[Insight-users] Resampling 64-bit crash
Atwood, Robert C
r.atwood at imperial.ac.uk
Wed Feb 14 14:08:25 EST 2007
Hmm. The follwing program does not crash, but the output size is a bit
strange.
Similar results obtained in real-3d with x=1000, y=m*1000, z=1000
In my test prog, below, the size is multiplied by the 3rd command line
argument.
--Robert
./ResampleBig bshell176.png t.mhd 10
-rw-r--r-- 1 rcatwood staff8 1.4G Feb 14 18:46 t.raw
-rw-r--r-- 1 rcatwood staff8 260 Feb 14 18:46 t.mhd
./ResampleBig bshell176.png t.mhd 5
-rw-r--r-- 1 rcatwood staff8 259 Feb 14 18:50 t.mhd
-rw-r--r-- 1 rcatwood staff8 673M Feb 14 18:50 t.raw
./ResampleBig bshell176.png t.mhd 2
-rw-r--r-- 1 rcatwood staff8 259 Feb 14 18:54 t.mhd
-rw-r--r-- 1 rcatwood staff8 1.9G Feb 14 18:54 t.raw
So, it does appear that the amount of data in the image gets weird for
large sizes.
Alarmingly, using 3 or 4 gives an empty file:
./ResampleBig bshell176.png t.mhd 4
-rw-r--r-- 1 rcatwood staff8 0 Feb 14 19:00 t.raw
-rw-r--r-- 1 rcatwood staff8 278 Feb 14 19:00 t.mhd
itk_example_build]$ file t.raw
t.raw: empty
//BEGINNING of program .. Based on ResampleImageFilter.cxx example
#if defined(_MSC_VER)
#pragma warning ( disable : 4786 )
#endif
#ifdef __BORLANDC__
#define ITK_LEAN_AND_MEAN
#endif
#include "itkImage.h"
#include "itkImageFileReader.h"
#include "itkImageFileWriter.h"
#include "itkResampleImageFilter.h"
#include "itkAffineTransform.h"
#include "itkNearestNeighborInterpolateImageFunction.h"
int main( int argc, char * argv[] )
{
if( argc < 4 )
{
std::cerr << "Usage: " << std::endl;
std::cerr << argv[0] << " inputImageFile outputImageFile";
std::cerr << " multiplier " << std::endl;
return EXIT_FAILURE;
}
int mul = 1;
if( argc >= 4 )
{
mul = atoi( argv[3] );
}
const unsigned int Dimension = 2;
typedef unsigned char InputPixelType;
typedef unsigned char OutputPixelType;
typedef itk::Image< InputPixelType, Dimension > InputImageType;
typedef itk::Image< OutputPixelType, Dimension > OutputImageType;
typedef itk::ImageFileReader< InputImageType > ReaderType;
typedef itk::ImageFileWriter< OutputImageType > WriterType;
ReaderType::Pointer reader = ReaderType::New();
WriterType::Pointer writer = WriterType::New();
reader->SetFileName( argv[1] );
writer->SetFileName( argv[2] );
typedef itk::ResampleImageFilter<InputImageType,OutputImageType>
FilterType;
FilterType::Pointer filter = FilterType::New();
typedef itk::AffineTransform< double, Dimension > TransformType;
TransformType::Pointer transform = TransformType::New();
filter->SetTransform( transform );
typedef itk::NearestNeighborInterpolateImageFunction<
InputImageType, double > InterpolatorType;
InterpolatorType::Pointer interpolator = InterpolatorType::New();
filter->SetInterpolator( interpolator );
filter->SetDefaultPixelValue( 0 );
double spacing[ Dimension ];
spacing[0] = 1.0; // pixel spacing in millimeters along X
spacing[1] = 1.0; // pixel spacing in millimeters along Y
filter->SetOutputSpacing( spacing );
double origin[ Dimension ];
origin[0] = 0.0; // X space coordinate of origin
origin[1] = 0.0; // Y space coordinate of origin
filter->SetOutputOrigin( origin );
InputImageType::SizeType size;
size[0] = 1000 * 1000; // number of pixels along X
size[1] = mul * 1000; // number of pixels along Y
std::cout << " Size = " << size[0] * size [1] << std::endl;
std::cout << " Size : " << size << std::endl;
filter->SetSize( size );
std::cout << " Filter : " << filter << std::endl;
filter->SetInput( reader->GetOutput() );
writer->SetInput( filter->GetOutput() );
try{
writer->Update();
} catch(itk::ExceptionObject & e) {
std::cerr << "FAILED writer update: " << e << std::endl;
return EXIT_FAILURE;
}
return EXIT_SUCCESS;
}
//END of program
> -----Original Message-----
> From: Florian Pierron [mailto:F.Pierron at exeter.ac.uk]
> Sent: 14 February 2007 15:11
> To: Atwood, Robert C; insight-users at itk.org
> Subject: Re: [Insight-users] Resampling 64-bit crash
>
> Hi Robert,
>
> Thank you for your quick reply.
>
> I haven't changed the dimension, I'm still in 2D. And it's
> working fine
> for me when size[0] * size[1] is less than 2 GB but not when
> it's more
> than 3-4 GB :-(. So if you can try to make it work with a
> size of 5 GB
> on your configuration, it would be really good / helpful!
>
> Regards,
> Florian
>
>
> On 14/02/2007 14:58, Atwood, Robert C wrote:
> > Maybe I am being dumb here, but did you change 'dimension' to 3 as
> > well, or not? (Line 127)
> >
> > I don't think you can set 3d dimensions for a 2d filter? Maybe this
> > causes a compiler/OS dependent crash behaviour? If I do as you say
> > exactly, I get failure on output with weird messages (but maybe you
> > can't put a 3d image in a png file!) 'Reason: Success'
> seems like kind
> > of a bad reason to abort.
> >
> >
> > Using linux RedHat , but also AMD64 Dual core processors,
> and 16 Gb of
> > physical RAM.
> >
> > [itk_example_build]$ ./ResampleBig BrainSliceBinary.png
> > BrainSliceBinaryOutput.png 0
> > terminate called after throwing an instance of
> 'itk::ExceptionObject'
> > what(): /sources/local/ITK_cvs/Code/IO/itkPNGImageIO.cxx:503:
> > itk::ERROR: PNGImageIO(0xa00520): Error while writing Slice to file:
> > BrainSliceBinaryOutput.png
> > Reason: Success
> > Aborted
> >
> >
> >
> >
> >
> >
> >
> >
> >
> >> -----Original Message-----
> >> From: insight-users-bounces+r.atwood=imperial.ac.uk at itk.org
> >> [mailto:insight-users-bounces+r.atwood=imperial.ac.uk at itk.org]
> >> On Behalf Of Florian Pierron
> >> Sent: 14 February 2007 14:06
> >> To: insight-users at itk.org
> >> Subject: [Insight-users] Resampling 64-bit crash
> >>
> >> Dear ITK users and developers,
> >>
> >> We need to resample big data and we decided to port our
> >> application in
> >> 64-bit version. We're currently working on Windows Server 2003,
> >> Enterprise x64 Edition, Dual Core AMD Opteron and using
> >> ITK-3-0 branch
> >> with VC2005. Unfortunately our application crashes when trying to
> >> resample big data.
> >>
> >> We reproduced the crash with the ResampleImageFilter example
> >> (D:\InsightToolkit-3.0.0\Examples\Filtering\ResampleImageFilte
> >> r.cxx) by
> >> changing the size of the output image to be more than 3-4 GB:
> >> Line 279: size[0] = 5 * 1000 * 1000; // number of
> pixels along X
> >> Line 280: size[1] = 1 * 1000; // number of pixels along Y
> >>
> >> We run this example by setting the working directory to
> >> "D:\InsightToolkit-3.0.0\Testing\Data\Input" and the command line
> >> arguments to
> >> "BrainSliceBinary.png BrainSliceBinaryOutput.png 0" (a
> random image I
> >> found in the ITK folder).
> >>
> >> 1) If I run this example with the modified size above (5 GB),
> >> it crashes
> >> immediately in:
> >>
> >> /** Set the pixel. */
> >> inline void Set(TType & output, const TType & input) const
> >> {output = input;}
> >>
> >> with this call stack:
> >>
> >> ResampleImageFilter.exe!itk::DefaultPixelAccessor<unsigned
> >> char>::Set(unsigned char & output=, const unsigned char &
> >> input=0) Line
> >> 67 + 0x1d bytes
> >>
> >> ResampleImageFilter.exe!itk::DefaultPixelAccessorFunctor<itk::
> >> Image<unsigned
> >> char,2> >::Set(unsigned char & output=, const unsigned char &
> >> input=0)
> >> Line 77
> >>
> >> ResampleImageFilter.exe!itk::ImageLinearIteratorWithIndex<itk:
> >> :Image<unsigned
> >> char,2> >::Set(const unsigned char & value=0) Line 106 +
> 0x47 bytes
> >>
> >>
> ResampleImageFilter.exe!itk::ResampleImageFilter<itk::Image<unsigned
> >> char,2>,itk::Image<unsigned
> >> char,2>,double>::LinearThreadedGenerateData(const
> >> itk::ImageRegion<2> &
> >> outputRegionForThread={...}, int threadId=2) Line 481
> >>
> >>
> ResampleImageFilter.exe!itk::ResampleImageFilter<itk::Image<unsigned
> >> char,2>,itk::Image<unsigned
> >> char,2>,double>::ThreadedGenerateData(const
> >> itk::ImageRegion<2> & outputRegionForThread={...}, int
> >> threadId=2) Line 192
> >> ResampleImageFilter.exe!itk::ImageSource<itk::Image<unsigned
> >> char,2> >::ThreaderCallback(void * arg=0x0000000002c2f4f8)
> Line 282
> >>
> >> ResampleImageFilter.exe!itk::MultiThreader::SingleMethodProxy(void
> >> * arg=0x0000000002c2f4f8) Line 748
> >> msvcr80d.dll!_callthreadstartex() Line 348 + 0x17 bytes
> >> msvcr80d.dll!_threadstartex(void *
> >> ptd=0x0000000002c3c8f0) Line 331
> >>
> >>
> >> 2) If I change the size to be 2GB, it's running fine. The
> >> limit between
> >> crashing and not crashing seems to be between 2 and 3 GB
> >> (with 8 threads).
> >>
> >> 3) If I force the SetNumberOfTheads to 1, it doesn't crash
> >> immediately
> >> (I think it crashes later, but it's quite slow so most of
> the time I
> >> killed it before). The funny thing is that when the number of
> >> threads is
> >> equal to 1:
> >> - if the size is 4 GB, then 4 GB of memory is allocated immediately
> >> - but if the size is 5 GB, only 700 MB is allocated
> >> - for 7 GB, 2.65 GB is allocated
> >> - for 10 GB, 1.4 GB is allocated (which is weirdly twice the 5GB)
> >> I have no idea if this is meaningful at all, I was just
> wondering if
> >> there's a problem during memory allocation when the 4GB limit
> >> is reached...
> >>
> >>
> >> Any ideas?
> >>
> >> Cheers,
> >> Florian
> >>
> >> _______________________________________________
> >> Insight-users mailing list
> >> Insight-users at itk.org
> >> http://www.itk.org/mailman/listinfo/insight-users
> >>
> >>
> >
> >
>
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