[Insight-users] ImageFilter problems
Fleysher, Lazar
lazar.fleysher at mountsinai.org
Sat Dec 24 06:45:56 EST 2011
Hello Bill
Yes I am modifying your code. The only difference between your code and mine
was the use of a pointer to access the filtered data... (was there anything else that I missed?)
For laplacian example simply replace
typedef itk::OptimalSharpeningImageFilter<ImageType,ImageType > sharpeningFilter;
with
typedef itk::LaplacianSharpeningImageFilter<ImageType,ImageType > sharpeningFilter;
Same result: seg fault on Update...
Thanks
Lazar
________________________________________
From: Bill Lorensen [bill.lorensen at gmail.com]
Sent: Friday, December 23, 2011 17:52
To: Fleysher, Lazar
Cc: Insight-users at itk.org
Subject: Re: [Insight-users] ImageFilter problems
You are modifying my code, correct?
Please send the code with the LaplacianSharpening.
On Fri, Dec 23, 2011 at 5:47 PM, Fleysher, Lazar
<lazar.fleysher at mountsinai.org> wrote:
> 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
>>>>>>> _____________________________________
>>>>>>> Powered by www.kitware.com
>>>>>>>
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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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>> Unpaid intern in BillsBasement at noware dot com
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