From nasil122002 at yahoo.de  Thu Nov  9 14:59:10 2017
From: nasil122002 at yahoo.de (Yusuf OEZBEK)
Date: Thu, 9 Nov 2017 19:59:10 +0000 (UTC)
Subject: [ITK-dev] itk::fem updating displacements
References: <587898442.10039537.1510257550772.ref@mail.yahoo.com>
Message-ID: <587898442.10039537.1510257550772@mail.yahoo.com>

Dear ITK users,I have another question. In order to visualize the deformation, I want to replace the old node coordinates with the new one after generating the solution, like in UpdateDisplacements() function in itkFemSolver.hxx 610-651
The code-block, which generates solution:m_FemSolver->Update();
//m_FemSolver->UpdateDisplacements();
const unsigned int invalidId= itk::fem::Element::InvalidDegreeOfFreedomID;
int numberOfNodes= m_FemSolver->GetInput()->GetNumberOfNodes();

for(int i= 0; i< numberOfNodes; i++)
{
  itk::fem::Element::Node::Pointer node= m_FemSolver->GetInput()->GetNode(i);
  std::cout<<"FEM Mesh Node: "<< node->GetGlobalNumber() << " Coordinates: "<< node->GetCoordinates()<<std::endl;
  
  for(unsigned int j= 0, dof; (dof= node->GetDegreeOfFreedom(j))!= invalidId; j++)
  {
    cout <<"FEM Mesh Solution: "<< m_FemSolver->GetSolution(dof)<<endl;
  }
}
gives me following output, that shows, I have some solutions for nodes 69 and 70:FEM Mesh Node: 68 Coordinates: -61.1098 -139.262 211.9
FEM Mesh Node: 69 Coordinates: -61.0742 -139.319 211.9
FEM Mesh Solution: 82.6806
FEM Mesh Solution: -32.5517
FEM Mesh Solution: 6.36021
FEM Mesh Node: 70 Coordinates: -61.3429 -138.832 211.9
FEM Mesh Solution: 0.798099
FEM Mesh Solution: 37.6971
FEM Mesh Solution: -4.36149
FEM Mesh Node: 71 Coordinates: -61.5039 -138.402 211.509
FEM Mesh Node: 72 Coordinates: -61.6232 -138.402 211.9
if I want to update the displacements://itk::fem::LinearSystemWrapper::Pointer wrapper;
VectorType replacedNodeVector(3);
for(int i= 0; i< numberOfNodes; i++)
{
  TetrahedronNodeType::Pointer node= m_FemSolver->GetInput()->GetNode(i);
  //itk::fem::Element::Node::Pointer node= m_Fem3dSolver->GetInput()->GetNode(i);

  for(unsigned int j= 0; j< 3; j++)
  {
    std::cout<<"FEM Mesh Solution Vector: "<<m_FemSolver->GetSolution(node->GetDegreeOfFreedom(j))<<std::endl;
    replacedNodeVector[j] = node->GetCoordinates()[j] +  m_FemSolver->GetSolution(node->GetDegreeOfFreedom(j));
  //replacedNodeVector[j] = node->GetCoordinates()[j] + m_ls->GetSolutionValue(node->GetDegreeOfFreedom(j));
  }
  node->SetCoordinates(replacedNodeVector);
  std::cout<<"FEM Mesh New Node: "<< node->GetGlobalNumber() << " Coordinates: "<< node->GetCoordinates()<<std::endl;
}
I get as output:FEM Mesh New Node: 67 Coordinates: -61.0742 -139.262 211.797 
FEM Mesh Solution Vector: 0
FEM Mesh Solution Vector: 0
FEM Mesh Solution Vector: 0
FEM Mesh New Node: 68 Coordinates: -61.1098 -139.262 211.9
FEM Mesh Solution Vector: 82.6806
FEM Mesh Solution Vector: -32.5517
FEM Mesh Solution Vector: 6.36021
FEM Mesh New Node: 69 Coordinates: 21.6064 -171.871 218.26
FEM Mesh Solution Vector: 0.798099
FEM Mesh Solution Vector: 37.6971
FEM Mesh Solution Vector: -4.36149
FEM Mesh New Node: 70 Coordinates: -60.5448 -101.135 207.539
FEM Mesh Solution Vector: 0
FEM Mesh Solution Vector: 0
FEM Mesh Solution Vector: 0
My questions are:
Do I do it correct for the replacements, if I sum the old node coordinate with the generated solution vector for that spacial node?:replacedNodeVector[j] = node->GetCoordinates()[j] + m_FemSolver->GetSolution(node->GetDegreeOfFreedom(j));
In my test application, I apply some force at node 1( loadNode->SetNode(1); ) but in generated solution it shows that the force doesn?t act on node 1 and nodes around it but for nodes 68, 69, 82, and 83. All the other solutions are zero. My test mesh contains 86 nodes and 162 elements. If I want to apply the force except node 1,eg at node 20, I get then segmentation fault.typedef itk::fem::LoadNode LoadNodeType;
LoadNodeType::Pointer loadNode= LoadNodeType::New();
loadNode->SetElement(tetrahedronElement.GetPointer());
loadNode->SetGlobalNumber(3);
loadNode->SetNode(1);

vnl_vector<double> force(3);
force[0]= 110.0;
force[1]= 20.0;
force[2]= 31.0;
loadNode->SetForce(force);
m_FemObject->AddNextLoad(loadNode);
For detailed information please see runnable test code:vtkUGridToFemMesh.zip
  
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Thank you for any help!
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From e.a.g.pfaehler at umcg.nl  Tue Nov 21 10:12:44 2017
From: e.a.g.pfaehler at umcg.nl (Pfaehler, EAG (ngmb))
Date: Tue, 21 Nov 2017 15:12:44 +0000
Subject: [ITK-dev] Problem calculating oriented bounding box,
	itk::ShapeLabelObject
Message-ID: <FB00E28D0DFA214FB31273A13543E1AA315D5FCC@WPZKH0217.zkh.umcg.intra>

Dear all,

I need the size of the oriented bounding box of a mask.
I created a shape label object and extracted already some attributes (like nr. of pixels etc), what works pretty fine.
Now I wanted to get the size of the oriented bounding box. But whatever I do and no matter which object I use, I always get the result [0, 0, 0]
Is there a trick?

Thanks a lot for your answer.

Regards

Elli

My code:


        typedef itk::CastImageFilter<ImageType, intImage> CastFilterType;
        typedef itk::CastImageFilter<ImageType, uCharImage> uCharCastFilterType;
        typedef itk::ConnectedComponentImageFilter <intImage, intImage> ConnectedComponentFilterType;
        typedef itk::LabelImageToShapeLabelMapFilter<intImage> LabelImageToShapeLabelMapFilterType;

        typedef int LabelType;
        typedef itk::ShapeLabelObject<LabelType, R> ShapeLabelObjectType;
        typedef itk::LabelMap<ShapeLabelObjectType> LabelMapType;
    typename ConnectedComponentFilterType::Pointer connectedComponentImageFilter = ConnectedComponentFilterType::New();
    connectedComponentImageFilter->SetInput(castFilter->GetOutput());
    connectedComponentImageFilter->Update();
    /*!
    With the label image to shape label map filter the mask is converted to a labeled image
    */
    typename LabelImageToShapeLabelMapFilterType::Pointer labelImageToShapeLabelMapFilter = LabelImageToShapeLabelMapFilterType::New();
    labelImageToShapeLabelMapFilter->SetInput(connectedComponentImageFilter->GetOutput());
    labelImageToShapeLabelMapFilter->SetComputePerimeter(true);
    labelImageToShapeLabelMapFilter->Update();

    LabelMapType *labelMap = labelImageToShapeLabelMapFilter->GetOutput();
    labelMap->Update();
    /*!
    For every connected component a labelObject is created
    Because we are only interested in the object with the label one, we check the label number
    */
    for(unsigned int n = 0; n < labelMap->GetNumberOfLabelObjects(); n++){
        ShapeLabelObjectType *labelObject = labelMap->GetNthLabelObject(n);
        int labelNr = labelObject->GetLabel();
        if(labelNr ==1){
#ifdef _WIN32
            volume = labelObject->GetPhysicalSize();
            principalMoments = labelObject->GetPrincipalMoments();
            nrPixels = labelObject->GetNumberOfPixels();
            surface = labelObject->GetNumberOfPixelsOnBorder()*imageSpacingX*imageSpacingY*imageSpacingZ;
            std::cout << "nr Pixels border" << labelObject->GetOrientedBoundingBoxOrigin() << std::endl;
________________________________
De inhoud van dit bericht is vertrouwelijk en alleen bestemd voor de geadresseerde(n). Anderen dan de geadresseerde(n) mogen geen gebruik maken van dit bericht, het niet openbaar maken of op enige wijze verspreiden of vermenigvuldigen. Het UMCG kan niet aansprakelijk gesteld worden voor een incomplete aankomst of vertraging van dit verzonden bericht.

The contents of this message are confidential and only intended for the eyes of the addressee(s). Others than the addressee(s) are not allowed to use this message, to make it public or to distribute or multiply this message in any way. The UMCG cannot be held responsible for incomplete reception or delay of this transferred message.
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From dzenanz at gmail.com  Tue Nov 21 12:46:17 2017
From: dzenanz at gmail.com (=?UTF-8?B?RMW+ZW5hbiBadWtpxIc=?=)
Date: Tue, 21 Nov 2017 12:46:17 -0500
Subject: [ITK-dev] Problem calculating oriented bounding box,
	itk::ShapeLabelObject
In-Reply-To: <FB00E28D0DFA214FB31273A13543E1AA315D5FCC@WPZKH0217.zkh.umcg.intra>
References: <FB00E28D0DFA214FB31273A13543E1AA315D5FCC@WPZKH0217.zkh.umcg.intra>
Message-ID: <CAPf2UMQY1avfOSpO_=A2jq9XoFBfPhXYCHPx28nEwZmiPwWYNg@mail.gmail.com>

Hi Elli,

can you repost on discourse <https://discourse.itk.org/>? We have moved
there.

Regards,
D?enan

On Tue, Nov 21, 2017 at 10:12 AM, Pfaehler, EAG (ngmb) <
e.a.g.pfaehler at umcg.nl> wrote:

> Dear all,
>
> I need the size of the oriented bounding box of a mask.
> I created a shape label object and extracted already some attributes (like
> nr. of pixels etc), what works pretty fine.
> Now I wanted to get the size of the oriented bounding box. But whatever I
> do and no matter which object I use, I always get the result [0, 0, 0]
> Is there a trick?
>
> Thanks a lot for your answer.
>
> Regards
>
> Elli
>
> My code:
>
>
>         typedef itk::CastImageFilter<ImageType, intImage> CastFilterType;
>         typedef itk::CastImageFilter<ImageType, uCharImage>
> uCharCastFilterType;
>         typedef itk::ConnectedComponentImageFilter <intImage, intImage>
> ConnectedComponentFilterType;
>         typedef itk::LabelImageToShapeLabelMapFilter<intImage>
> LabelImageToShapeLabelMapFilterType;
>
>         typedef int LabelType;
>         typedef itk::ShapeLabelObject<LabelType, R> ShapeLabelObjectType;
>         typedef itk::LabelMap<ShapeLabelObjectType> LabelMapType;
>     typename ConnectedComponentFilterType::Pointer
> connectedComponentImageFilter = ConnectedComponentFilterType::New();
>     connectedComponentImageFilter->SetInput(castFilter->GetOutput());
>     connectedComponentImageFilter->Update();
>     /*!
>     With the label image to shape label map filter the mask is converted
> to a labeled image
>     */
>     typename LabelImageToShapeLabelMapFilterType::Pointer
> labelImageToShapeLabelMapFilter = LabelImageToShapeLabelMapFilte
> rType::New();
>     labelImageToShapeLabelMapFilter->SetInput(
> connectedComponentImageFilter->GetOutput());
>     labelImageToShapeLabelMapFilter->SetComputePerimeter(true);
>     labelImageToShapeLabelMapFilter->Update();
>
>     LabelMapType *labelMap = labelImageToShapeLabelMapFilter->GetOutput();
>     labelMap->Update();
>     /*!
>     For every connected component a labelObject is created
>     Because we are only interested in the object with the label one, we
> check the label number
>     */
>     for(unsigned int n = 0; n < labelMap->GetNumberOfLabelObjects(); n++){
>         ShapeLabelObjectType *labelObject = labelMap->GetNthLabelObject(n)
> ;
>         int labelNr = labelObject->GetLabel();
>         if(labelNr ==1){
> #ifdef _WIN32
>             volume = labelObject->GetPhysicalSize();
>             principalMoments = labelObject->GetPrincipalMoments();
>             nrPixels = labelObject->GetNumberOfPixels();
>             surface = labelObject->GetNumberOfPixelsOnBorder()*
> imageSpacingX*imageSpacingY*imageSpacingZ;
>             std::cout << "nr Pixels border" << labelObject->GetOrientedBoundingBoxOrigin()
> << std::endl;
> ------------------------------
> De inhoud van dit bericht is vertrouwelijk en alleen bestemd voor de
> geadresseerde(n). Anderen dan de geadresseerde(n) mogen geen gebruik maken
> van dit bericht, het niet openbaar maken of op enige wijze verspreiden of
> vermenigvuldigen. Het UMCG kan niet aansprakelijk gesteld worden voor een
> incomplete aankomst of vertraging van dit verzonden bericht.
>
> The contents of this message are confidential and only intended for the
> eyes of the addressee(s). Others than the addressee(s) are not allowed to
> use this message, to make it public or to distribute or multiply this
> message in any way. The UMCG cannot be held responsible for incomplete
> reception or delay of this transferred message.
>
> The ITK community is transitioning from this mailing list to
> discourse.itk.org. Please join us there!
> ______________________________________
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>
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