[Insight-users] ConnectedThresholdImageFilter does take into accopunt the configuration
Luis Ibanez
luis.ibanez at kitware.com
Thu Oct 8 09:42:51 EDT 2009
Hi Vincent,
Thanks for the additional information.
You made an interesting observation,
It is very strange and suspicious that
the values printed by filter->Print()
do not correspond to the values of
Lower/Upper/DebugOn and that you
are setting.
It looks like the filter is created in two
separate places and we are looking at
two different pieces of code.
Any chance that you can run this in
Debug mode ?
It will be really helpful to locate the
exact line where it is crashing (inside
the Update() method call), AND to
look at the callstack to trace back
what method call lead to that point.
Please let us know if you can do that,
Thanks
Luis
--------------------------------------------------------
On Thu, Oct 8, 2009 at 9:32 AM, Daanen Vincent <daanen at koelis.com> wrote:
> Hi Luis,
>
> Thanks for your input.
>
>> An easy way to verify this, would be to pass the image to
>> an itkImageFileWriter<> and to save it to disk.
>
> I follow your requirement and thus, i could write my image on the disk ...I
> checked the image and it is ok.
>
>> BTW: It is normal for the connected threshold filter not to
>> offer the full connectivity option when ITK has been configured
>> with REVIEW off. The reason is that this is a new feature, that
>> relies on a new Iterator class that is currently in the Code/Review
>> directory.
>
> OK
>
>> In particular, you want to review the code of
>>
>> TItkInterface::Gmcao2Itk(*l_pImg);
>>
>> and make sure that the ITK image produced by the ImportFilter
>> is held ALL THE TIME by a SmartPointer.
> Yes it is
>
>>
>> Also, please double check the settings of the boolean flag that
>> defines who will be responsible for releasing the memory of
>> the imported image. (Wrongly setting this boolean is also
>> a common mistake when importing images).
>
> The application is responsible for releasing the memory of
>> the imported image and since I can write the imported image on the disk ,I
> think it's ok.
>
> The crash occurs on the following line:
> l_pFilter->Update();
> So during the filter processing I guess ....
>
> Hereafter the output of the call to l_pFilter->Print() method:
>
> ConnectedThresholdImageFilter (003E7E48)
> RTTI typeinfo: class itk::ConnectedThresholdImageFilter<class
> itk::Image<unsigned char,3>,class itk::Image<unsigned char,3> >
> Reference Count: 1
> Modified Time: 53
> Debug: On
> Observers:none
> Number Of Required Inputs: 1
> Number Of Required Outputs: 1
> Number Of Threads: 2
> ReleaseDataFlag: Off
> ReleaseDataBeforeUpdateFlag: Off
> Input 0: (003EA538)
> Input 1: (003E81C8)
> Input 2: (003ECF80)
> Output 0: (003E7F28)
> AbortGenerateData: Off
> Progress: 0
> Multithreader:
> RTTI typeinfo: class itk::MultiThreader
> Reference Count: 1
> Modified Time: 27
> Debug: Off
> Observers:
> none
> Thread Count: 2
> Global Maximum Number Of Threads: 128
> Global Default Number Of Threads: 2
> Upper: 255
> Lower: 0
> ReplaceValue: 1
> Connectivity: 0
>
> As you can see, Lower/Upper = [0 255] but I explicitly set them to 100/130
> Debug is also OFF but I set it to on just before the call to Print ...
>
> Any Idea ?
>
> Vincent
>>
>>
>>
>> Regards,
>>
>>
>> Luis
>>
>>
>> ------------------
>> On Wed, Oct 7, 2009 at 2:17 AM, Daanen Vincent
>> <daanen at koelis.com> wrote:
>> > Hi Itk users,
>> >
>> > I want to use itk::ConnectedThresholdImageFilter to extract
>> a object from a
>> > 3D image.
>> > I first load the image and convert it from our own image
>> format into itk
>> > image format. The call to CItkInterface::Gmcao2Itk is just
>> a wrapper to
>> > ItkImageimportFilter.
>> > I can say it is ok (I play several tests to check that all
>> the data are
>> > correctly converted...)
>> >
>> > I then instantiate a itk::ConnectedThresholdImageFilter
>> ,set its input, the
>> > thresholds and the seed. (My code is nearly the same that
>> the one in the itk
>> > user guide)
>> >
>> > When I call Update, the software crashes with messages in a
>> window but I
>> > can't read them totally ...:(
>> >
>> > So, before calling update, I print the component on screen
>> (using Print
>> > method) and I can see that the thresholds are not the one I
>> set (low = 0;
>> > high = 255) instead of (L/H = 100/130).
>> > I also saw that there is not method to set the connectivity
>> unless itk is
>> > compiled with ITK_USE_REVIEW. Is this normal ? I can not see why the
>> > connectivity is link to the REVIEW flag
>> >
>> > How can I find why the filter exit without making its work ?
>> >
>> > Thx for help
>> >
>> > Vince
>> >
>> > PS : the code I wrote. If someone sees something wrong,
>> please tell me
>> >
>> > void Test()
>> > {
>> >
>> > /// Our Own core work
>> > typedef gmcao::CImage<BYTE,3> TImage;
>> > CSmartPtr<TImage> l_pImg(new TImage);
>> >
>> > if
>> (!gmcao::CImageTools<TImage>::ReadImage(*l_pImg,"Img.hdr"))
>> > {
>> > std::cout<<"Could not read image"<<std::endl;
>> > return;
>> > }
>> >
>> > typedef CItkInterface<TImage::TValue, TImage::Dim>
>> TItkInterface;
>> > TItkInterface::TItkImage::Pointer l_pIktImg =
>> > TItkInterface::Gmcao2Itk(*l_pImg);
>> > if (l_pIktImg.IsNull())
>> > {
>> > std::cout<<"Error converting Gmcao ->
>> Itk"<<std::endl;
>> > return;
>> > }
>> > ///
>> >
>> > /// Itk filter
>> > typedef
>> >
>> itk::ConnectedThresholdImageFilter<TItkInterface::TItkImage,TI
>> tkInterface::T
>> > ItkImage> TFilter;
>> > TFilter::Pointer l_pFilter=TFilter::New();
>> > if (l_pFilter.IsNull())
>> > {
>> > std::cout<<"Could not create filter"<<std::endl;
>> > return;
>> > }
>> >
>> > l_pFilter->SetInput(l_pIktImg);
>> > l_pFilter->SetLower(100);
>> > l_pFilter->SetUpper(130);
>> >
>> > TFilter::IndexType l_Seed;
>> > l_Seed[0] = l_pImg->GetWidths()[0]>>1;
>> > l_Seed[1] = l_pImg->GetWidths()[1]>>1;
>> > l_Seed[2] = l_pImg->GetWidths()[2]>>1;
>> >
>> > l_pFilter->SetSeed(l_Seed);
>> >
>> > l_pFilter->DebugOn();
>> > l_pFilter->Print(std::cout);
>> >
>> > try
>> > { l_pFilter->Update();}
>> > catch( itk::ExceptionObject &excep )
>> > {
>> > std::cerr << "Exception caught !" << std::endl;
>> > std::cerr << excep << std::endl;
>> > }
>> > }
>> >
>> > --------------------------------------------
>> > Vincent Daanen, PhD
>> > D&D Manager
>> >
>> > --------------------------------------------
>> > KOELIS
>> > 5, avenue du Grand Sablon 38700 La Tronche
>> > www.koelis.com - daanen at koelis.com
>> > Tel .+33(0) 476637588 Fax .+33(0) 476637592
>> > --------------------------------------------
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