[ITK] ITK-4.6 problem - OffsetValueType

[Gib Bogle]

Hi,

I've been digging into the code, and trying to track down where the memory access problem occurs.  By putting some printf statements in itkImage.hxx and itkImageBase.h I think I've got close to the source.  As I suspected it is in the Image::Allocate() function.  As the program output below shows, with N=1625 GetOffsetTable() returns the correct size of the image, but with N=1626 it returns 1626^3 - 2^32.  The problem is that OffsetValueType is only 4 bytes.  I'm reluctant to go further with this because I don't want to risk breaking something, but somebody should know why OffsetValueType has this size and how to increase it to 8 bytes in the case of ITK_USE_64BITS_IDS on.

itkImage.hxx:

void
Image< TPixel, VImageDimension >
::Allocate(bool initializePixels)
{
  SizeValueType num;

  this->ComputeOffsetTable();
  num = static_cast<SizeValueType>(this->GetOffsetTable()[VImageDimension]);
  printf("Image::Allocate: GetOffsetTable(): %lld\n",this->GetOffsetTable()[VImageDimension]); //Gib
  printf("Image::Allocate: num: %lld\n",num); //Gib
  m_Buffer->Reserve(num, initializePixels);
}

itkImageBase.h:

  const OffsetValueType * GetOffsetTable() const { 
  printf("Image::Allocate: sizeof(OffsetValueType): %d\n",sizeof(OffsetValueType));	//Gib
	  return m_OffsetTable; }


D:\testing\ITK\bigtiff>Release\makebig.exe zzz-4.6.tif 1625 1
Output image file: zzz-4.6.tif
Desired image dimensions: width, height, depth: 1625 1625 1625
Image::Allocate: sizeof(OffsetValueType): 4
Image::Allocate: sizeof(OffsetValueType): 4
Image::Allocate: GetOffsetTable(): 4291015625
Image::Allocate: num: 4291015625
Requested image dimensions: width, height, depth: 1625 1625 1625
imregion size(0): 1625
imregion size(1): 1625
imregion size(2): 1625
Image::FillBuffer: numberOfPixels: 4291015625

D:\testing\ITK\bigtiff>Release\makebig.exe zzz-4.6.tif 1626 1
Output image file: zzz-4.6.tif
Desired image dimensions: width, height, depth: 1626 1626 1626
Image::Allocate: sizeof(OffsetValueType): 4
Image::Allocate: sizeof(OffsetValueType): 4
Image::Allocate: GetOffsetTable(): 3975080
Image::Allocate: num: 3975080
Requested image dimensions: width, height, depth: 1626 1626 1626
imregion size(0): 1626
imregion size(1): 1626
imregion size(2): 1626
Image::FillBuffer: numberOfPixels: 3975080
________________________________________
From: Community [community-bounces at itk.org] on behalf of Gib Bogle [g.bogle at auckland.ac.nz]
Sent: Wednesday, 17 September 2014 10:39 a.m.
To: Matt McCormick
Cc: community at itk.org
Subject: Re: [ITK] ITK-4.6 problem

Update on the bug in the version of ITK-4.6 installed by Slicer:

What can we make of this:

    ImageType::Pointer im = ImageType::New();
    ImageType::SizeType imsize;
    imsize[0] = width;
    imsize[1] = height;
    imsize[2] = depth;
    ImageType::IndexType imstart;
    imstart[0] = 0;
    imstart[1] = 0;
    imstart[2] = 0;
    ImageType::RegionType imregion;
    imregion.SetSize(imsize);
    imregion.SetIndex(imstart);
    im->SetRegions(imregion);
    im->Allocate();
    p = (unsigned char *)(im->GetBufferPointer());

    width = im->GetLargestPossibleRegion().GetSize()[0];
    height = im->GetLargestPossibleRegion().GetSize()[1];
    depth = im->GetLargestPossibleRegion().GetSize()[2];
    printf("Requested image dimensions: width, height, depth: %d %d %d\n",width,height,depth);

    printf("imregion size(0): %d\n",imregion.GetSize(0));
    printf("imregion size(1): %d\n",imregion.GetSize(1));
    printf("imregion size(2): %d\n",imregion.GetSize(2));

    int i = 195000000;
    for (int i=197160890; i<200000000;i++) {
        printf("offset: %d\n",i);
        p[i] = 0;
    }

yields (reproducibly):

D:\testing\ITK\bigtiff>Release\makebig.exe big1650c-4.6.tif 1650 0
...
Requested image dimensions: width, height, depth: 1650 1650 1650
imregion size(0): 1650
imregion size(1): 1650
imregion size(2): 1650
offset: 197160890
offset: 197160891
offset: 197160892
offset: 197160893
offset: 197160894
offset: 197160895
offset: 197160896
<crash>

(If instead of writing to the image buffer I do this: im->FillBuffer(0) the program crashes when it attempts writer->Update().)

Varying the size of the image (NxNxN) I find that N = 1625 is OK, N = 1626 crashes at z=2, buffer offset = 5287752 (clearly the offset index is insignificant).  1626^3 is slightly bigger than 2^32.

I checked that the ITK build definitely had ITKV3_COMPATIBILITY off and therefore ITK_USE_64BITS_IDS on.

I'm wondering if the image buffer allocation  im->Allocate() is successful in the cases that crash.  How can I check that?

I'd appreciate some pointers.

Thanks
Gib

________________________________________
From: Matt McCormick [matt.mccormick at kitware.com]
Sent: Wednesday, 17 September 2014 1:48 a.m.
To: Gib Bogle
Cc: community at itk.org
Subject: Re: [ITK] ITK-4.6 problem

Hi Gib,

>
> There is something a bit funny about the installed ITK-4.6, in that the
> compiler complained about some missing include files, vnl_*.h and others,
> which are in my ITK-4.0 installation but not in 4.6.  I just copied them
> across - I hope this is not a problem.
>

This is probably a problem.  Did the ITK 4.6 build complete
successfully and the install complete successfully?

Thanks,
Matt
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