[Insight-users] Re: Passing pixel data from or to itk filter

[Bill Lorensen]

Reinhard,
I added a test Testing/Code/Common/itkImportContainerTest that exercises the
ImportImageContainer class. As it turns out, the code coverage was fairly
low for this class. As I wrote it, I discovered that the class can be tricky
to use.

If you are on a linux system, I suggest that you run your code with
valgrind,s memtest. http://valgrind.org/

I suspect that your code is mucking improperly with the import pointer. If
you can't run valgrind, perhaps you could post a small program that
illustrates the error and we could help analyze it.

Bill
On Dec 9, 2007 5:55 PM, Reinhard Hameeteman <k.hameeteman+maillist at gmail.com>
wrote:

> Hi Luis,
>
> Thanks for taking a look.
>
> Let me try to untangle things by reducing it to one method:
>
> I want to pass the output buffer of the itk filter (an itk::Image<
> itk::Vector< float, 3>, 3> image) to my application. So the itk filter
> is responsible for allocating the buffer, but is told not to
> deallocate the buffer when getting out of scope like this:
>
> // create my own image
> CustomImageType m_MemberImage.;
>
> // pointer to an aray of 3 floats
> vecf3 * pixelPointer;
>
> // get pointer to itk output buffer
> pixelPointer =
>  itkFilter->GetOutput()->GetPixelContainer()->GetImportPointer();
>
> // pass the itk buffer to my own application
> m_MemberImage.setData( pixelPointer );
>
> // tell itk filter not to destroy the buffer
>
> itkFilter->GetOutput()->GetPixelContainer()->SetContainerManageMemory(false);
>
> This works fine until I want to deallocated the image buffer using:
> delete[] pixelPointer;
>
> I've used this method before with itk::Image< short, 3> images and it
> worked fine, but now with the vector image my program crashes upon
> deleting the buffer.
>
> Sorry for the confusing, I hope this clarifies it a bit.
>
> Reinhard
>
>
> On Dec 9, 2007 2:37 AM, Luis Ibanez <luis.ibanez at kitware.com> wrote:
> >
> > Hi Reinhard,
> >
> >
> > I'm afraid that by now,
> > your questions are too entangled to address them correctly.
> >
> >
> > Let me rephrase the questions and please correct me if I'm getting
> > them wrong.
> >
> >
> > 1) you are running an ITK pipeline and you want the output of the
> >     pipeline to store its result in a block of memory that you have
> >     pre-allocated from your application.
> >
> >
> > 2) You want to do this with a filter that produces as output an
> >     image whose pixel type is Vector<float,3>.
> >
> >
> > 3) You are attempting to use the following method:
> >
> >      m_Filter->GetOutput()->SetRegions(region);
> >
> >      m_Filter->GetOutput()->GetPixelContainer()->SetImportPointer(
> >          static_cast< OutputPixelType * >( applicationAllocatedBuffer ),
> >          totalNumberOfPixels, false);
> >
> >      m_Filter->GetOutput()->Allocate( );
> >
> >
> > 4) When you run it, it crashes at the moment of dealocating the
> >     memory.
> >
> >
> >
> > Is that right ?
> >
> >
> > If so, this leads to suspect that
> >
> >
> > A) you have not allocated the right size of memory in your application
> >
> >
> > or
> >
> >
> > B) your assumptions about the organization of the pixel components
> >     in memory are not correct.
> >
> >
> >
> > Please provide a fresh description of the state of your problem.
> >
> >
> >    Thanks
> >
> >
> >
> >       Luis
> >
> >
> >
> >
> > ---------------------------
> >
> > Reinhard Hameeteman wrote:
> > > To comment on my own questions:
> > > The error in the second approach, was due to an invalid pointer the
> > > was passed to the itk filter.
> > > However the other 2 questions still remain. And since this approach
> > > preferable because you allocate the memory once it is needed and not
> > > long before that (depending on your filter), I would very much get
> > > some comments on those issues.
> > > Is someone capable of doing so?
> > >
> > > Reinhard
> > >
> > >
> > > On Dec 3, 2007 11:50 AM, Reinhard Hameeteman
> > > <k.hameeteman+maillist at gmail.com> wrote:
> > >
> > >>Hi,
> > >>
> > >>I am experiencing similar problems as described in
> > >>http://www.itk.org/pipermail/insight-users/2005-December/016027.html.
> > >>I use an itk pipeline within another image processing framework
> > >>(MeVisLab). To avoid unnecessary memory copying I want to pass a
> > >>pointer to the image data output from a itk filter output to an other
> > >>data structure. As Luis described in e.g.
> > >>http://www.itk.org/pipermail/insight-users/2007-May/022343.html there
> > >>are 2 methods:
> > >>1) Mummify the buffer of the output filter
> > >>2) Provide the memory buffer to the output filter so when it computes
> > >>the output image, it is already stored in the buffer that you
> > >>provided.
> > >>
> > >>Until now, I used method 1 with success. Like this:
> > >>CustomDatatType m_MemberImage.;
> > >>m_MemberImage.setData(
> > >>itkFilter->GetOutput()->GetPixelContainer()->GetImportPointer() );
> >
> >>itkFilter->GetOutput()->GetPixelContainer()->SetContainerManageMemory(false);
> > >>
> > >>However this only works when I have a scalar voxel type and now I have
> > >>created a pipeline that produces a  itk::Image< itk::Vector< float, 3
> > >>
> > >>>, 3> image. The creation of the image and the passing of the pointer
> > >>
> > >>to my own data structure works fine. But as soon as I try to release
> > >>the memory, my program crashes. This does not happen when the voxel
> > >>type is of type int which is still unexplained.
> > >>
> > >>I used the second method as mentioned by Luis like this:
> > >>
> > >>   CustomDatatType m_MemberImage;
> > >>   // Set size of m_MemberImage and allocate memory
> > >>
> > >>   // Set size of itk output image
> > >>   region.SetSize( size );
> > >>   region.SetIndex( start );
> > >>   itkFilter->GetOutput(1)->SetRegions( region);
> > >>
> > >>   // Set pointer of filter image to allocated data
> > >>   ItkFilterType::VectorVoxelType * pixelData;
> > >>   pixelData = static_cast<ItkFilterType::VectorVoxelType* >(
> > >>m_MemberImage.getData() );
> > >>   itkFilter->GetOutput(1)->
> > >>                 GetPixelContainer()->
> > >>                 SetImportPointer(pixelData, m_MemberImage.getSize(),
> false);
> > >>
> > >>Using this method, there is still a problem with the vector voxel
> > >>typed image. Using an image with int voxels things works fine, but as
> > >>soon as the mentioned vector voxel type is used, access violations
> > >>occur when the itk filter writes to the output buffer. This suggests
> > >>that somehow the size of the buffer or the datatype is not set
> > >>correctly. I checked both and they are ok.
> > >>
> > >>My questions:
> > >>- Could someone comment on the difference in deleting a scalar and
> > >>vector voxel typed image buffer.
> > >>- Is there more generally, any difference in the memory management of
> > >>scalar and multiple component voxel typed images?
> > >>- Are there any suggestions on where to look for the problem in the
> > >>second approach?
> > >>
> > >>Thanks a lot.
> > >>
> > >
> > > _______________________________________________
> > > Insight-users mailing list
> > > Insight-users at itk.org
> > > http://www.itk.org/mailman/listinfo/insight-users
> > >
> >
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