[Insight-users] Segmenation Error--after set advection image by GVF flow
Baoyun Li
baoyun_li123 at yahoo.com
Fri Mar 6 12:38:01 EST 2009
Dear Amardeep:
Finally, my code can work now.
I have to add geodesicActiveContour->GenerateSpeedImage(). Without it, the program always shows segmentation error.
Can you please share some experience about the selection of GVF parameters for 3D images"
> > m_GVFFilter->SetNoiseLevel(500);
> > m_GVFFilter->SetTimeStep(0.05);
> > m_GVFFilter->SetIterationNum(5);
Thanks for your help.
Baoyun
________________________________
From: Amardeep Singh <amar.singh at gmx.de>
To: Baoyun Li <baoyun_li123 at yahoo.com>; insight-users at itk.org
Sent: Friday, March 6, 2009 10:44:54 AM
Subject: Re: Segmenation Error--after set advection image by GVF flow
Dear Baoyun
I am not sure, I understand what you mean by saying "Since you just recently fixed the GVF as advection term".
I had hacked the code, because I did not know of the flag "SetAutoGenerateSpeedAdvection(...)". In the end, I ended up using the same code as you.
You might want to have a look at the full posting:
http://www.nabble.com/Use-of-advection-image-to-guide-geodesic-level-set-td22083962.html#a22159804
Best regards
Amardeep
Baoyun Li wrote:
> Dear Amardeep:
> Thank you for your help. Since you just recently fixed the GVF as advection term, can you please send me a copy of your test code.
> I saw your original code (GVFtest.cc) pasted on the web. But that is not the working version.
> Thanks.
> Baoyun
>
> ------------------------------------------------------------------------
> *From:* Amardeep Singh <amar.singh at gmx.de>
> *To:* Baoyun Li <baoyun_li123 at yahoo.com>
> *Cc:* insight-users at itk.org
> *Sent:* Friday, March 6, 2009 4:36:35 AM
> *Subject:* Re: Segmenation Error--after set advection image by GVF flow
>
> Dear Baoyun
>
> Unfortunately, I have not yet encountered your error message, so I am not sure, if I can help you..
> I would try to save the gradient vector field as a *.vtk file, not in Analyze format, as the gradient vector flow output is a vector field. Can Analyze deal with that? (I don't know.)
> Furthermore, I would suggest that you encapsulate every Update() call in a try-catch block:
> try
> {
> ...->Update();
> }
> catch( itk::ExceptionObject & excep )
> {
> std::cerr << "Exception caught !" << std::endl;
> std::cerr << excep << std::endl;
> }
>
> This might give you more meaningful error messages.
>
> Best regards
> Amardeep
>
> Baoyun Li wrote:
> > Dear All:
> > The error message is: Program *received* signal *SIGFPE*, *Arithmetic exception*.
> > It happens in itkImageHelp.h
> > index[NLoop] = static_cast<IndexValueType>(offset / offsetTable[NLoop]);
> > inline static void ComputeIndexInner(const IndexType &bufferedRegionIndex,
> > OffsetValueType &offset,
> > const OffsetValueType offsetTable[],
> > IndexType &index,
> > const UniqueTypeBoolFalse& )
> > {
> > index[NLoop] = static_cast<IndexValueType>(offset / offsetTable[NLoop]);
> > offset = offset - (index[NLoop] * offsetTable[NLoop]);
> > index[NLoop] = index[NLoop] + bufferedRegionIndex[NLoop];
> > ImageHelper<NImageDimension, NLoop-1>::
> > ComputeIndexInner(bufferedRegionIndex,
> > offset,
> > offsetTable,
> > index,
> > Concept::Detail::UniqueType_bool<(NLoop==1)>());
> > }
> > Does this mean some overflow, or my datatype has some problme.
> > Thanks
> > Baoyun
> >
> > > ------------------------------------------------------------------------
> > *From:* Baoyun Li <baoyun_li123 at yahoo.com <mailto:baoyun_li123 at yahoo.com>>
> > *To:* Amardeep Singh <amar.singh at gmx.de <mailto:amar.singh at gmx.de>>
> > *Cc:* insight-users at itk.org <mailto:insight-users at itk.org>
> > *Sent:* Thursday, March 5, 2009 4:51:41 PM
> > *Subject:* Re: Segmenation Error--after set advection image by GVF flow
> >
> > Dear Amardeep:
> > After I called
> >
> > geodesicActiveContour->SetAdvectionImage(castflowfilter->GetOutput());
> > Do I need to call GenerateAdvectioniImage() since Atumatic Generate is set off.
> > After I add : geodesicActiveContour->GenerateAdvectionImage();
> > I still got error, please give me some suggestions.
> > Baoyun
> > ------------------------------------------------------------------------
> > *From:* Baoyun Li <baoyun_li123 at yahoo.com <mailto:baoyun_li123 at yahoo.com>>
> > *To:* Amardeep Singh <amar.singh at gmx.de <mailto:amar.singh at gmx.de>>
> > *Cc:* insight-users at itk.org <mailto:insight-users at itk.org>
> > *Sent:* Thursday, March 5, 2009 3:25:12 PM
> > *Subject:* Segmenation Error--after set advection image by GVF flow
> >
> > Dear Amardeep and All:
> > Now I can build the program after seting advection image by GVF flow. However, when I run the program, the program shows segmeation error when geodesicActiveContour->Update();
> > The program stop at: itkSegmentationLevelSetFunction_txx at return ( m_AdvectionImage->GetPixel(idx) );
> > template <class TImageType, class TFeatureImageType>
> > typename SegmentationLevelSetFunction<TImageType, TFeatureImageType>::VectorType
> > SegmentationLevelSetFunction<TImageType, TFeatureImageType>
> > ::AdvectionField(const NeighborhoodType &neighborhood,
> > const FloatOffsetType &offset, GlobalDataStruct *) const
> > {
> > IndexType idx = neighborhood.GetIndex();
> > ContinuousIndexType cdx;
> > for (unsigned i = 0; i < ImageDimension; ++i)
> > {
> > cdx[i] = static_cast<double>(idx[i]) - offset[i];
> > }
> > if ( m_VectorInterpolator->IsInsideBuffer(cdx) )
> > {
> > return ( m_VectorCast(m_VectorInterpolator->EvaluateAtContinuousIndex(cdx)));
> > }
> > //Just return the default else
> > return ( m_AdvectionImage->GetPixel(idx) );
> > }
> > Clearly, something is still wrong with SetAdvectionImage. Below is related code.
> > Can you please help me figure out which setting is wrong?
> > Thanks
> > Baoyun
> >
> > typedef itk::CovariantVector<double, Dim> myGradientType;
> > typedef itk::Image<myGradientType, Dim> myGradientImageType;
> > typedef itk::GradientVectorFlowImageFilter<myGradientImageType, myGradientImageType>
> > myGVFFilterType;
> > typedef itk::GradientImageFilter<DoublelImageType, double,double>
> > myGFilterType;
> > typedef itk::GradientToMagnitudeImageFilter<myGradientImageType, DoublelImageType>
> > myGToMFilterType;
> >
> > typedef itk::GradientRecursiveGaussianImageFilter<
> > DoublelImageType,
> > myGradientImageType
> > > myFilterType;
> > typedef typename GeodesicActiveContourFilterType::VectorImageType AdvectionImageType;
> > typedef itk::CastImageFilter<myGradientImageType,AdvectionImageType>
> > CastFlowFilterType;
> > typedef itk::LaplacianImageFilter<DoublelImageType, DoublelImageType> myLaplacianFilterType;
> > typename myFilterType::Pointer filter = myFilterType::New();
> > typename myGFilterType::Pointer gfilter = myGFilterType::New();
> > typename myGToMFilterType::Pointer gtomfilter = myGToMFilterType::New();
> > typename myLaplacianFilterType::Pointer m_LFilter = myLaplacianFilterType::New();
> > typename myGVFFilterType::Pointer m_GVFFilter = myGVFFilterType::New();
> > typename CastFlowFilterType::Pointer castflowfilter = CastFlowFilterType::New();
> > typedef itk::ImageFileWriter< myGradientImageType > WriterType2;
> > typename WriterType2::Pointer writer21=WriterType2::New();
> > > typename WriterType1::Pointer writer4=WriterType1::New();
> > writer4->SetInput(caster11->GetOutput());
> > writer4->SetFileName("../data/intial_contour.hdr");
> > writer4->Update();
> >
> > sigmoid->SetOutputMinimum( 0.0 );
> > sigmoid->SetOutputMaximum( 1.0 );
> > caster12->SetInput(inputfilter);
> > smoothing->SetInput(caster12->GetOutput() );
> > gradientMagnitude->SetInput( smoothing->GetOutput() );
> > sigmoid->SetInput( gradientMagnitude->GetOutput() );
> > caster31->SetInput(inputfilter);
> > filter->SetInput( caster31->GetOutput() ); //caster short to double
> > filter->SetSigma( 1.0);
> > filter->Update();
> > gtomfilter->SetInput(filter->GetOutput());
> > gtomfilter->Update();
> > gfilter->SetInput(gtomfilter->GetOutput());
> > gfilter->Update();
> > m_GVFFilter->SetInput(gfilter->GetOutput());
> > m_GVFFilter->SetLaplacianFilter(m_LFilter);
> > m_GVFFilter->SetNoiseLevel(500);
> > m_GVFFilter->SetTimeStep(0.05);
> > m_GVFFilter->SetIterationNum(5);
> > m_GVFFilter->Update();
> > writer21->SetInput(m_GVFFilter->GetOutput());
> > writer21->SetFileName("../data/GVF_flow.hdr");
> > writer21->Update();
> > //to get gradient manitude of GVF low
> > geodesicActiveContour->SetAutoGenerateSpeedAdvection(false);
> > //typename myGradientImageType::Pointer m_GVFField;
> > //m_GVFField = m_GVFFilter->GetOutput();
> > castflowfilter->SetInput(m_GVFFilter->GetOutput());
> > geodesicActiveContour->SetAdvectionImage(castflowfilter->GetOutput());
> > // geodesicActiveContour->GenerateSpeedImage();
> > //geodesicActiveContour->SetAdvectionImage(m_GVFFilter->GetOutput());
> > geodesicActiveContour->SetInput( caster11->GetOutput() );
> > geodesicActiveContour->SetFeatureImage( sigmoid->GetOutput() );
> > geodesicActiveContour->GenerateSpeedImage();
> > geodesicActiveContour->Update();
> > thresholder->SetInput( geodesicActiveContour->GetOutput() );
> > thresholder->Update();
> > outputfilter=thresholder->GetOutput();
> >
> >
> >
> >
>
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