[Insight-developers] HDF5 writer streaming

[Bradley Lowekamp]

This article  may be of some use too:
http://www.insight-journal.org/browse/publication/729
On Dec 30, 2013, at 1:40 AM, David Froger <david.froger at inria.fr> wrote:

> Hi all,
> 
> I would like to add writer streaming support to the HDF5 module. Writer
> streaming would includes:
> 
> 1) Write a whole array in a new HDF5 file by iteration on subregion writting.
> For example: write NZ times an array of dimension (NY*NX) in a new HDF5 file
> that will finally store an array of dimensions (NZ*NY*NX).
> 
> 2) Paste (override) a subregion in an existing HDF5 file. (This require to
> open the file in a different mode).
> 
> I know how to do it in HDF5, I've looked at the source code of the HDF5 ITK
> module, and have some questions on how to patch the HDF5 module.
> 
> To support reading and writing subregion, HDF5 manipulates simple arrays
> defining the start and the size of the region to read/write. These arrays are
> 'HDFSize' and 'offset' in the method HDF5ImageIO::SetupStreaming of the file
> itkHDF5ImageIO.cxx, and their values are set according to the size and index
> of the region 'this->GetIORegion()':
> 
>   void
>   HDF5ImageIO
>   ::SetupStreaming(H5::DataSpace *imageSpace, H5::DataSpace *slabSpace)
>   {
>     ImageIORegion            regionToRead = this->GetIORegion();
>     ImageIORegion::SizeType  size = regionToRead.GetSize();
>     ImageIORegion::IndexType start = regionToRead.GetIndex();
>     //
>     int numComponents = this->GetNumberOfComponents();
> 
>     const int HDFDim(this->GetNumberOfDimensions() +
>                      (numComponents > 1 ? 1 : 0));
>     hsize_t *offset = new hsize_t[HDFDim];
>     hsize_t *HDFSize = new hsize_t[HDFDim];
>     int limit;
>     //
>     // fastest moving dimension is intra-voxel
>     // index
>     if(numComponents > 1)
>       {
>       limit = HDFDim - 1;
>       offset[limit] = 0;
>       HDFSize[limit] = numComponents;
>       }
>     else
>       {
>       limit = HDFDim;
>       }
>     for(int i=0; i < limit; i++)
>       {
>       offset[limit - i - 1] = start[i];
>       HDFSize[limit - i - 1] = size[i];
>       }
>     slabSpace->setExtentSimple(HDFDim,HDFSize);
>     imageSpace->selectHyperslab(H5S_SELECT_SET,HDFSize,offset);
>     delete[] HDFSize;
>     delete[] offset;
>   }
> 
> When reading a file, 'this->GetIORegion()' can be modified by calling
>   reader->GetOutput()->SetRequestedRegion(requestedRegion);
> which enables input streaming.
> 
> But how to modifiy 'this->GetIORegion()' when writing in a file, for case 1)
> and 2)?
> 
> Which example / source code can I look to get started with writer streaming?
> 
> Thanks for your help!
> 
> David
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