[Insight-users] ImageFilter problems
Fleysher, Lazar
lazar.fleysher at mountsinai.org
Fri Dec 23 15:42:14 EST 2011
Dear Bill
You suggest to feed the output of filter directly into the writer without
the use of an intermediate storage. While in my end application
this will not work, I have tried it here and the same thing happens.
The segmentation violation is generated on filter->update() call...
There is something wong with ITK or libc
What do you think?
Lazar
________________________________________
From: Bill Lorensen [bill.lorensen at gmail.com]
Sent: Friday, December 23, 2011 15:01
To: Fleysher, Lazar
Cc: Insight-users at itk.org
Subject: Re: [Insight-users] ImageFilter problems
Try my attached version
On Fri, Dec 23, 2011 at 2:48 PM, Fleysher, Lazar
<lazar.fleysher at mountsinai.org> wrote:
> Hello Bill
>
> Sorry for not being clear. Attached is the example which I am trying to work out.
>
> The way to execute is :
>
> TestFilter blah.nii.gz r16slice.nii.gz
>
> (unfortunately the image file is too large to be accepted by the mailing list)
>
> The function reads the file r16slice and applies filter to it and saves it on disk into blah.nii.gz
>
> If I do not exectute shFilter->Update(); than averageimage has no pixels just before write.
> If I do execute shFilter->Update(); then this causes segmentation violation.
> If I do not execute shFilter->Update(); and do not execute averageimage = shFilter->GetOutput();
> then the function works as copy and blah.nii.gz is identical to the r16slice.nii.gz....
>
> Thank you very much for your help
>
> Lazar
> ________________________________________
> From: Bill Lorensen [bill.lorensen at gmail.com]
> Sent: Friday, December 23, 2011 12:44
> To: Fleysher, Lazar
> Cc: Insight-users at itk.org
> Subject: Re: [Insight-users] ImageFilter problems
>
> itk is a demand driven pipelined system. Typically you set the input
> to the next filter to be the output of the previous filter. Setting
> the input/output chain just establishes the pipeline and does not
> execute it. When you do an Updtae() on the last filter, the pipeline
> executes.
>
> averageimage=shFilter->GetOutput() is OK, but in your first email you had said:
> shFilter->SetInput( averageimage );
> shFilter->SetSValue(0.5);
> // shFilter->Update();
> averageimage = shFilter->GetOutput();
>
> This modified averageimage was was the input to shFilter.
>
>
> Please post a complete small, compilable example that fails. Including
> snippets in e-mails is too prone to error and misinterpretation.
>
> thanks,
>
> Bill
>
> On Fri, Dec 23, 2011 at 11:39 AM, Fleysher, Lazar
> <lazar.fleysher at mountsinai.org> wrote:
>> 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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>>
>>
>>
>> --
>> Unpaid intern in BillsBasement at noware dot com
>
>
>
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