[Insight-users] ImageFilter problems
Fleysher, Lazar
lazar.fleysher at mountsinai.org
Fri Dec 23 11:39:44 EST 2011
Dear Bill Lorensen
averageimage is decleared as float 3D and then it is read from a (NIFTI) file....
typename ImageFileReader::Pointer reader = ImageFileReader::New();
reader->SetFileName(argv[bigimage]);
reader->Update();
averageimage=reader->GetOutput();
If I understood you correctly, I should run filter-> Update()
than to save the image do writer->SetInput(shFilter->GetOutput());
What is wrong with doing averageimage=shFilter->GetOutput()
followed by writer->SetInput(averageimage) ?
Regardless, shFilter->Update() generates a segmentation violation.
If I comment out the filter part, the image gets saved in to a file
and everything seem to work correctly.
So there is something strange with the filter ... but what?
Here is the output of gdb. Definitely there is a problem with some threads...
[New Thread 2122320192 (LWP 15648)]
[New Thread 46912496267840 (LWP 15512)]
[New Thread 46913547483456 (LWP 15649)]
[New Thread 46914596063552 (LWP 15650)]
[Thread 2122320192 (LWP 15648) exited]
[Thread 46914596063552 (LWP 15650) exited]
[Thread 46913547483456 (LWP 15649) exited]
Program received signal SIGSEGV, Segmentation fault.
[Switching to Thread 46912496267840 (LWP 15512)]
0x0000003482c076e8 in pthread_join () from /lib64/libpthread.so.0
Here we see that the filter created 4 threads, but could not join them correctly.
Furthermore:
(gdb) where
#0 0x0000003482c076e8 in pthread_join () from /lib64/libpthread.so.0
#1 0x00000000007dd2b5 in itk::MultiThreader::WaitForSingleMethodThread (this=0x1a11160, threadHandle=3)
at /work/home/xxx/ANTS/ITK_SOURCE/ITK/Modules/Core/Common/src/itkMultiThreaderPThreads.cxx:210
#2 0x00000000007dd9af in itk::MultiThreader::SingleMethodExecute (this=0x1a11160)
at /work/home/xxx/ANTS/ITK_SOURCE/ITK/Modules/Core/Common/src/itkMultiThreader.cxx:332
#3 0x00000000007207fb in itk::ImageSource<itk::Image<double, 3u> >::GenerateData (this=0x19cf700)
at /work/home/xxx/ANTS/ITK_SOURCE/ITK/Modules/Core/Common/include/itkImageSource.hxx:275
#4 0x00000000007d36a6 in itk::ProcessObject::UpdateOutputData (this=0x19cf700)
at /work/home/xxx/ANTS/ITK_SOURCE/ITK/Modules/Core/Common/src/itkProcessObject.cxx:1500
#5 0x00000000007e18f8 in itk::DataObject::UpdateOutputData (this=0x19c3830) at /work/home/xxx/ANTS/ITK_SOURCE/ITK/Modules/Core/Common/src/itkDataObject.cxx:434
#6 0x0000000000705f43 in itk::ImageBase<3u>::UpdateOutputData (this=0x19c3830) at /work/home/xxx/ANTS/ITK_SOURCE/ITK/Modules/Core/Common/include/itkImageBase.hxx:285
#7 0x00000000007e1816 in itk::DataObject::Update (this=0x19c3830) at /work/home/xxx/ANTS/ITK_SOURCE/ITK/Modules/Core/Common/src/itkDataObject.cxx:359
#8 0x00000000007d3bc1 in itk::ProcessObject::Update (this=0x19cf700) at /work/home/xxx/ANTS/ITK_SOURCE/ITK/Modules/Core/Common/src/itkProcessObject.cxx:1096
#9 0x000000000077a82a in itk::OptimalSharpeningImageFilter<itk::Image<float, 3u>, itk::Image<float, 3u> >::GenerateData (this=0x19ce520)
at /work/home/xxx/ANTS/ANTS_SOURCE/ANTS/Examples/../Utilities/itkOptimalSharpeningImageFilter.hxx:142
#10 0x00000000007d36a6 in itk::ProcessObject::UpdateOutputData (this=0x19ce520)
at /work/home/xxx/ANTS/ITK_SOURCE/ITK/Modules/Core/Common/src/itkProcessObject.cxx:1500
#11 0x00000000007e18f8 in itk::DataObject::UpdateOutputData (this=0x19b52b0) at /work/home/xxx/ANTS/ITK_SOURCE/ITK/Modules/Core/Common/src/itkDataObject.cxx:434
#12 0x0000000000705f43 in itk::ImageBase<3u>::UpdateOutputData (this=0x19b52b0) at /work/home/xxx/ANTS/ITK_SOURCE/ITK/Modules/Core/Common/include/itkImageBase.hxx:285
#13 0x00000000007e1816 in itk::DataObject::Update (this=0x19b52b0) at /work/home/xxx/ANTS/ITK_SOURCE/ITK/Modules/Core/Common/src/itkDataObject.cxx:359
#14 0x00000000007d3bc1 in itk::ProcessObject::Update (this=0x19ce520) at /work/home/xxx/ANTS/ITK_SOURCE/ITK/Modules/Core/Common/src/itkProcessObject.cxx:1096
#15 0x000000000077d9ad in AverageImages1<3u, 1u> (argc=10, argv=0x7fffffffd7f8) at /work/home/xxx/ANTS/ANTS_SOURCE/ANTS/Examples/AverageImages.cxx:121
#16 0x0000000000633770 in main (argc=10, argv=0x7fffffffd7f8) at /work/home/xxx/ANTS/ANTS_SOURCE/ANTS/Examples/AverageImages.cxx:308
Does this provide some information about what is happening????
The system I am running on is CentOS5, I guess:
cat /etc/redhat-release
Red Hat Enterprise Linux ES release 5
cat /etc/redhat-release.CENTOS5.orig
CentOS release 5.4 (Final)
yum gives me this:
yum list|grep libc
glibc.i686 2.5-42 installed
glibc.x86_64 2.5-42 installed
glibc-common.x86_64 2.5-42 installed
glibc-devel.i386 2.5-42 installed
glibc-devel.x86_64 2.5-42 installed
glibc-headers.x86_64 2.5-42 installed
Is this a problem with libc6?
Thanks
Lazar
________________________________________
From: Bill Lorensen [bill.lorensen at gmail.com]
Sent: Friday, December 23, 2011 08:37
To: Fleysher, Lazar
Cc: Insight-users at itk.org
Subject: Re: [Insight-users] ImageFilter problems
For a filter to run, you must either explicitly call Update() on it,
or a filter down stream.
Can you show the code that creates averageimage?
Also, you should remove the statement:
averageimage = shFilter->GetOutput();
It is already used as input to your filter. You are probably
introducing some sort of cycle in the pipeline.
Try
writer->SetInput(shFilter->GetOutput());
On Fri, Dec 23, 2011 at 8:19 AM, Fleysher, Lazar
<lazar.fleysher at mountsinai.org> wrote:
>
>
> Hello insight-users at itk.org.
>
> I am new to ITK and I am experiencing a strange problem with the image filters.
> So I was wondering if someone could shed some light on this.
>
> I have this code
>
>
> typedef itk::OptimalSharpeningImageFilter<ImageType,ImageType > sharpeningFilter;
> typename sharpeningFilter::Pointer shFilter = sharpeningFilter::New();
> shFilter->SetInput( averageimage );
> shFilter->SetSValue(0.5);
> // shFilter->Update();
> averageimage = shFilter->GetOutput();
>
>
> which should filter the averageimage.
>
> Unfortunately, when I run this code the resulting averageimage contains zero pixels.
> If I uncomment the "Update()" call (which I do not know if is needed) then
> the Update() generates a segmentation violation.
>
>
> I have ITK installed from sources using git clone git://itk.org/ITK.git from
> 2 days ago. I think it is version 4.1.
>
> Also, I have noticed that if I do not call Update() and try to save the image with
>
> typename writertype::Pointer writer = writertype::New();
> writer->SetFileName("aaa");
> writer->SetInput( averageimage );
> writer->Update();
>
> writer->Update() never returns. That is, it cannot write an empty image.
>
> Am I doing something wrong? What is going on?
>
> Thank you very much for your help
>
> Lazar
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