store data >> in C++, if not the default way for most users. Vectors are extremely common >> as well. Why are we still held back by using C type arrays? >> >> On Mon, May 9, 2016 at 12:58 PM, David <[email protected]> wrote: >> >>> 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 >>>> >>>> _______________________________________________ >>>> Hdf-forum is for HDF software users discussion. >>>> [email protected] >>>> http://lists.hdfgroup.org/mailman/listinfo/hdf-forum_lists.hdfgroup.org >>>> Twitter: https://twitter.com/hdf5 >>>> >>> >>> >>> _______________________________________________ >>> Hdf-forum is for HDF software users discussion. >>> [email protected] >>> http://lists.hdfgroup.org/mailman/listinfo/hdf-forum_lists.hdfgroup.org >>> Twitter: https://twitter.com/hdf5 >>> >> >> >> _______________________________________________ >> Hdf-forum is for HDF software users discussion. >> [email protected] >> http://lists.hdfgroup.org/mailman/listinfo/hdf-forum_lists.hdfgroup.org >> Twitter: https://twitter.com/hdf5 >> > > > _______________________________________________ > Hdf-forum is for HDF software users discussion. > [email protected] > http://lists.hdfgroup.org/mailman/listinfo/hdf-forum_lists.hdfgroup.org > Twitter: https://twitter.com/hdf5 >
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