[Insight-users] ImageFilter problems
Bill Lorensen
bill.lorensen at gmail.com
Fri Dec 23 15:01:04 EST 2011
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
-------------- next part --------------
#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;
}
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