[Insight-users] ImageFilter problems
Fleysher, Lazar
lazar.fleysher at mountsinai.org
Sat Dec 24 10:18:25 EST 2011
Hello Bill
I am definitely missing something...
Below is the code I use. There is a line with // which shows the Laplacian filter
I tried to use with the same outcome....
Thanks
Lazar
--------------------------------
start code
--------------------------------
#include "itkArray.h"
#include "itkVariableLengthVector.h"
#include "itkImage.h"
#include "itkImageRegionConstIterator.h"
#include "itkImageFileReader.h"
#include "itkImageFileWriter.h"
#include "itkImageRegionIteratorWithIndex.h"
#include "itkOptimalSharpeningImageFilter.h"
#include "itkLaplacianSharpeningImageFilter.h"
/////////////////////////////////////////////////////
template <unsigned int ImageDimension,unsigned int NVectorComponents>
int TestFilter(unsigned int argc, char *argv[])
{
std::cout << "testFilter executed" << std::endl;
typedef float PixelType;
typedef itk::Image<PixelType, ImageDimension> ImageType;
typedef itk::ImageRegionIteratorWithIndex<ImageType> Iterator;
typedef itk::ImageFileReader<ImageType> ImageFileReader;
typedef itk::ImageFileWriter<ImageType> writertype;
typename ImageType::Pointer averageimage = NULL;
typename ImageFileReader::Pointer reader = ImageFileReader::New();
reader->SetFileName(argv[2]); // load this image...
reader->Update();
averageimage=reader->GetOutput();
typedef itk::OptimalSharpeningImageFilter<ImageType,ImageType > sharpeningFilter;
// typedef itk::LaplacianSharpeningImageFilter<ImageType,ImageType > sharpeningFilter;
typename sharpeningFilter::Pointer shFilter = sharpeningFilter::New();
shFilter->SetInput( averageimage );
shFilter->SetSValue(0.5);
std::cout << "before" << std::endl;
shFilter->Update();
std::cout << "after" << std::endl;
std::cout << " writing output ";
{
typename writertype::Pointer writer = writertype::New();
writer->SetFileName(argv[1]); // save into this name....
writer->SetInput( shFIlter->GetOutput() );
writer->Update();
}
return 0;
}
/////////////////////////////////////////////////////
int main(int argc, char * argv[])
{
TestFilter<3,1>(argc,argv);
return 0;
}
---------------------------------------------------
end of code
--------------------------------------------------
________________________________________
From: Bill Lorensen [bill.lorensen at gmail.com]
Sent: Saturday, December 24, 2011 07:52
To: Fleysher, Lazar
Cc: Insight-users at itk.org
Subject: Re: [Insight-users] ImageFilter problems
Please send me your code.
On Sat, Dec 24, 2011 at 6:45 AM, Fleysher, Lazar
<lazar.fleysher at mountsinai.org> wrote:
> 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
>>>>>>>> _____________________________________
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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
>>>>
>>>>
>>>>
>>>> --
>>>> 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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