[Insight-users] Reading portion of the image without loading the whole image into the memory

[yan xu]

  Hi, Matt,
       According to CanStreamRead, right now only MetaImageIO and
VTKImageIO are streamable right? What does it need to be a streaming
reader? Thank you!
  Yan

On Tue, Aug 14, 2012 at 5:03 PM, Matt McCormick
<matt.mccormick at kitware.com>wrote:

> Hi Yan,
>
> Streaming will only occur if the filter is streamable and it has been
> implemented as a streamable filter.  Unfortunately the NrrdImageIO is
> not implemented as a streaming reader at this time, so it will always
> load the entire image to memory.  For more information, see the
> CanStreamRead method on itk::ImageIOBase.
>
> HTH,
> Matt
>
> On Tue, Aug 14, 2012 at 9:22 PM, yan xu <xy198908 at gmail.com> wrote:
> >  Hi, David,
> >         I'm afraid it doesn't work, the codes are following for 16bit
> nrrd.
> > The memory still increases up to the size of the image not the region of
> > image I defined. Is it due to the image type or something? The codes are
> > following:
> >
> > UShortImageType::IndexType index;
> > index[0] = startX;
> > index[1] = startY;
> > index[2] = startZ;
> >
> > UShortImageType::SizeType size;
> > size[0] = sizeX;
> > size[1] = sizeY;
> > size[2] = sizeZ;
> >
> > UShortImageType::RegionType region;
> > region.SetIndex( index);
> > region.SetSize( size);
> >
> > ushortImageReader::Pointer reader = ushortImageReader::New();
> > reader->SetFileName(fileName);
> > reader->GetOutput()->SetRequestedRegion(region);
> >
> > try
> > {
> > reader->Update();
> > }
> > catch ( itk::ExceptionObject &err)
> > {
> > std::cout << "Error in bin_image_writer: " << err << std::endl;
> > }
> >
> >
> > Yan
> >
> >
> > On Tue, Aug 14, 2012 at 4:08 PM, David Doria <daviddoria at gmail.com>
> wrote:
> >>
> >> On Tue, Aug 14, 2012 at 4:59 PM, yan xu <xy198908 at gmail.com> wrote:
> >>>
> >>> Hi, all
> >>>       I'm facing a problem to read only portion of the image to test
> the
> >>> algorithm since the whole image is too big for the memory. I have tried
> >>> using the itk pipeline through extractimage filter, but I don't think
> it
> >>> works. The memory still goes larger and larger. My image type is 16bit
> nrrd.
> >>> What I hope is that the only the desired region of the image is loaded
> into
> >>> the memory. Is there a solution for that? Thank you!
> >>
> >>
> >> I've never done it, but you could try this:
> >>
> >> http://www.itk.org/Wiki/ITK/Examples/SimpleOperations/RequestedRegion
> >>
> >> on your ImageReader.
> >>
> >> David
> >
> >
> >
> >
> > --
> > Yan Xu
> > Research Assistant
> > Bio-Image Analytics Laboratory
> > Department of Electrical and Computer Engineering
> > University of Houston
> >
> >
> >
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>



-- 
Yan Xu
Research Assistant
Bio-Image Analytics Laboratory
Department of Electrical and Computer Engineering
University of Houston
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