[Insight-users] ImageFilter problems
Fleysher, Lazar
lazar.fleysher at mountsinai.org
Fri Dec 23 17:47:46 EST 2011
Dear Bill
I did try catching am exception, but none is generated.
The filter was there in the code. I tried to put another one (laplacian), but
Result is the same: seg fault inside Update()....
Lazar
________________________________________
From: Bill Lorensen [bill.lorensen at gmail.com]
Sent: Friday, December 23, 2011 17:21
To: Fleysher, Lazar
Cc: Insight-users at itk.org
Subject: Re: [Insight-users] ImageFilter problems
Where did you get the filter: OptimalSharpeningImageFilter?
On Fri, Dec 23, 2011 at 4:41 PM, Bill Lorensen <bill.lorensen at gmail.com> wrote:
> Put a try/catch block around your code:
> try
> {
> your code
> catch (itk::ExceptionObject& e)
> {
> std::cerr << "Exception detected: " << e;
> return EXIT_FAILURE;
> }
>
> On Fri, Dec 23, 2011 at 4:23 PM, Fleysher, Lazar
> <lazar.fleysher at mountsinai.org> wrote:
>> Hello Bill
>>
>> Yes of course I have tried your version. As I said, I will not be
>> able to use your approach in the final application, but for test
>> purposes I did run your program with the same segmentation violation.
>> (in my final application I will need the pointer to filtered image as I will
>> do more things to it)
>>
>> ProcessObject::UpdateOutputData and calls inside it
>> cause segmentation violation whether update() is called directly or not.
>>
>> Thank you very much for your help
>>
>> Lazar
>> ________________________________________
>> From: Bill Lorensen [bill.lorensen at gmail.com]
>> Sent: Friday, December 23, 2011 16:09
>> To: Fleysher, Lazar
>> Cc: Insight-users at itk.org
>> Subject: Re: [Insight-users] ImageFilter problems
>>
>> itk does not use intermediate storage. When you say image1 = image2 it
>> is just assigning pointers.
>>
>> I'll try compiling and running your test program if I get a chance.
>>
>> Did you try my test program?
>>
>> On Fri, Dec 23, 2011 at 3:42 PM, Fleysher, Lazar
>> <lazar.fleysher at mountsinai.org> wrote:
>>> 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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>>>>>>
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>>>>>
>>>>>
>>>>>
>>>>> --
>>>>> Unpaid intern in BillsBasement at noware dot com
>>>>
>>>>
>>>>
>>>> --
>>>> Unpaid intern in BillsBasement at noware dot com
>>>
>>>
>>>
>>> --
>>> Unpaid intern in BillsBasement at noware dot com
>>
>>
>>
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>> Unpaid intern in BillsBasement at noware dot com
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