[hdf-forum] How to write hyperslabs?

[Natalie Happenhofer]

Hi!
I´ve tried to work with boost::multiarray, but it does not work either,that´s what I´m trying to do:

typedef boost::multi_array<double, 2> array;
array AData (boost::extents[xdims][ydims]);

status = H5Dwrite(dataset, H5T_NATIVE_FLOAT, H5S_ALL, H5S_ALL, H5P_DEFAULT, AData);


AData is the array I want to write to my .h5-file, and this is the error I get:
c:\dokumente und einstellungen\natalie happenhofer\eigene dateien\atox_main.cpp(428) : error C2664: 'H5Dwrite': conversion of parameter 6  'array' in 'const void *' not possible.

the problem is that I need a structure working with the HDF5-Api!

greetings,
NH



> Date: Thu, 16 Oct 2008 14:29:15 +0200
> From: diepen at astron.nl
> To: hdf-forum at hdfgroup.org; nataliehapp at hotmail.com
> Subject: Re: [hdf-forum] How to write hyperslabs?
> 
> Hi Natalie,
> 
> Below is an extract from a class HDF5DataSet I've written some time ago for the casacore package. It writes a hyperslab.
> I hope you more or less understand the code. Block is similar to the std::vector.
> I can point you to the code if you would like to see more or use it.
> 
> Why don't you use something like Blitz++ or boost::multi_array (or casacore::Array) instead of struggling with C pointers? All do full array arithmetic, etc.
> 
> Cheers,
> Ger
> 
>   void HDF5DataSet::put (const Slicer& section, const void* buf)
>   {
>     // Define the data set selection.
>     Block<hsize_t> offset = fromShape(section.start());
>     Block<hsize_t> count  = fromShape(section.length());
>     Block<hsize_t> stride = fromShape(section.stride());
>     if (H5Sselect_hyperslab (itsDSid, H5S_SELECT_SET, offset.storage(),
> 			     stride.storage(), count.storage(), NULL) < 0) {
>       throw HDF5Error("invalid data set array selection");
>     }
>     // Define a data space for the memory buffer.
>     HDF5HidDataSpace memspace (H5Screate_simple (count.size(),
> 						 count.storage(), NULL));
>     // Define memory selection.
>     offset = 0;
>     if (H5Sselect_hyperslab (memspace, H5S_SELECT_SET, offset.storage(),
> 			     NULL, count.storage(), NULL) < 0) {
>       throw HDF5Error("setting slab of memory buffer");
>     }
>     // Read the data.
>     if (H5Dwrite (getHid(), itsDataType.getHidMem(), memspace, itsDSid,
> 		  H5P_DEFAULT, buf) < 0) {
>       throw HDF5Error("writing slab into data set array");
>     }
>   }
>  
>  
> >>> Natalie Happenhofer <nataliehapp at hotmail.com> 10/16/08 1:50 PM >>> 
> 
> Hi!
> I need to write a 2-dimensional .h5 file, the data in it should look like the following array (concerning shape)
> 
> 1 2 3 2 4 
> 1 2 5 2 4 
> 1 1 4 2 4 
> 
> My problem is that I need to allocate the space for my data array dynamically, i.e. it looks like this in C++:
> 
> float** Data = new float* [xdims]
> for(int i=1; i<xdims; i++) Data[i] = new float [ydims];
> 
> as my data array is not necessarily contiguous in memory, I need a way to write it to my .h5 file with hyperslabs, as someone hinted earlier - I would write xdims rows with ydims values, but how do I write a hyperslab, which functions do I have to use? In the HDF5 Users Guide I have just found how to read hyperslabs from already existing data.
> 
> thx,
> NH
> 
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