[Insight-users] Segmenation Error--after set advection image by GVF flow
Amardeep Singh
amar.singh at gmx.de
Fri Mar 6 13:15:09 EST 2009
Dear Baoyun
I would suggest, you have a look at the following posting by Luis Ibanez:
http://www.nabble.com/units-of-SetNoiseLevel-in-itkGradientVectorFlowImageFilter-td21957034.html
So, you can leave out the SetTimeStep(). I found that a small number of
iterations may be sufficient. At least, it was for me.
The exact amount of the noise level depends highly on your data. On a
synthetic example, a value as high as 20000 worked for me.
On real data, I used values between 20 and 200 mostly, but I have not
finished evaluating the best parameters yet. So, you should just give it
a try and see what works best for you.
Best regards
Amardeep
Baoyun Li wrote:
> 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 <http://gvftest.cc/>) pasted
> on the web. But that is not the working version.
> > Thanks.
> > Baoyun
> >
> > ------------------------------------------------------------------------
> > *From:* Amardeep Singh <amar.singh at gmx.de <mailto:amar.singh at gmx.de>>
> > *To:* Baoyun Li <baoyun_li123 at yahoo.com <mailto:baoyun_li123 at yahoo.com>>
> > *Cc:* insight-users at itk.org <mailto: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> <mailto: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>
> <mailto:amar.singh at gmx.de <mailto:amar.singh at gmx.de>>>
> > > *Cc:* insight-users at itk.org <mailto:insight-users at itk.org>
> <mailto: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> <mailto: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>
> <mailto:amar.singh at gmx.de <mailto:amar.singh at gmx.de>>>
> > > *Cc:* insight-users at itk.org <mailto:insight-users at itk.org>
> <mailto: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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