From brufsc at hotmail.com  Wed Nov  1 19:42:26 2017
From: brufsc at hotmail.com (bsouza)
Date: Wed, 1 Nov 2017 16:42:26 -0700 (MST)
Subject: [ITK-users] Simplex Mesh Deformable Model doesn't change
Message-ID: <1509579746285-0.post@n2.nabble.com>

Dear itk-developers,

I'm trying to use the itkDeformableSimplexMesh3D filter to make a local
adjustment of a simplex mesh. The mesh that I want to deform using this
filter is already initialized close to the target structure in the image.
However, after playing with all parameter values of the filter, it seems
that there is not significant differences between the input and output
meshes.

I'm reading the mesh from a file (stl or vtk extension) and I want to deform
it using a brain MRI (nifiti format) image as a reference. After the filter
application, the result seems to not approximate the mesh to the local
structure in the image (only occurs a small smoothness of the model). I've
tried to change the parameters (alpha, beta, gamma, rigidity, number of
iterations) values to check if some change would occur, but the result
always seems the same. I would like that deformation to be able to move the
mesh to closer to the structure in the image. My code is below. Is there
something wrong with my code? Why it seems that the external force has no
influence in the mesh deform result?

The image and the mesh I'm using in this test is available in the link below
(I don't know how much time until the link expires):

http://www73.zippyshare.com/v/sqQ6cgjN/file.html

Here is my code:

=================================================================
enum PARAMS {
    PROGRAM_NAME = 0,
    IMAGE_FILENAME,
    INPUT_MESH_FILENAME,
    OUTPUT_MESH_FILENAME,
    NUM_ARGS
};


using namespace std;

int main( int argc, char *argv[] )
{

    if( argc < NUM_ARGS )
    {
        std::cerr << "\n\n";
        std::cerr << "Usage: " << argv[PROGRAM_NAME] << " imageFileName
inputMeshFileName ouputMeshFileName";
        std::cerr << "\n\n";
        return 1;
    }

    itk::STLMeshIOFactory::RegisterOneFactory();

  const int dimension = 3;

  typedef float PixelType;
  typedef itk::Image<PixelType, dimension> ImageType;

  typedef itk::DefaultDynamicMeshTraits<PixelType, dimension>      
TriangleMeshTraits;
  typedef itk::DefaultDynamicMeshTraits<PixelType, dimension>      
SimplexMeshTraits;
  typedef itk::Mesh<PixelType, dimension, TriangleMeshTraits>      
TriangleMeshType;
  typedef itk::SimplexMesh<PixelType, dimension, SimplexMeshTraits>
SimplexMeshType;

  typedef itk::TriangleMeshToSimplexMeshFilter<TriangleMeshType,
SimplexMeshType> TriangleToSimplexFilterType;
  typedef itk::SimplexMeshToTriangleMeshFilter<SimplexMeshType,
TriangleMeshType> SimplexToTriangleFilterType;

  typedef itk::DeformableSimplexMesh3DFilter<SimplexMeshType,
SimplexMeshType> DeformFilterType;
  typedef DeformFilterType::GradientImageType                                 
GradientType;

  typedef itk::GradientAnisotropicDiffusionImageFilter <ImageType,
ImageType> DiffusionFilterType;

  typedef itk::GradientAnisotropicDiffusionImageFilter < ImageType,
ImageType >  GradientAnisotropicImageType;
  typedef itk::GradientMagnitudeRecursiveGaussianImageFilter < ImageType,
ImageType >  GradientMagnitudeType;
  typedef itk::SigmoidImageFilter< ImageType, ImageType > SigmoidImageType;
  typedef itk::GradientRecursiveGaussianImageFilter<ImageType,GradientType>
GradientFilterType;

  typedef itk::ImageFileReader<ImageType>       ImageReaderType;
  typedef itk::ImageFileWriter<ImageType>       ImageWriterType;
  typedef itk::MeshFileReader<TriangleMeshType> MeshReaderType;
  typedef itk::MeshFileWriter<TriangleMeshType>  MeshWriterType;


  ImageReaderType::Pointer imageReader = ImageReaderType::New();
  imageReader->SetFileName(argv[IMAGE_FILENAME]);
  imageReader->Update();

  MeshReaderType::Pointer meshReader = MeshReaderType::New();
  meshReader->SetFileName(argv[INPUT_MESH_FILENAME]);
  meshReader->Update();

  std::cout << " starting to Filter Image" << std::endl;
  GradientAnisotropicImageType::Pointer gradientanisotropicfilter =
GradientAnisotropicImageType::New();
  gradientanisotropicfilter->SetInput(imageReader->GetOutput());
  gradientanisotropicfilter->SetNumberOfIterations(5);
  gradientanisotropicfilter->SetTimeStep(0.0625);
  gradientanisotropicfilter->SetConductanceParameter(3);
  gradientanisotropicfilter->Update();
  std::cout << "GradientAnisotropicDiffusion is DONE!" << std::endl;

  GradientMagnitudeType::Pointer gradientmagnitudefilter =
GradientMagnitudeType::New();
  gradientmagnitudefilter->SetInput( gradientanisotropicfilter->GetOutput()
);
  gradientmagnitudefilter->SetSigma(1.0);
  gradientmagnitudefilter->Update();
  std::cout << "GradientMagnitude is DONE!" << std::endl;

  SigmoidImageType::Pointer sigmoidimagefilter = SigmoidImageType::New();
  sigmoidimagefilter->SetInput( gradientmagnitudefilter->GetOutput());
  sigmoidimagefilter->SetOutputMinimum(0);
  sigmoidimagefilter->SetOutputMaximum(1);
  sigmoidimagefilter->SetAlpha(10);
  sigmoidimagefilter->SetBeta(100);
  sigmoidimagefilter->Update();
  std::cout << "Sigmoid is DONE!" << std::endl;

  GradientFilterType::Pointer gradientFilter = GradientFilterType::New();
  gradientFilter->SetInput( sigmoidimagefilter->GetOutput() );
  gradientFilter->SetSigma(1.0);
  gradientFilter->Update();
  std::cout << "GradientMagnitude is DONE!" << std::endl;

  std::cout << "Gradient filter ok\n";

  TriangleToSimplexFilterType::Pointer triangleToSimplexFilter =
TriangleToSimplexFilterType::New();
  triangleToSimplexFilter->SetInput(meshReader->GetOutput());
  triangleToSimplexFilter->Update();

  GradientType::Pointer gradientImage    = gradientFilter->GetOutput();
  SimplexMeshType::Pointer simplexMesh   =
triangleToSimplexFilter->GetOutput();
  DeformFilterType::Pointer deformFilter = DeformFilterType::New();

  const unsigned int numberOfCycles = 100;

  for (unsigned int i = 0; i < numberOfCycles; i++)
    {
    // must disconnect the pipeline
    simplexMesh->DisconnectPipeline();
    deformFilter->SetInput( simplexMesh );
    deformFilter->SetGradient( gradientImage );
    deformFilter->SetAlpha(0.1);
    deformFilter->SetBeta(-0.1);
    deformFilter->SetIterations(5);
    deformFilter->SetRigidity(1);
    deformFilter->Update();
    }
  SimplexMeshType::Pointer deformResult =  deformFilter->GetOutput();


   SimplexToTriangleFilterType::Pointer simplexToTriangleFilter =
SimplexToTriangleFilterType::New();
   simplexToTriangleFilter->SetInput(deformResult);
   simplexToTriangleFilter->Update();
   TriangleMeshType::Pointer conversionResult =
simplexToTriangleFilter->GetOutput();

  conversionResult->DisconnectPipeline();

  MeshWriterType::Pointer meshWriter = MeshWriterType::New();
  meshWriter->SetFileName(argv[OUTPUT_MESH_FILENAME]);
  meshWriter->SetInput(conversionResult);
  meshWriter->Update();

  return EXIT_SUCCESS;
}

=================================================================

I really appreciate any help you can provide me. 

Thank you very much,
Breno




--
Sent from: http://itk-insight-users.2283740.n2.nabble.com/

From dzenanz at gmail.com  Thu Nov  2 11:19:17 2017
From: dzenanz at gmail.com (=?UTF-8?B?RMW+ZW5hbiBadWtpxIc=?=)
Date: Thu, 2 Nov 2017 11:19:17 -0400
Subject: [ITK-users] Simplex Mesh Deformable Model doesn't change
In-Reply-To: <1509579746285-0.post@n2.nabble.com>
References: <1509579746285-0.post@n2.nabble.com>
Message-ID: <CAPf2UMQja_kbreGuH0eAnLDgZ1QZX3CqT98wKNv3smaAzz11ww@mail.gmail.com>

Hi Breno,

can you provide a link via some service which does not require installation
of some adware to download the file? I think that most could storage
providers have a free version (e.g. Dropbox or Google Drive).

Also, we are trying to switch to Discourse <https://discourse.itk.org/>,
can you re-post the message with updated link there?

Regards,
D?enan

On Wed, Nov 1, 2017 at 7:42 PM, bsouza <brufsc at hotmail.com> wrote:

> Dear itk-developers,
>
> I'm trying to use the itkDeformableSimplexMesh3D filter to make a local
> adjustment of a simplex mesh. The mesh that I want to deform using this
> filter is already initialized close to the target structure in the image.
> However, after playing with all parameter values of the filter, it seems
> that there is not significant differences between the input and output
> meshes.
>
> I'm reading the mesh from a file (stl or vtk extension) and I want to
> deform
> it using a brain MRI (nifiti format) image as a reference. After the filter
> application, the result seems to not approximate the mesh to the local
> structure in the image (only occurs a small smoothness of the model). I've
> tried to change the parameters (alpha, beta, gamma, rigidity, number of
> iterations) values to check if some change would occur, but the result
> always seems the same. I would like that deformation to be able to move the
> mesh to closer to the structure in the image. My code is below. Is there
> something wrong with my code? Why it seems that the external force has no
> influence in the mesh deform result?
>
> The image and the mesh I'm using in this test is available in the link
> below
> (I don't know how much time until the link expires):
>
> http://www73.zippyshare.com/v/sqQ6cgjN/file.html
>
> Here is my code:
>
> =================================================================
> enum PARAMS {
>     PROGRAM_NAME = 0,
>     IMAGE_FILENAME,
>     INPUT_MESH_FILENAME,
>     OUTPUT_MESH_FILENAME,
>     NUM_ARGS
> };
>
>
> using namespace std;
>
> int main( int argc, char *argv[] )
> {
>
>     if( argc < NUM_ARGS )
>     {
>         std::cerr << "\n\n";
>         std::cerr << "Usage: " << argv[PROGRAM_NAME] << " imageFileName
> inputMeshFileName ouputMeshFileName";
>         std::cerr << "\n\n";
>         return 1;
>     }
>
>     itk::STLMeshIOFactory::RegisterOneFactory();
>
>   const int dimension = 3;
>
>   typedef float PixelType;
>   typedef itk::Image<PixelType, dimension> ImageType;
>
>   typedef itk::DefaultDynamicMeshTraits<PixelType, dimension>
> TriangleMeshTraits;
>   typedef itk::DefaultDynamicMeshTraits<PixelType, dimension>
> SimplexMeshTraits;
>   typedef itk::Mesh<PixelType, dimension, TriangleMeshTraits>
> TriangleMeshType;
>   typedef itk::SimplexMesh<PixelType, dimension, SimplexMeshTraits>
> SimplexMeshType;
>
>   typedef itk::TriangleMeshToSimplexMeshFilter<TriangleMeshType,
> SimplexMeshType> TriangleToSimplexFilterType;
>   typedef itk::SimplexMeshToTriangleMeshFilter<SimplexMeshType,
> TriangleMeshType> SimplexToTriangleFilterType;
>
>   typedef itk::DeformableSimplexMesh3DFilter<SimplexMeshType,
> SimplexMeshType> DeformFilterType;
>   typedef DeformFilterType::GradientImageType
> GradientType;
>
>   typedef itk::GradientAnisotropicDiffusionImageFilter <ImageType,
> ImageType> DiffusionFilterType;
>
>   typedef itk::GradientAnisotropicDiffusionImageFilter < ImageType,
> ImageType >  GradientAnisotropicImageType;
>   typedef itk::GradientMagnitudeRecursiveGaussianImageFilter < ImageType,
> ImageType >  GradientMagnitudeType;
>   typedef itk::SigmoidImageFilter< ImageType, ImageType > SigmoidImageType;
>   typedef itk::GradientRecursiveGaussianImage
> Filter<ImageType,GradientType>
> GradientFilterType;
>
>   typedef itk::ImageFileReader<ImageType>       ImageReaderType;
>   typedef itk::ImageFileWriter<ImageType>       ImageWriterType;
>   typedef itk::MeshFileReader<TriangleMeshType> MeshReaderType;
>   typedef itk::MeshFileWriter<TriangleMeshType>  MeshWriterType;
>
>
>   ImageReaderType::Pointer imageReader = ImageReaderType::New();
>   imageReader->SetFileName(argv[IMAGE_FILENAME]);
>   imageReader->Update();
>
>   MeshReaderType::Pointer meshReader = MeshReaderType::New();
>   meshReader->SetFileName(argv[INPUT_MESH_FILENAME]);
>   meshReader->Update();
>
>   std::cout << " starting to Filter Image" << std::endl;
>   GradientAnisotropicImageType::Pointer gradientanisotropicfilter =
> GradientAnisotropicImageType::New();
>   gradientanisotropicfilter->SetInput(imageReader->GetOutput());
>   gradientanisotropicfilter->SetNumberOfIterations(5);
>   gradientanisotropicfilter->SetTimeStep(0.0625);
>   gradientanisotropicfilter->SetConductanceParameter(3);
>   gradientanisotropicfilter->Update();
>   std::cout << "GradientAnisotropicDiffusion is DONE!" << std::endl;
>
>   GradientMagnitudeType::Pointer gradientmagnitudefilter =
> GradientMagnitudeType::New();
>   gradientmagnitudefilter->SetInput( gradientanisotropicfilter->
> GetOutput()
> );
>   gradientmagnitudefilter->SetSigma(1.0);
>   gradientmagnitudefilter->Update();
>   std::cout << "GradientMagnitude is DONE!" << std::endl;
>
>   SigmoidImageType::Pointer sigmoidimagefilter = SigmoidImageType::New();
>   sigmoidimagefilter->SetInput( gradientmagnitudefilter->GetOutput());
>   sigmoidimagefilter->SetOutputMinimum(0);
>   sigmoidimagefilter->SetOutputMaximum(1);
>   sigmoidimagefilter->SetAlpha(10);
>   sigmoidimagefilter->SetBeta(100);
>   sigmoidimagefilter->Update();
>   std::cout << "Sigmoid is DONE!" << std::endl;
>
>   GradientFilterType::Pointer gradientFilter = GradientFilterType::New();
>   gradientFilter->SetInput( sigmoidimagefilter->GetOutput() );
>   gradientFilter->SetSigma(1.0);
>   gradientFilter->Update();
>   std::cout << "GradientMagnitude is DONE!" << std::endl;
>
>   std::cout << "Gradient filter ok\n";
>
>   TriangleToSimplexFilterType::Pointer triangleToSimplexFilter =
> TriangleToSimplexFilterType::New();
>   triangleToSimplexFilter->SetInput(meshReader->GetOutput());
>   triangleToSimplexFilter->Update();
>
>   GradientType::Pointer gradientImage    = gradientFilter->GetOutput();
>   SimplexMeshType::Pointer simplexMesh   =
> triangleToSimplexFilter->GetOutput();
>   DeformFilterType::Pointer deformFilter = DeformFilterType::New();
>
>   const unsigned int numberOfCycles = 100;
>
>   for (unsigned int i = 0; i < numberOfCycles; i++)
>     {
>     // must disconnect the pipeline
>     simplexMesh->DisconnectPipeline();
>     deformFilter->SetInput( simplexMesh );
>     deformFilter->SetGradient( gradientImage );
>     deformFilter->SetAlpha(0.1);
>     deformFilter->SetBeta(-0.1);
>     deformFilter->SetIterations(5);
>     deformFilter->SetRigidity(1);
>     deformFilter->Update();
>     }
>   SimplexMeshType::Pointer deformResult =  deformFilter->GetOutput();
>
>
>    SimplexToTriangleFilterType::Pointer simplexToTriangleFilter =
> SimplexToTriangleFilterType::New();
>    simplexToTriangleFilter->SetInput(deformResult);
>    simplexToTriangleFilter->Update();
>    TriangleMeshType::Pointer conversionResult =
> simplexToTriangleFilter->GetOutput();
>
>   conversionResult->DisconnectPipeline();
>
>   MeshWriterType::Pointer meshWriter = MeshWriterType::New();
>   meshWriter->SetFileName(argv[OUTPUT_MESH_FILENAME]);
>   meshWriter->SetInput(conversionResult);
>   meshWriter->Update();
>
>   return EXIT_SUCCESS;
> }
>
> =================================================================
>
> I really appreciate any help you can provide me.
>
> Thank you very much,
> Breno
>
>
>
>
> --
> Sent from: http://itk-insight-users.2283740.n2.nabble.com/
> The ITK community is transitioning from this mailing list to
> discourse.itk.org. Please join us there!
> ________________________________
> Powered by www.kitware.com
>
> Visit other Kitware open-source projects at
> http://www.kitware.com/opensource/opensource.html
>
> Kitware offers ITK Training Courses, for more information visit:
> http://www.kitware.com/products/protraining.php
>
> Please keep messages on-topic and check the ITK FAQ at:
> http://www.itk.org/Wiki/ITK_FAQ
>
> Follow this link to subscribe/unsubscribe:
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>
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From srbn.ghosh99 at gmail.com  Fri Nov  3 13:56:41 2017
From: srbn.ghosh99 at gmail.com (shrabani99)
Date: Fri, 3 Nov 2017 10:56:41 -0700 (MST)
Subject: [ITK-users] Writing DICOM from non-DICOM
In-Reply-To: <93FF79329C2BBB4F87A133EB17807A17494165630A@backend.visus-tt.com>
References: <93FF79329C2BBB4F87A133EB17807A17494165630A@backend.visus-tt.com>
Message-ID: <1509731801468-0.post@n7.nabble.com>

Actually for me, my images are in PNG series. So, I need to convert each PNG
image in dicom image. Is there any itk code for this to do?



--
Sent from: http://itk-users.7.n7.nabble.com/

From dzenanz at gmail.com  Fri Nov  3 14:16:20 2017
From: dzenanz at gmail.com (=?UTF-8?B?RMW+ZW5hbiBadWtpxIc=?=)
Date: Fri, 3 Nov 2017 14:16:20 -0400
Subject: [ITK-users] Writing DICOM from non-DICOM
In-Reply-To: <1509731801468-0.post@n7.nabble.com>
References: <93FF79329C2BBB4F87A133EB17807A17494165630A@backend.visus-tt.com>
 <1509731801468-0.post@n7.nabble.com>
Message-ID: <CAPf2UMSJ-i4mLYST1em349SVzvwdLniu7_Cptrvjp6fB0KqTsQ@mail.gmail.com>

I don't know of an example which does exactly that. But starting with the
examples I mentioned, it should be mostly a simplification.

Regards,
D?enan

On Fri, Nov 3, 2017 at 1:56 PM, shrabani99 <srbn.ghosh99 at gmail.com> wrote:

> Actually for me, my images are in PNG series. So, I need to convert each
> PNG
> image in dicom image. Is there any itk code for this to do?
>
>
>
> --
> Sent from: http://itk-users.7.n7.nabble.com/
> The ITK community is transitioning from this mailing list to
> discourse.itk.org. Please join us there!
> ________________________________
> Powered by www.kitware.com
>
> Visit other Kitware open-source projects at
> http://www.kitware.com/opensource/opensource.html
>
> Kitware offers ITK Training Courses, for more information visit:
> http://www.kitware.com/products/protraining.php
>
> Please keep messages on-topic and check the ITK FAQ at:
> http://www.itk.org/Wiki/ITK_FAQ
>
> Follow this link to subscribe/unsubscribe:
> http://public.kitware.com/mailman/listinfo/insight-users
>
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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-users] 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
  
|  
|   
|   
|   |    |

   |

  |
|  
|    |  
vtkUGridToFemMesh.zip
 Shared with Dropbox  |   |

  |

  |

 
Thank you for any help!
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From bxt161230 at utdallas.edu  Fri Nov 10 02:05:36 2017
From: bxt161230 at utdallas.edu (bipul)
Date: Fri, 10 Nov 2017 00:05:36 -0700 (MST)
Subject: [ITK-users] Watershed filter: vary level parameter without running
	update
Message-ID: <1510297536805-0.post@n2.nabble.com>

Hi,

The documentation for the watershed filter says that

/"The Level parameter can be used to create a hierarchy of output images in
constant time once an initial segmentation is done. A typical scenario might
go like this: For the initial execution of the filter, set the Level to the
maximum saliency value that you anticipate might be of interest. Once the
initial Update() of this process object has finished, the Level can be
manipulated anywhere below the initial setting without triggering a full
update of the segmentation mini-pipeline. All that is now be required to
produce the new output is a simple relabeling of the output image."/

I was interested in knowing how to access these hierarchy of output images,
once the update has been performed.

Thank you.

Best,
Bipul Tarafdar



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From dzenanz at gmail.com  Fri Nov 10 09:43:01 2017
From: dzenanz at gmail.com (=?UTF-8?B?RMW+ZW5hbiBadWtpxIc=?=)
Date: Fri, 10 Nov 2017 09:43:01 -0500
Subject: [ITK-users] Watershed filter: vary level parameter without
 running update
In-Reply-To: <1510297536805-0.post@n2.nabble.com>
References: <1510297536805-0.post@n2.nabble.com>
Message-ID: <CAPf2UMT06EMp6j78EnEeAB-CoDU3V6jASARjbZY7DxfmaL-nMQ@mail.gmail.com>

Hi Bipul,

the way I understood that is this:

watershed->SetInput(inImage);
watershed->SetLevel(0.8);
watershed->Update(); //the initial segmentation, slow
seg8=watershed->GetOutput();
seg8->DisconnectPipeline(); //might not be needed

watershed->SetLevel(0.6);
watershed->Update(); //simple relabeling, quick
seg6=watershed->GetOutput();
seg6->DisconnectPipeline(); //might not be needed

watershed->SetLevel(0.55);
watershed->Update(); //simple relabeling, quick
seg55=watershed->GetOutput();
seg55->DisconnectPipeline(); //might not be needed

Give it a try, and if you run into issues ask for help on the new forum
<https://discourse.itk.org/>, to which we are transitioning.

Regards,
D?enan

On Fri, Nov 10, 2017 at 2:05 AM, bipul <bxt161230 at utdallas.edu> wrote:

> Hi,
>
> The documentation for the watershed filter says that
>
> /"The Level parameter can be used to create a hierarchy of output images in
> constant time once an initial segmentation is done. A typical scenario
> might
> go like this: For the initial execution of the filter, set the Level to the
> maximum saliency value that you anticipate might be of interest. Once the
> initial Update() of this process object has finished, the Level can be
> manipulated anywhere below the initial setting without triggering a full
> update of the segmentation mini-pipeline. All that is now be required to
> produce the new output is a simple relabeling of the output image."/
>
> I was interested in knowing how to access these hierarchy of output images,
> once the update has been performed.
>
> Thank you.
>
> Best,
> Bipul Tarafdar
>
>
>
> --
> Sent from: http://itk-insight-users.2283740.n2.nabble.com/
> The ITK community is transitioning from this mailing list to
> discourse.itk.org. Please join us there!
> ________________________________
> Powered by www.kitware.com
>
> Visit other Kitware open-source projects at
> http://www.kitware.com/opensource/opensource.html
>
> Kitware offers ITK Training Courses, for more information visit:
> http://www.kitware.com/products/protraining.php
>
> Please keep messages on-topic and check the ITK FAQ at:
> http://www.itk.org/Wiki/ITK_FAQ
>
> Follow this link to subscribe/unsubscribe:
> http://public.kitware.com/mailman/listinfo/insight-users
>
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From swetha.bsharma at gmail.com  Fri Nov 17 09:54:29 2017
From: swetha.bsharma at gmail.com (Swetha Sharma)
Date: Fri, 17 Nov 2017 20:24:29 +0530
Subject: [ITK-users] extract middle slice from dicom files
Message-ID: <CACDHZES_6-EffS1thDcJQO40ej1Fj12JoqrdkPOY91M=r=q8-g@mail.gmail.com>

Hi ,

I want to know how to get the image values from middle slice of dicom
series.
-swetha
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From dzenanz at gmail.com  Fri Nov 17 14:25:45 2017
From: dzenanz at gmail.com (=?UTF-8?B?RMW+ZW5hbiBadWtpxIc=?=)
Date: Fri, 17 Nov 2017 14:25:45 -0500
Subject: [ITK-users] extract middle slice from dicom files
In-Reply-To: <CACDHZES_6-EffS1thDcJQO40ej1Fj12JoqrdkPOY91M=r=q8-g@mail.gmail.com>
References: <CACDHZES_6-EffS1thDcJQO40ej1Fj12JoqrdkPOY91M=r=q8-g@mail.gmail.com>
Message-ID: <CAPf2UMQqngQS_ACeYr954h34ORw6Woe8sQezYvDy7YEbzRe+Ug@mail.gmail.com>

Hi Swetha,

the simplest, but not computationally most efficient, is to load
<https://itk.org/ITKExamples/src/IO/GDCM/ReadDICOMSeriesAndWrite3DImage/Documentation.html>
the series as a 3D image and then access the middle slice:

image3d=reader->GetOutput();
ImageType::IndexType ind=image3d->GetBufferedRegion().GetIndex();
ind[2]=image3d->GetBufferedRegion().GetSize()[2]/2; //middle
slicePixel00=image3d->GetPixel(ind);

Less computation, but more code would be to examine spatial position of
each slice in seriesUID and then just load the one closest to the middle.

We are in the process of switching to discourse <https://discourse.itk.org/>,
please post follow-up questions there.

Regards,
D?enan

On Fri, Nov 17, 2017 at 9:54 AM, Swetha Sharma <swetha.bsharma at gmail.com>
wrote:

> Hi ,
>
> I want to know how to get the image values from middle slice of dicom
> series.
> -swetha
>
> The ITK community is transitioning from this mailing list to
> discourse.itk.org. Please join us there!
> ________________________________
> Powered by www.kitware.com
>
> Visit other Kitware open-source projects at
> http://www.kitware.com/opensource/opensource.html
>
> Kitware offers ITK Training Courses, for more information visit:
> http://www.kitware.com/products/protraining.php
>
> Please keep messages on-topic and check the ITK FAQ at:
> http://www.itk.org/Wiki/ITK_FAQ
>
> Follow this link to subscribe/unsubscribe:
> http://public.kitware.com/mailman/listinfo/insight-users
>
>
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From cyril.mory at creatis.insa-lyon.fr  Wed Nov 22 04:41:35 2017
From: cyril.mory at creatis.insa-lyon.fr (Cyril Mory)
Date: Wed, 22 Nov 2017 10:41:35 +0100
Subject: [ITK-users] VariableLengthVector and multiplication
Message-ID: <4740afa6-0730-728f-5a66-46cea25229ee@creatis.insa-lyon.fr>

Dear ITK users,

I am using itk::VectorImage in some of my code, which uses 
itk::VariableLengthVector as pixel type. And I am wondering why 
itk::VariableLengthVector has so little support for multiplication. 
Currently, the * operator only supports multiplication by a scalar.

It probably isn't simple, but I would need three additional kinds of 
multiplication:

- dot product with another VariableLengthVector (that has the same 
length, although it is probably a waste of time to perform the check 
every time), returning a scalar

- component-wise multiplication, returning a VariableLengthVector of the 
same length

- left or right multiplication with a matrix (possibly an 
itk::VariableSizeMatrix) that has the correct size, but I understand 
that this is probably the most complex one, and since it only occurs 
rarely in my code, I can handle it with conversions to vnl::vector and 
vnl::matrix

Are there constraints that prevent at least the dot product and 
component-wise multiplication operators from being implemented ? If not, 
then I'd be happy to give it a try. Since both differ only by the return 
type, two different operators would have to be used (I guess). Do you 
have suggestions (which one should use *, and what should be the other 
operator) ? In itk::Vector and itk::CovariantVector, the * operator is 
used for dot product.

Regards,

Cyril



From blowekamp at mail.nih.gov  Wed Nov 22 08:38:41 2017
From: blowekamp at mail.nih.gov (Lowekamp, Bradley (NIH/NLM/LHC) [C])
Date: Wed, 22 Nov 2017 13:38:41 +0000
Subject: [ITK-users] VariableLengthVector and multiplication
In-Reply-To: <4740afa6-0730-728f-5a66-46cea25229ee@creatis.insa-lyon.fr>
References: <4740afa6-0730-728f-5a66-46cea25229ee@creatis.insa-lyon.fr>
Message-ID: <26BF12F6-67F6-4488-81AC-14DDA1581CC3@mail.nih.gov>

Hello,

There are an incredible number of different per-pixel operations that could be implemented as ITK filters. We cannot provide them all. Many of the basic operations are implemented as ITK filters these include performing the basic C++ operators, such as +, -, * and /, on a per-pixel basis.

As you indicate there are many possible meanings for multiplication of vector images, which can lead to confusion.

ITK has a flexible set of Unary[1], Binary[2] functor filters. Classes like the MultiplyImageFilter[3], are implemented by deriving from the base functor classes. However it is easier to just use the base functor filter and set the proper or custom functor, as in this example [4].

It is fairly easy to write a functor for your specific purposes by following the existing set [5]. It is common for filters to internally define a private functor to perform one step in a large filter. Moving from writing for loops on pixels to writing custom functors is part of good usage of ITK.


Brad


[1] https://itk.org/Doxygen/html/classitk_1_1UnaryFunctorImageFilter.html
[2] https://itk.org/Doxygen/html/classitk_1_1BinaryFunctorImageFilter.html
[3] https://itk.org/Doxygen/html/classitk_1_1MultiplyImageFilter.html
[4] https://itk.org/Doxygen/html/WikiExamples_2ImageProcessing_2BinaryFunctorImageFilter_8cxx-example.html#_a1

On 11/22/17, 5:15 AM, "Cyril Mory" <cyril.mory at creatis.insa-lyon.fr> wrote:

    Dear ITK users,
    
    I am using itk::VectorImage in some of my code, which uses 
    itk::VariableLengthVector as pixel type. And I am wondering why 
    itk::VariableLengthVector has so little support for multiplication. 
    Currently, the * operator only supports multiplication by a scalar.
    
    It probably isn't simple, but I would need three additional kinds of 
    multiplication:
    
    - dot product with another VariableLengthVector (that has the same 
    length, although it is probably a waste of time to perform the check 
    every time), returning a scalar
    
    - component-wise multiplication, returning a VariableLengthVector of the 
    same length
    
    - left or right multiplication with a matrix (possibly an 
    itk::VariableSizeMatrix) that has the correct size, but I understand 
    that this is probably the most complex one, and since it only occurs 
    rarely in my code, I can handle it with conversions to vnl::vector and 
    vnl::matrix
    
    Are there constraints that prevent at least the dot product and 
    component-wise multiplication operators from being implemented ? If not, 
    then I'd be happy to give it a try. Since both differ only by the return 
    type, two different operators would have to be used (I guess). Do you 
    have suggestions (which one should use *, and what should be the other 
    operator) ? In itk::Vector and itk::CovariantVector, the * operator is 
    used for dot product.
    
    Regards,
    
    Cyril
    
    
    The ITK community is transitioning from this mailing list to discourse.itk.org. Please join us there!
    ________________________________
    Powered by www.kitware.com
    
    Visit other Kitware open-source projects at
    http://www.kitware.com/opensource/opensource.html
    
    Kitware offers ITK Training Courses, for more information visit:
    http://www.kitware.com/products/protraining.php
    
    Please keep messages on-topic and check the ITK FAQ at:
    http://www.itk.org/Wiki/ITK_FAQ
    
    Follow this link to subscribe/unsubscribe:
    http://public.kitware.com/mailman/listinfo/insight-users
    


From cyril.mory at creatis.insa-lyon.fr  Wed Nov 22 09:54:49 2017
From: cyril.mory at creatis.insa-lyon.fr (Cyril Mory)
Date: Wed, 22 Nov 2017 15:54:49 +0100
Subject: [ITK-users] VariableLengthVector and multiplication
In-Reply-To: <26BF12F6-67F6-4488-81AC-14DDA1581CC3@mail.nih.gov>
References: <4740afa6-0730-728f-5a66-46cea25229ee@creatis.insa-lyon.fr>
 <26BF12F6-67F6-4488-81AC-14DDA1581CC3@mail.nih.gov>
Message-ID: <23954cc4-a874-7213-471e-b817cab250aa@creatis.insa-lyon.fr>

Thanks for this answer.

I am trying the approach you suggested, and would like to write a dot 
product functor that would work either on scalars (in which case it 
would perform a simple product) or on itk::VariableLengthVector of 
scalars (in which case it would perform a dot product).

I found the "itk::NumericTraits<TPixel>::GetLength()" method, which 
works in both cases, and so I tried this:


namespace Functor
{
 ? template< class TPixel, class TInternal>
 ? class DotProduct
 ? {
 ? public:
 ??? DotProduct() {}
 ??? ~DotProduct() {}
 ??? bool operator!=(const DotProduct &) const
 ??? {
 ????? return false;
 ??? }

 ??? bool operator==(const DotProduct & other) const
 ??? {
 ????? return !( *this != other );
 ??? }

 ??? inline TInternal operator()(const TPixel & A, const TPixel & B) const
 ??? {
 ??? TInternal out = 0;
 ??? for (unsigned int component=0; component < 
itk::NumericTraits<TPixel>::GetLength(); component++)
 ????? {
 ????? out += A[component] * B[component];
 ????? }
 ??? return out;
 ??? }
 ? };
} // end namespace functor


But it does not compile with itk::Image inputs, since the pixels A and B 
have no [ ] operator. Is there a standard way around this problem ?

Regards,
Cyril

On 22/11/2017 14:38, Lowekamp, Bradley (NIH/NLM/LHC) [C] wrote:
> Hello,
>
> There are an incredible number of different per-pixel operations that could be implemented as ITK filters. We cannot provide them all. Many of the basic operations are implemented as ITK filters these include performing the basic C++ operators, such as +, -, * and /, on a per-pixel basis.
>
> As you indicate there are many possible meanings for multiplication of vector images, which can lead to confusion.
>
> ITK has a flexible set of Unary[1], Binary[2] functor filters. Classes like the MultiplyImageFilter[3], are implemented by deriving from the base functor classes. However it is easier to just use the base functor filter and set the proper or custom functor, as in this example [4].
>
> It is fairly easy to write a functor for your specific purposes by following the existing set [5]. It is common for filters to internally define a private functor to perform one step in a large filter. Moving from writing for loops on pixels to writing custom functors is part of good usage of ITK.
>
>
> Brad
>
>
> [1] https://itk.org/Doxygen/html/classitk_1_1UnaryFunctorImageFilter.html
> [2] https://itk.org/Doxygen/html/classitk_1_1BinaryFunctorImageFilter.html
> [3] https://itk.org/Doxygen/html/classitk_1_1MultiplyImageFilter.html
> [4] https://itk.org/Doxygen/html/WikiExamples_2ImageProcessing_2BinaryFunctorImageFilter_8cxx-example.html#_a1
>
> On 11/22/17, 5:15 AM, "Cyril Mory" <cyril.mory at creatis.insa-lyon.fr> wrote:
>
>      Dear ITK users,
>      
>      I am using itk::VectorImage in some of my code, which uses
>      itk::VariableLengthVector as pixel type. And I am wondering why
>      itk::VariableLengthVector has so little support for multiplication.
>      Currently, the * operator only supports multiplication by a scalar.
>      
>      It probably isn't simple, but I would need three additional kinds of
>      multiplication:
>      
>      - dot product with another VariableLengthVector (that has the same
>      length, although it is probably a waste of time to perform the check
>      every time), returning a scalar
>      
>      - component-wise multiplication, returning a VariableLengthVector of the
>      same length
>      
>      - left or right multiplication with a matrix (possibly an
>      itk::VariableSizeMatrix) that has the correct size, but I understand
>      that this is probably the most complex one, and since it only occurs
>      rarely in my code, I can handle it with conversions to vnl::vector and
>      vnl::matrix
>      
>      Are there constraints that prevent at least the dot product and
>      component-wise multiplication operators from being implemented ? If not,
>      then I'd be happy to give it a try. Since both differ only by the return
>      type, two different operators would have to be used (I guess). Do you
>      have suggestions (which one should use *, and what should be the other
>      operator) ? In itk::Vector and itk::CovariantVector, the * operator is
>      used for dot product.
>      
>      Regards,
>      
>      Cyril
>      
>      
>      The ITK community is transitioning from this mailing list to discourse.itk.org. Please join us there!
>      ________________________________
>      Powered by www.kitware.com
>      
>      Visit other Kitware open-source projects at
>      http://www.kitware.com/opensource/opensource.html
>      
>      Kitware offers ITK Training Courses, for more information visit:
>      http://www.kitware.com/products/protraining.php
>      
>      Please keep messages on-topic and check the ITK FAQ at:
>      http://www.itk.org/Wiki/ITK_FAQ
>      
>      Follow this link to subscribe/unsubscribe:
>      http://public.kitware.com/mailman/listinfo/insight-users
>      
>
>


From dzenanz at gmail.com  Wed Nov 22 10:17:15 2017
From: dzenanz at gmail.com (=?UTF-8?B?RMW+ZW5hbiBadWtpxIc=?=)
Date: Wed, 22 Nov 2017 10:17:15 -0500
Subject: [ITK-users] VariableLengthVector and multiplication
In-Reply-To: <23954cc4-a874-7213-471e-b817cab250aa@creatis.insa-lyon.fr>
References: <4740afa6-0730-728f-5a66-46cea25229ee@creatis.insa-lyon.fr>
 <26BF12F6-67F6-4488-81AC-14DDA1581CC3@mail.nih.gov>
 <23954cc4-a874-7213-471e-b817cab250aa@creatis.insa-lyon.fr>
Message-ID: <CAPf2UMQ-t2oucnZC2=0En2gGtLzOdtYmPVFar9WdCBZ=u1y+KA@mail.gmail.com>

Hi Cyril,

Francois has recently used compileif construct. That might help you. But I
can't find an instance of it right now.

Also, we are moving to discourse <https://discourse.itk.org/>. Please post
follow-ups there.

Regards,
D?enan

On Wed, Nov 22, 2017 at 9:54 AM, Cyril Mory <cyril.mory at creatis.insa-lyon.fr
> wrote:

> Thanks for this answer.
>
> I am trying the approach you suggested, and would like to write a dot
> product functor that would work either on scalars (in which case it would
> perform a simple product) or on itk::VariableLengthVector of scalars (in
> which case it would perform a dot product).
>
> I found the "itk::NumericTraits<TPixel>::GetLength()" method, which works
> in both cases, and so I tried this:
>
>
> namespace Functor
> {
>   template< class TPixel, class TInternal>
>   class DotProduct
>   {
>   public:
>     DotProduct() {}
>     ~DotProduct() {}
>     bool operator!=(const DotProduct &) const
>     {
>       return false;
>     }
>
>     bool operator==(const DotProduct & other) const
>     {
>       return !( *this != other );
>     }
>
>     inline TInternal operator()(const TPixel & A, const TPixel & B) const
>     {
>     TInternal out = 0;
>     for (unsigned int component=0; component <
> itk::NumericTraits<TPixel>::GetLength(); component++)
>       {
>       out += A[component] * B[component];
>       }
>     return out;
>     }
>   };
> } // end namespace functor
>
>
> But it does not compile with itk::Image inputs, since the pixels A and B
> have no [ ] operator. Is there a standard way around this problem ?
>
> Regards,
> Cyril
>
>
> On 22/11/2017 14:38, Lowekamp, Bradley (NIH/NLM/LHC) [C] wrote:
>
>> Hello,
>>
>> There are an incredible number of different per-pixel operations that
>> could be implemented as ITK filters. We cannot provide them all. Many of
>> the basic operations are implemented as ITK filters these include
>> performing the basic C++ operators, such as +, -, * and /, on a per-pixel
>> basis.
>>
>> As you indicate there are many possible meanings for multiplication of
>> vector images, which can lead to confusion.
>>
>> ITK has a flexible set of Unary[1], Binary[2] functor filters. Classes
>> like the MultiplyImageFilter[3], are implemented by deriving from the base
>> functor classes. However it is easier to just use the base functor filter
>> and set the proper or custom functor, as in this example [4].
>>
>> It is fairly easy to write a functor for your specific purposes by
>> following the existing set [5]. It is common for filters to internally
>> define a private functor to perform one step in a large filter. Moving from
>> writing for loops on pixels to writing custom functors is part of good
>> usage of ITK.
>>
>>
>> Brad
>>
>>
>> [1] https://itk.org/Doxygen/html/classitk_1_1UnaryFunctorImageFilter.html
>> [2] https://itk.org/Doxygen/html/classitk_1_1BinaryFunctorImageF
>> ilter.html
>> [3] https://itk.org/Doxygen/html/classitk_1_1MultiplyImageFilter.html
>> [4] https://itk.org/Doxygen/html/WikiExamples_2ImageProcessing_2
>> BinaryFunctorImageFilter_8cxx-example.html#_a1
>>
>> On 11/22/17, 5:15 AM, "Cyril Mory" <cyril.mory at creatis.insa-lyon.fr>
>> wrote:
>>
>>      Dear ITK users,
>>           I am using itk::VectorImage in some of my code, which uses
>>      itk::VariableLengthVector as pixel type. And I am wondering why
>>      itk::VariableLengthVector has so little support for multiplication.
>>      Currently, the * operator only supports multiplication by a scalar.
>>           It probably isn't simple, but I would need three additional
>> kinds of
>>      multiplication:
>>           - dot product with another VariableLengthVector (that has the
>> same
>>      length, although it is probably a waste of time to perform the check
>>      every time), returning a scalar
>>           - component-wise multiplication, returning a
>> VariableLengthVector of the
>>      same length
>>           - left or right multiplication with a matrix (possibly an
>>      itk::VariableSizeMatrix) that has the correct size, but I understand
>>      that this is probably the most complex one, and since it only occurs
>>      rarely in my code, I can handle it with conversions to vnl::vector
>> and
>>      vnl::matrix
>>           Are there constraints that prevent at least the dot product and
>>      component-wise multiplication operators from being implemented ? If
>> not,
>>      then I'd be happy to give it a try. Since both differ only by the
>> return
>>      type, two different operators would have to be used (I guess). Do you
>>      have suggestions (which one should use *, and what should be the
>> other
>>      operator) ? In itk::Vector and itk::CovariantVector, the * operator
>> is
>>      used for dot product.
>>           Regards,
>>           Cyril
>>                The ITK community is transitioning from this mailing list
>> to discourse.itk.org. Please join us there!
>>      ________________________________
>>      Powered by www.kitware.com
>>           Visit other Kitware open-source projects at
>>      http://www.kitware.com/opensource/opensource.html
>>           Kitware offers ITK Training Courses, for more information visit:
>>      http://www.kitware.com/products/protraining.php
>>           Please keep messages on-topic and check the ITK FAQ at:
>>      http://www.itk.org/Wiki/ITK_FAQ
>>           Follow this link to subscribe/unsubscribe:
>>      http://public.kitware.com/mailman/listinfo/insight-users
>>
>>
>>
> The ITK community is transitioning from this mailing list to
> discourse.itk.org. Please join us there!
> ________________________________
> Powered by www.kitware.com
>
> Visit other Kitware open-source projects at
> http://www.kitware.com/opensource/opensource.html
>
> Kitware offers ITK Training Courses, for more information visit:
> http://www.kitware.com/products/protraining.php
>
> Please keep messages on-topic and check the ITK FAQ at:
> http://www.itk.org/Wiki/ITK_FAQ
>
> Follow this link to subscribe/unsubscribe:
> http://public.kitware.com/mailman/listinfo/insight-users
>
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From dzenanz at gmail.com  Wed Nov 22 12:42:44 2017
From: dzenanz at gmail.com (=?UTF-8?B?RMW+ZW5hbiBadWtpxIc=?=)
Date: Wed, 22 Nov 2017 12:42:44 -0500
Subject: [ITK-users] VariableLengthVector and multiplication
In-Reply-To: <CAPf2UMQ-t2oucnZC2=0En2gGtLzOdtYmPVFar9WdCBZ=u1y+KA@mail.gmail.com>
References: <4740afa6-0730-728f-5a66-46cea25229ee@creatis.insa-lyon.fr>
 <26BF12F6-67F6-4488-81AC-14DDA1581CC3@mail.nih.gov>
 <23954cc4-a874-7213-471e-b817cab250aa@creatis.insa-lyon.fr>
 <CAPf2UMQ-t2oucnZC2=0En2gGtLzOdtYmPVFar9WdCBZ=u1y+KA@mail.gmail.com>
Message-ID: <CAPf2UMQ6pi=FzyhHhR4hYQ2uPGHJ=zKAnkdSWmePRh7NZQib1A@mail.gmail.com>

I found it. Construct is called *EnableIf*, and you can see how it is used
in *ITK\Modules\Core\Common\test\itkEnableIfTest.cxx*

Regards

On Wed, Nov 22, 2017 at 10:17 AM, D?enan Zuki? <dzenanz at gmail.com> wrote:

> Hi Cyril,
>
> Francois has recently used compileif construct. That might help you. But I
> can't find an instance of it right now.
>
> Also, we are moving to discourse <https://discourse.itk.org/>. Please
> post follow-ups there.
>
> Regards,
> D?enan
>
> On Wed, Nov 22, 2017 at 9:54 AM, Cyril Mory <cyril.mory at creatis.insa-lyon.
> fr> wrote:
>
>> Thanks for this answer.
>>
>> I am trying the approach you suggested, and would like to write a dot
>> product functor that would work either on scalars (in which case it would
>> perform a simple product) or on itk::VariableLengthVector of scalars (in
>> which case it would perform a dot product).
>>
>> I found the "itk::NumericTraits<TPixel>::GetLength()" method, which
>> works in both cases, and so I tried this:
>>
>>
>> namespace Functor
>> {
>>   template< class TPixel, class TInternal>
>>   class DotProduct
>>   {
>>   public:
>>     DotProduct() {}
>>     ~DotProduct() {}
>>     bool operator!=(const DotProduct &) const
>>     {
>>       return false;
>>     }
>>
>>     bool operator==(const DotProduct & other) const
>>     {
>>       return !( *this != other );
>>     }
>>
>>     inline TInternal operator()(const TPixel & A, const TPixel & B) const
>>     {
>>     TInternal out = 0;
>>     for (unsigned int component=0; component <
>> itk::NumericTraits<TPixel>::GetLength(); component++)
>>       {
>>       out += A[component] * B[component];
>>       }
>>     return out;
>>     }
>>   };
>> } // end namespace functor
>>
>>
>> But it does not compile with itk::Image inputs, since the pixels A and B
>> have no [ ] operator. Is there a standard way around this problem ?
>>
>> Regards,
>> Cyril
>>
>>
>> On 22/11/2017 14:38, Lowekamp, Bradley (NIH/NLM/LHC) [C] wrote:
>>
>>> Hello,
>>>
>>> There are an incredible number of different per-pixel operations that
>>> could be implemented as ITK filters. We cannot provide them all. Many of
>>> the basic operations are implemented as ITK filters these include
>>> performing the basic C++ operators, such as +, -, * and /, on a per-pixel
>>> basis.
>>>
>>> As you indicate there are many possible meanings for multiplication of
>>> vector images, which can lead to confusion.
>>>
>>> ITK has a flexible set of Unary[1], Binary[2] functor filters. Classes
>>> like the MultiplyImageFilter[3], are implemented by deriving from the base
>>> functor classes. However it is easier to just use the base functor filter
>>> and set the proper or custom functor, as in this example [4].
>>>
>>> It is fairly easy to write a functor for your specific purposes by
>>> following the existing set [5]. It is common for filters to internally
>>> define a private functor to perform one step in a large filter. Moving from
>>> writing for loops on pixels to writing custom functors is part of good
>>> usage of ITK.
>>>
>>>
>>> Brad
>>>
>>>
>>> [1] https://itk.org/Doxygen/html/classitk_1_1UnaryFunctorImageFi
>>> lter.html
>>> [2] https://itk.org/Doxygen/html/classitk_1_1BinaryFunctorImageF
>>> ilter.html
>>> [3] https://itk.org/Doxygen/html/classitk_1_1MultiplyImageFilter.html
>>> [4] https://itk.org/Doxygen/html/WikiExamples_2ImageProcessing_2
>>> BinaryFunctorImageFilter_8cxx-example.html#_a1
>>>
>>> On 11/22/17, 5:15 AM, "Cyril Mory" <cyril.mory at creatis.insa-lyon.fr>
>>> wrote:
>>>
>>>      Dear ITK users,
>>>           I am using itk::VectorImage in some of my code, which uses
>>>      itk::VariableLengthVector as pixel type. And I am wondering why
>>>      itk::VariableLengthVector has so little support for multiplication.
>>>      Currently, the * operator only supports multiplication by a scalar.
>>>           It probably isn't simple, but I would need three additional
>>> kinds of
>>>      multiplication:
>>>           - dot product with another VariableLengthVector (that has the
>>> same
>>>      length, although it is probably a waste of time to perform the check
>>>      every time), returning a scalar
>>>           - component-wise multiplication, returning a
>>> VariableLengthVector of the
>>>      same length
>>>           - left or right multiplication with a matrix (possibly an
>>>      itk::VariableSizeMatrix) that has the correct size, but I understand
>>>      that this is probably the most complex one, and since it only occurs
>>>      rarely in my code, I can handle it with conversions to vnl::vector
>>> and
>>>      vnl::matrix
>>>           Are there constraints that prevent at least the dot product and
>>>      component-wise multiplication operators from being implemented ? If
>>> not,
>>>      then I'd be happy to give it a try. Since both differ only by the
>>> return
>>>      type, two different operators would have to be used (I guess). Do
>>> you
>>>      have suggestions (which one should use *, and what should be the
>>> other
>>>      operator) ? In itk::Vector and itk::CovariantVector, the * operator
>>> is
>>>      used for dot product.
>>>           Regards,
>>>           Cyril
>>>                The ITK community is transitioning from this mailing list
>>> to discourse.itk.org. Please join us there!
>>>      ________________________________
>>>      Powered by www.kitware.com
>>>           Visit other Kitware open-source projects at
>>>      http://www.kitware.com/opensource/opensource.html
>>>           Kitware offers ITK Training Courses, for more information
>>> visit:
>>>      http://www.kitware.com/products/protraining.php
>>>           Please keep messages on-topic and check the ITK FAQ at:
>>>      http://www.itk.org/Wiki/ITK_FAQ
>>>           Follow this link to subscribe/unsubscribe:
>>>      http://public.kitware.com/mailman/listinfo/insight-users
>>>
>>>
>>>
>> The ITK community is transitioning from this mailing list to
>> discourse.itk.org. Please join us there!
>> ________________________________
>> Powered by www.kitware.com
>>
>> Visit other Kitware open-source projects at
>> http://www.kitware.com/opensource/opensource.html
>>
>> Kitware offers ITK Training Courses, for more information visit:
>> http://www.kitware.com/products/protraining.php
>>
>> Please keep messages on-topic and check the ITK FAQ at:
>> http://www.itk.org/Wiki/ITK_FAQ
>>
>> Follow this link to subscribe/unsubscribe:
>> http://public.kitware.com/mailman/listinfo/insight-users
>>
>
>
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From grothausmann.roman at mh-hannover.de  Fri Nov 24 06:26:38 2017
From: grothausmann.roman at mh-hannover.de (Grothausmann, Roman Dr.)
Date: Fri, 24 Nov 2017 12:26:38 +0100
Subject: [ITK-users] watershed on surface meshs
Message-ID: <67d53e88-3783-6a6b-faae-cab064883d9d@mh-hannover.de>

Dear mailing list members,


I need to separate a mesh at "curved corners" (see attached PNG, using the 
colored labels from a facet analysis do not suffice but go in the right 
direction). So my current thought is to run vtkCurvature to get a Gaussian 
curvature value per point/vertex and then try to separate regions of positive 
values around local maxima. Just thresholding the result of vtkCurvature does 
not fully separate each local max from neighboring ones, but to my understanding 
a surface watershed would. I found two publications by Mangan and Whitaker on this:

Partitioning 3D surface meshes using watershed:
http://teacher.en.rmutt.ac.th/ktw/Resources/Full%20paper%20PDF/Partitioning%203D%20surface%20meshes%20using%20watershed%20segmentation.pdf

Surface Segmentation Using Morphological Watersheds:
https://www.google.de/url?sa=t&rct=j&q=&esrc=s&source=web&cd=4&cad=rja&uact=8&ved=0ahUKEwjD0by1lafWAhVUGsAKHZ2MAbUQFgg_MAM&url=http%3A%2F%2Fciteseerx.ist.psu.edu%2Fviewdoc%2Fdownload%3Fdoi%3D10.1.1.464.2788%26rep%3Drep1%26type%3Dpdf&usg=AFQjCNGX-p9-ElQFcpsUyBRO0pCjBKCmNg

Does anybody know about an implementation for this in VTK/ITK or another 
open-source library? If not, would it be possible to transfer the ITK watershed 
implementation for voxel data to mesh data, e.g. to crate a VTKmorphWatershedFilter?

Thanks for any help or hints.
Roman


-- 
Dr. Roman Grothausmann

Tomographie und Digitale Bildverarbeitung
Tomography and Digital Image Analysis

Medizinische Hochschule Hannover
Institut f?r Funktionelle und Angewandte Anatomie
OE 4120, Carl-Neuberg-Str. 1, 30625 Hannover, Deutschland

Tel. +49 511 532-2900
grothausmann.roman at mh-hannover.de
http://www.mh-hannover.de/anatomie.html
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From cyril.mory at creatis.insa-lyon.fr  Fri Nov 24 06:54:25 2017
From: cyril.mory at creatis.insa-lyon.fr (Cyril Mory)
Date: Fri, 24 Nov 2017 12:54:25 +0100
Subject: [ITK-users] VariableLengthVector and multiplication
In-Reply-To: <CAPf2UMQ6pi=FzyhHhR4hYQ2uPGHJ=zKAnkdSWmePRh7NZQib1A@mail.gmail.com>
References: <4740afa6-0730-728f-5a66-46cea25229ee@creatis.insa-lyon.fr>
 <26BF12F6-67F6-4488-81AC-14DDA1581CC3@mail.nih.gov>
 <23954cc4-a874-7213-471e-b817cab250aa@creatis.insa-lyon.fr>
 <CAPf2UMQ-t2oucnZC2=0En2gGtLzOdtYmPVFar9WdCBZ=u1y+KA@mail.gmail.com>
 <CAPf2UMQ6pi=FzyhHhR4hYQ2uPGHJ=zKAnkdSWmePRh7NZQib1A@mail.gmail.com>
Message-ID: <eeb55a03-93ed-28c4-f4ee-a23661dda7ed@creatis.insa-lyon.fr>

Thanks.

Here is the solution I used, which works but may be sub-optimal:

namespace Functor
{
 ? template< class TPixel, class TInternal>
 ? class DotProduct
 ? {
 ? public:
 ??? DotProduct() {}
 ??? ~DotProduct() {}
 ??? bool operator!=(const DotProduct &) const
 ??? {
 ????? return false;
 ??? }

 ??? bool operator==(const DotProduct & other) const
 ??? {
 ????? return !( *this != other );
 ??? }

 ? template<typename T = TPixel>
 ? inline
 ? typename itk::mpl::EnableIf<itk::mpl::IsSame<T, TInternal>, 
TInternal>::Type
 ? operator()(const TInternal & A, const TInternal & B) const
 ? { return static_cast<TInternal>( A * B ); }

 ? template<typename T = TPixel>
 ? typename itk::mpl::DisableIf<itk::mpl::IsSame<T, TInternal>, 
TInternal>::Type
 ? operator()(const TPixel & A, const TPixel & B) const
 ??? {
 ??? TInternal out = 0;
 ??? for (unsigned int component=0; component < 
itk::NumericTraits<TPixel>::GetLength(A); component++)
 ????? {
 ????? out += A[component] * B[component];
 ????? }
 ??? return out;
 ??? }
 ? };
} // end namespace functor


On 22/11/2017 18:42, D?enan Zuki? wrote:
> I found it. Construct is called *EnableIf*, and you can see how it is 
> used in /ITK\Modules\Core\Common\test\itkEnableIfTest.cxx/
>
> Regards
>
> On Wed, Nov 22, 2017 at 10:17 AM, D?enan Zuki? <dzenanz at gmail.com 
> <mailto:dzenanz at gmail.com>> wrote:
>
>     Hi Cyril,
>
>     Francois has recently used compileif construct. That might help
>     you. But I can't find an instance of it right now.
>
>     Also, we are moving to discourse <https://discourse.itk.org/>.
>     Please post follow-ups there.
>
>     Regards,
>     D?enan
>
>     On Wed, Nov 22, 2017 at 9:54 AM, Cyril Mory
>     <cyril.mory at creatis.insa-lyon.fr
>     <mailto:cyril.mory at creatis.insa-lyon.fr>> wrote:
>
>         Thanks for this answer.
>
>         I am trying the approach you suggested, and would like to
>         write a dot product functor that would work either on scalars
>         (in which case it would perform a simple product) or on
>         itk::VariableLengthVector of scalars (in which case it would
>         perform a dot product).
>
>         I found the "itk::NumericTraits<TPixel>::GetLength()" method,
>         which works in both cases, and so I tried this:
>
>
>         namespace Functor
>         {
>         ? template< class TPixel, class TInternal>
>         ? class DotProduct
>         ? {
>         ? public:
>         ??? DotProduct() {}
>         ??? ~DotProduct() {}
>         ??? bool operator!=(const DotProduct &) const
>         ??? {
>         ????? return false;
>         ??? }
>
>         ??? bool operator==(const DotProduct & other) const
>         ??? {
>         ????? return !( *this != other );
>         ??? }
>
>         ??? inline TInternal operator()(const TPixel & A, const TPixel
>         & B) const
>         ??? {
>         ??? TInternal out = 0;
>         ??? for (unsigned int component=0; component <
>         itk::NumericTraits<TPixel>::GetLength(); component++)
>         ????? {
>         ????? out += A[component] * B[component];
>         ????? }
>         ??? return out;
>         ??? }
>         ? };
>         } // end namespace functor
>
>
>         But it does not compile with itk::Image inputs, since the
>         pixels A and B have no [ ] operator. Is there a standard way
>         around this problem ?
>
>         Regards,
>         Cyril
>
>
>         On 22/11/2017 14:38, Lowekamp, Bradley (NIH/NLM/LHC) [C] wrote:
>
>             Hello,
>
>             There are an incredible number of different per-pixel
>             operations that could be implemented as ITK filters. We
>             cannot provide them all. Many of the basic operations are
>             implemented as ITK filters these include performing the
>             basic C++ operators, such as +, -, * and /, on a per-pixel
>             basis.
>
>             As you indicate there are many possible meanings for
>             multiplication of vector images, which can lead to confusion.
>
>             ITK has a flexible set of Unary[1], Binary[2] functor
>             filters. Classes like the MultiplyImageFilter[3], are
>             implemented by deriving from the base functor classes.
>             However it is easier to just use the base functor filter
>             and set the proper or custom functor, as in this example [4].
>
>             It is fairly easy to write a functor for your specific
>             purposes by following the existing set [5]. It is common
>             for filters to internally define a private functor to
>             perform one step in a large filter. Moving from writing
>             for loops on pixels to writing custom functors is part of
>             good usage of ITK.
>
>
>             Brad
>
>
>             [1]
>             https://itk.org/Doxygen/html/classitk_1_1UnaryFunctorImageFilter.html
>             <https://itk.org/Doxygen/html/classitk_1_1UnaryFunctorImageFilter.html>
>             [2]
>             https://itk.org/Doxygen/html/classitk_1_1BinaryFunctorImageFilter.html
>             <https://itk.org/Doxygen/html/classitk_1_1BinaryFunctorImageFilter.html>
>             [3]
>             https://itk.org/Doxygen/html/classitk_1_1MultiplyImageFilter.html
>             <https://itk.org/Doxygen/html/classitk_1_1MultiplyImageFilter.html>
>             [4]
>             https://itk.org/Doxygen/html/WikiExamples_2ImageProcessing_2BinaryFunctorImageFilter_8cxx-example.html#_a1
>             <https://itk.org/Doxygen/html/WikiExamples_2ImageProcessing_2BinaryFunctorImageFilter_8cxx-example.html#_a1>
>
>             On 11/22/17, 5:15 AM, "Cyril Mory"
>             <cyril.mory at creatis.insa-lyon.fr
>             <mailto:cyril.mory at creatis.insa-lyon.fr>> wrote:
>
>             ? ? ?Dear ITK users,
>             ? ? ? ? ? I am using itk::VectorImage in some of my code,
>             which uses
>             ? ? ?itk::VariableLengthVector as pixel type. And I am
>             wondering why
>             ? ? ?itk::VariableLengthVector has so little support for
>             multiplication.
>             ? ? ?Currently, the * operator only supports
>             multiplication by a scalar.
>             ? ? ? ? ? It probably isn't simple, but I would need three
>             additional kinds of
>             ? ? ?multiplication:
>             ? ? ? ? ? - dot product with another VariableLengthVector
>             (that has the same
>             ? ? ?length, although it is probably a waste of time to
>             perform the check
>             ? ? ?every time), returning a scalar
>             ? ? ? ? ? - component-wise multiplication, returning a
>             VariableLengthVector of the
>             ? ? ?same length
>             ? ? ? ? ? - left or right multiplication with a matrix
>             (possibly an
>             ? ? ?itk::VariableSizeMatrix) that has the correct size,
>             but I understand
>             ? ? ?that this is probably the most complex one, and since
>             it only occurs
>             ? ? ?rarely in my code, I can handle it with conversions
>             to vnl::vector and
>             ? ? ?vnl::matrix
>             ? ? ? ? ? Are there constraints that prevent at least the
>             dot product and
>             ? ? ?component-wise multiplication operators from being
>             implemented ? If not,
>             ? ? ?then I'd be happy to give it a try. Since both differ
>             only by the return
>             ? ? ?type, two different operators would have to be used
>             (I guess). Do you
>             ? ? ?have suggestions (which one should use *, and what
>             should be the other
>             ? ? ?operator) ? In itk::Vector and itk::CovariantVector,
>             the * operator is
>             ? ? ?used for dot product.
>             ? ? ? ? ? Regards,
>             ? ? ? ? ? Cyril
>             ? ? ? ? ? ? ? ?The ITK community is transitioning from
>             this mailing list to discourse.itk.org
>             <http://discourse.itk.org>. Please join us there!
>             ? ? ?________________________________
>             ? ? ?Powered by www.kitware.com <http://www.kitware.com>
>             ? ? ? ? ? Visit other Kitware open-source projects at
>             http://www.kitware.com/opensource/opensource.html
>             <http://www.kitware.com/opensource/opensource.html>
>             ? ? ? ? ? Kitware offers ITK Training Courses, for more
>             information visit:
>             http://www.kitware.com/products/protraining.php
>             <http://www.kitware.com/products/protraining.php>
>             ? ? ? ? ? Please keep messages on-topic and check the ITK
>             FAQ at:
>             http://www.itk.org/Wiki/ITK_FAQ
>             <http://www.itk.org/Wiki/ITK_FAQ>
>             ? ? ? ? ? Follow this link to subscribe/unsubscribe:
>             http://public.kitware.com/mailman/listinfo/insight-users
>             <http://public.kitware.com/mailman/listinfo/insight-users>
>
>
>
>         The ITK community is transitioning from this mailing list to
>         discourse.itk.org <http://discourse.itk.org>. Please join us
>         there!
>         ________________________________
>         Powered by www.kitware.com <http://www.kitware.com>
>
>         Visit other Kitware open-source projects at
>         http://www.kitware.com/opensource/opensource.html
>         <http://www.kitware.com/opensource/opensource.html>
>
>         Kitware offers ITK Training Courses, for more information visit:
>         http://www.kitware.com/products/protraining.php
>         <http://www.kitware.com/products/protraining.php>
>
>         Please keep messages on-topic and check the ITK FAQ at:
>         http://www.itk.org/Wiki/ITK_FAQ <http://www.itk.org/Wiki/ITK_FAQ>
>
>         Follow this link to subscribe/unsubscribe:
>         http://public.kitware.com/mailman/listinfo/insight-users
>         <http://public.kitware.com/mailman/listinfo/insight-users>
>
>
>

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From dzenanz at gmail.com  Fri Nov 24 08:46:05 2017
From: dzenanz at gmail.com (=?UTF-8?B?RMW+ZW5hbiBadWtpxIc=?=)
Date: Fri, 24 Nov 2017 08:46:05 -0500
Subject: [ITK-users] VariableLengthVector and multiplication
In-Reply-To: <eeb55a03-93ed-28c4-f4ee-a23661dda7ed@creatis.insa-lyon.fr>
References: <4740afa6-0730-728f-5a66-46cea25229ee@creatis.insa-lyon.fr>
 <26BF12F6-67F6-4488-81AC-14DDA1581CC3@mail.nih.gov>
 <23954cc4-a874-7213-471e-b817cab250aa@creatis.insa-lyon.fr>
 <CAPf2UMQ-t2oucnZC2=0En2gGtLzOdtYmPVFar9WdCBZ=u1y+KA@mail.gmail.com>
 <CAPf2UMQ6pi=FzyhHhR4hYQ2uPGHJ=zKAnkdSWmePRh7NZQib1A@mail.gmail.com>
 <eeb55a03-93ed-28c4-f4ee-a23661dda7ed@creatis.insa-lyon.fr>
Message-ID: <CAPf2UMRCBxpWz9wY27o8K5h9GbB_o3Z_qyVQFY5jhegnLCcF_Q@mail.gmail.com>

That looks about right. Thanks for sharing your solution.

Regards,
D?enan

On Fri, Nov 24, 2017 at 6:54 AM, Cyril Mory <cyril.mory at creatis.insa-lyon.fr
> wrote:

> Thanks.
>
> Here is the solution I used, which works but may be sub-optimal:
>
> namespace Functor
> {
>   template< class TPixel, class TInternal>
>   class DotProduct
>   {
>   public:
>     DotProduct() {}
>     ~DotProduct() {}
>     bool operator!=(const DotProduct &) const
>     {
>       return false;
>     }
>
>     bool operator==(const DotProduct & other) const
>     {
>       return !( *this != other );
>     }
>
>   template<typename T = TPixel>
>   inline
>   typename itk::mpl::EnableIf<itk::mpl::IsSame<T, TInternal>,
> TInternal>::Type
>   operator()(const TInternal & A, const TInternal & B) const
>   { return static_cast<TInternal>( A * B ); }
>
>   template<typename T = TPixel>
>   typename itk::mpl::DisableIf<itk::mpl::IsSame<T, TInternal>,
> TInternal>::Type
>   operator()(const TPixel & A, const TPixel & B) const
>     {
>     TInternal out = 0;
>     for (unsigned int component=0; component < itk::NumericTraits<TPixel>::GetLength(A);
> component++)
>       {
>       out += A[component] * B[component];
>       }
>     return out;
>     }
>   };
> } // end namespace functor
>
>
> On 22/11/2017 18:42, D?enan Zuki? wrote:
>
> I found it. Construct is called *EnableIf*, and you can see how it is
> used in *ITK\Modules\Core\Common\test\itkEnableIfTest.cxx*
>
> Regards
>
> On Wed, Nov 22, 2017 at 10:17 AM, D?enan Zuki? <dzenanz at gmail.com> wrote:
>
>> Hi Cyril,
>>
>> Francois has recently used compileif construct. That might help you. But
>> I can't find an instance of it right now.
>>
>> Also, we are moving to discourse <https://discourse.itk.org/>. Please
>> post follow-ups there.
>>
>> Regards,
>> D?enan
>>
>> On Wed, Nov 22, 2017 at 9:54 AM, Cyril Mory <
>> cyril.mory at creatis.insa-lyon.fr> wrote:
>>
>>> Thanks for this answer.
>>>
>>> I am trying the approach you suggested, and would like to write a dot
>>> product functor that would work either on scalars (in which case it would
>>> perform a simple product) or on itk::VariableLengthVector of scalars (in
>>> which case it would perform a dot product).
>>>
>>> I found the "itk::NumericTraits<TPixel>::GetLength()" method, which
>>> works in both cases, and so I tried this:
>>>
>>>
>>> namespace Functor
>>> {
>>>   template< class TPixel, class TInternal>
>>>   class DotProduct
>>>   {
>>>   public:
>>>     DotProduct() {}
>>>     ~DotProduct() {}
>>>     bool operator!=(const DotProduct &) const
>>>     {
>>>       return false;
>>>     }
>>>
>>>     bool operator==(const DotProduct & other) const
>>>     {
>>>       return !( *this != other );
>>>     }
>>>
>>>     inline TInternal operator()(const TPixel & A, const TPixel & B) const
>>>     {
>>>     TInternal out = 0;
>>>     for (unsigned int component=0; component <
>>> itk::NumericTraits<TPixel>::GetLength(); component++)
>>>       {
>>>       out += A[component] * B[component];
>>>       }
>>>     return out;
>>>     }
>>>   };
>>> } // end namespace functor
>>>
>>>
>>> But it does not compile with itk::Image inputs, since the pixels A and B
>>> have no [ ] operator. Is there a standard way around this problem ?
>>>
>>> Regards,
>>> Cyril
>>>
>>>
>>> On 22/11/2017 14:38, Lowekamp, Bradley (NIH/NLM/LHC) [C] wrote:
>>>
>>>> Hello,
>>>>
>>>> There are an incredible number of different per-pixel operations that
>>>> could be implemented as ITK filters. We cannot provide them all. Many of
>>>> the basic operations are implemented as ITK filters these include
>>>> performing the basic C++ operators, such as +, -, * and /, on a per-pixel
>>>> basis.
>>>>
>>>> As you indicate there are many possible meanings for multiplication of
>>>> vector images, which can lead to confusion.
>>>>
>>>> ITK has a flexible set of Unary[1], Binary[2] functor filters. Classes
>>>> like the MultiplyImageFilter[3], are implemented by deriving from the base
>>>> functor classes. However it is easier to just use the base functor filter
>>>> and set the proper or custom functor, as in this example [4].
>>>>
>>>> It is fairly easy to write a functor for your specific purposes by
>>>> following the existing set [5]. It is common for filters to internally
>>>> define a private functor to perform one step in a large filter. Moving from
>>>> writing for loops on pixels to writing custom functors is part of good
>>>> usage of ITK.
>>>>
>>>>
>>>> Brad
>>>>
>>>>
>>>> [1] https://itk.org/Doxygen/html/classitk_1_1UnaryFunctorImageFi
>>>> lter.html
>>>> [2] https://itk.org/Doxygen/html/classitk_1_1BinaryFunctorImageF
>>>> ilter.html
>>>> [3] https://itk.org/Doxygen/html/classitk_1_1MultiplyImageFilter.html
>>>> [4] https://itk.org/Doxygen/html/WikiExamples_2ImageProcessing_2
>>>> BinaryFunctorImageFilter_8cxx-example.html#_a1
>>>>
>>>> On 11/22/17, 5:15 AM, "Cyril Mory" <cyril.mory at creatis.insa-lyon.fr>
>>>> wrote:
>>>>
>>>>      Dear ITK users,
>>>>           I am using itk::VectorImage in some of my code, which uses
>>>>      itk::VariableLengthVector as pixel type. And I am wondering why
>>>>      itk::VariableLengthVector has so little support for multiplication.
>>>>      Currently, the * operator only supports multiplication by a scalar.
>>>>           It probably isn't simple, but I would need three additional
>>>> kinds of
>>>>      multiplication:
>>>>           - dot product with another VariableLengthVector (that has the
>>>> same
>>>>      length, although it is probably a waste of time to perform the
>>>> check
>>>>      every time), returning a scalar
>>>>           - component-wise multiplication, returning a
>>>> VariableLengthVector of the
>>>>      same length
>>>>           - left or right multiplication with a matrix (possibly an
>>>>      itk::VariableSizeMatrix) that has the correct size, but I
>>>> understand
>>>>      that this is probably the most complex one, and since it only
>>>> occurs
>>>>      rarely in my code, I can handle it with conversions to vnl::vector
>>>> and
>>>>      vnl::matrix
>>>>           Are there constraints that prevent at least the dot product
>>>> and
>>>>      component-wise multiplication operators from being implemented ?
>>>> If not,
>>>>      then I'd be happy to give it a try. Since both differ only by the
>>>> return
>>>>      type, two different operators would have to be used (I guess). Do
>>>> you
>>>>      have suggestions (which one should use *, and what should be the
>>>> other
>>>>      operator) ? In itk::Vector and itk::CovariantVector, the *
>>>> operator is
>>>>      used for dot product.
>>>>           Regards,
>>>>           Cyril
>>>>                The ITK community is transitioning from this mailing
>>>> list to discourse.itk.org. Please join us there!
>>>>      ________________________________
>>>>      Powered by www.kitware.com
>>>>           Visit other Kitware open-source projects at
>>>>      http://www.kitware.com/opensource/opensource.html
>>>>           Kitware offers ITK Training Courses, for more information
>>>> visit:
>>>>      http://www.kitware.com/products/protraining.php
>>>>           Please keep messages on-topic and check the ITK FAQ at:
>>>>      http://www.itk.org/Wiki/ITK_FAQ
>>>>           Follow this link to subscribe/unsubscribe:
>>>>      http://public.kitware.com/mailman/listinfo/insight-users
>>>>
>>>>
>>>>
>>> The ITK community is transitioning from this mailing list to
>>> discourse.itk.org. Please join us there!
>>> ________________________________
>>> Powered by www.kitware.com
>>>
>>> Visit other Kitware open-source projects at
>>> http://www.kitware.com/opensource/opensource.html
>>>
>>> Kitware offers ITK Training Courses, for more information visit:
>>> http://www.kitware.com/products/protraining.php
>>>
>>> Please keep messages on-topic and check the ITK FAQ at:
>>> http://www.itk.org/Wiki/ITK_FAQ
>>>
>>> Follow this link to subscribe/unsubscribe:
>>> http://public.kitware.com/mailman/listinfo/insight-users
>>>
>>
>>
>
>
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From dzenanz at gmail.com  Fri Nov 24 10:53:41 2017
From: dzenanz at gmail.com (=?UTF-8?B?RMW+ZW5hbiBadWtpxIc=?=)
Date: Fri, 24 Nov 2017 10:53:41 -0500
Subject: [ITK-users] watershed on surface meshs
In-Reply-To: <67d53e88-3783-6a6b-faae-cab064883d9d@mh-hannover.de>
References: <67d53e88-3783-6a6b-faae-cab064883d9d@mh-hannover.de>
Message-ID: <CAPf2UMSyhbTx=HdX40RtRvimD2aAxo_14iHWehFV=vz5qxyFkA@mail.gmail.com>

Hi Roman,

I don't know of any implementation of mesh watershed segmentation. ITK does
not really have mesh processing capabilities, it is mostly limited to
conversion between mesh and image representations.

A colleague <http://www.cg.informatik.uni-siegen.de/en/chiosa-iurie> worked
on something related, maybe he can provide the source code if you ask.

And we are moving to discourse <https://discourse.itk.org/>. Re-posting
this question there might be useful.

Regards,
D?enan

On Fri, Nov 24, 2017 at 6:26 AM, Grothausmann, Roman Dr. <
grothausmann.roman at mh-hannover.de> wrote:

> Dear mailing list members,
>
>
> I need to separate a mesh at "curved corners" (see attached PNG, using the
> colored labels from a facet analysis do not suffice but go in the right
> direction). So my current thought is to run vtkCurvature to get a Gaussian
> curvature value per point/vertex and then try to separate regions of
> positive values around local maxima. Just thresholding the result of
> vtkCurvature does not fully separate each local max from neighboring ones,
> but to my understanding a surface watershed would. I found two publications
> by Mangan and Whitaker on this:
>
> Partitioning 3D surface meshes using watershed:
> http://teacher.en.rmutt.ac.th/ktw/Resources/Full%20paper%20P
> DF/Partitioning%203D%20surface%20meshes%20using%20watershed%
> 20segmentation.pdf
>
> Surface Segmentation Using Morphological Watersheds:
> https://www.google.de/url?sa=t&rct=j&q=&esrc=s&source=web&cd
> =4&cad=rja&uact=8&ved=0ahUKEwjD0by1lafWAhVUGsAKHZ2MAbUQFgg_M
> AM&url=http%3A%2F%2Fciteseerx.ist.psu.edu%2Fviewdoc%2Fdownlo
> ad%3Fdoi%3D10.1.1.464.2788%26rep%3Drep1%26type%3Dpdf&usg=
> AFQjCNGX-p9-ElQFcpsUyBRO0pCjBKCmNg
>
> Does anybody know about an implementation for this in VTK/ITK or another
> open-source library? If not, would it be possible to transfer the ITK
> watershed implementation for voxel data to mesh data, e.g. to crate a
> VTKmorphWatershedFilter?
>
> Thanks for any help or hints.
> Roman
>
>
> --
> Dr. Roman Grothausmann
>
> Tomographie und Digitale Bildverarbeitung
> Tomography and Digital Image Analysis
>
> Medizinische Hochschule Hannover
> Institut f?r Funktionelle und Angewandte Anatomie
> OE 4120, Carl-Neuberg-Str. 1, 30625 Hannover, Deutschland
>
> Tel. +49 511 532-2900
> grothausmann.roman at mh-hannover.de
> http://www.mh-hannover.de/anatomie.html
>
> The ITK community is transitioning from this mailing list to
> discourse.itk.org. Please join us there!
> ________________________________
> Powered by www.kitware.com
>
> Visit other Kitware open-source projects at
> http://www.kitware.com/opensource/opensource.html
>
> Kitware offers ITK Training Courses, for more information visit:
> http://www.kitware.com/products/protraining.php
>
> Please keep messages on-topic and check the ITK FAQ at:
> http://www.itk.org/Wiki/ITK_FAQ
>
> Follow this link to subscribe/unsubscribe:
> http://public.kitware.com/mailman/listinfo/insight-users
>
>
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From richard.beare at gmail.com  Fri Nov 24 15:53:49 2017
From: richard.beare at gmail.com (Richard Beare)
Date: Sat, 25 Nov 2017 07:53:49 +1100
Subject: [ITK-users] watershed on surface meshs
In-Reply-To: <67d53e88-3783-6a6b-faae-cab064883d9d@mh-hannover.de>
References: <67d53e88-3783-6a6b-faae-cab064883d9d@mh-hannover.de>
Message-ID: <CA+V7QS9QiBXHtiyjNf107XZtt94G3-72bXHcpEpN51Z5m4R+YQ@mail.gmail.com>

I don't recall an implementation of this anywhere. However you may be able
to hack something together reasonably quickly. Watersheds are built around
minimal paths, so depending on what complexity is available in the
mesh-based shortest path tools. In the worst cast you could create a copy
of the mesh for each seed region, compute the minimal distance to each non
seed vertex, then do a vertex-wise min, tracking which mesh/seed region has
the minimum, and that's your label. Not very efficient because you compute
the entire mesh distance each time, and no obvious way to do a watershed
line consistently, but perhaps that doesn't matter for testing the idea.

On Fri, Nov 24, 2017 at 10:26 PM, Grothausmann, Roman Dr. <
grothausmann.roman at mh-hannover.de> wrote:

> Dear mailing list members,
>
>
> I need to separate a mesh at "curved corners" (see attached PNG, using the
> colored labels from a facet analysis do not suffice but go in the right
> direction). So my current thought is to run vtkCurvature to get a Gaussian
> curvature value per point/vertex and then try to separate regions of
> positive values around local maxima. Just thresholding the result of
> vtkCurvature does not fully separate each local max from neighboring ones,
> but to my understanding a surface watershed would. I found two publications
> by Mangan and Whitaker on this:
>
> Partitioning 3D surface meshes using watershed:
> http://teacher.en.rmutt.ac.th/ktw/Resources/Full%20paper%20P
> DF/Partitioning%203D%20surface%20meshes%20using%20watershed%
> 20segmentation.pdf
>
> Surface Segmentation Using Morphological Watersheds:
> https://www.google.de/url?sa=t&rct=j&q=&esrc=s&source=web&cd
> =4&cad=rja&uact=8&ved=0ahUKEwjD0by1lafWAhVUGsAKHZ2MAbUQFgg_
> MAM&url=http%3A%2F%2Fciteseerx.ist.psu.edu%2Fviewdoc%
> 2Fdownload%3Fdoi%3D10.1.1.464.2788%26rep%3Drep1%26type%
> 3Dpdf&usg=AFQjCNGX-p9-ElQFcpsUyBRO0pCjBKCmNg
>
> Does anybody know about an implementation for this in VTK/ITK or another
> open-source library? If not, would it be possible to transfer the ITK
> watershed implementation for voxel data to mesh data, e.g. to crate a
> VTKmorphWatershedFilter?
>
> Thanks for any help or hints.
> Roman
>
>
> --
> Dr. Roman Grothausmann
>
> Tomographie und Digitale Bildverarbeitung
> Tomography and Digital Image Analysis
>
> Medizinische Hochschule Hannover
> Institut f?r Funktionelle und Angewandte Anatomie
> OE 4120, Carl-Neuberg-Str. 1, 30625 Hannover, Deutschland
>
> Tel. +49 511 532-2900
> grothausmann.roman at mh-hannover.de
> http://www.mh-hannover.de/anatomie.html
>
> The ITK community is transitioning from this mailing list to
> discourse.itk.org. Please join us there!
> ________________________________
> Powered by www.kitware.com
>
> Visit other Kitware open-source projects at
> http://www.kitware.com/opensource/opensource.html
>
> Kitware offers ITK Training Courses, for more information visit:
> http://www.kitware.com/products/protraining.php
>
> Please keep messages on-topic and check the ITK FAQ at:
> http://www.itk.org/Wiki/ITK_FAQ
>
> Follow this link to subscribe/unsubscribe:
> http://public.kitware.com/mailman/listinfo/insight-users
>
>
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From richard.beare at gmail.com  Fri Nov 24 22:16:42 2017
From: richard.beare at gmail.com (Richard Beare)
Date: Sat, 25 Nov 2017 14:16:42 +1100
Subject: [ITK-users] watershed on surface meshs
In-Reply-To: <67d53e88-3783-6a6b-faae-cab064883d9d@mh-hannover.de>
References: <67d53e88-3783-6a6b-faae-cab064883d9d@mh-hannover.de>
Message-ID: <CA+V7QS9Xr0aWQ8MGD4s6zCSh+-qjUfXoLOLWWT5WhgbypexF_w@mail.gmail.com>

Just remembered something that may be useful for testing. I wrote the
following for doing watersheds on geospatial graphs using R/igraph.
Certainly isn't efficient, but may be useful for testing if you can turn
your mesh+curvature into something like a text file.

This was set up for allocating points on maps to destinations based on
travel time. It performed a kind of smoothing to smooth non-sensical travel
time estimates, but the basic algorithm is there. It will take some
fiddling. You could probably do something equivalent with python, probably
doing better than this priorty queue, but using much the same approach with
igraph.

library(liqueueR)

## Mostly a copy of PriorityQueue from liqueueR
StablePriorityQueue <- setRefClass("StablePriorityQueue",
                                   contains = "Queue",
                                   fields = list(
                                     count = "numeric",
                                     entries = "numeric",
                                     priorities = "numeric",
                                     prioritise = "function"
                                   ),
                                   methods = list(
                                     sort_ = function() {
                                       order = order(priorities, entries,
decreasing = TRUE, partial = size():1)
                                       #
                                       data <<- data[order]
                                       priorities <<- priorities[order]
                                       entries <<- entries[order]
                                     },
                                     push = function(item, priority = NULL)
{
                                       'Inserts element into the queue,
reordering according to priority.'
                                       callSuper(item)
                                       #
                                       if (is.null(priority)) priority =
prioritise(item)
                                       #
                                       priorities <<- c(priorities,
priority)
                                       entries <<- c(entries, count)
                                       count <<- count - 1
                                       #
                                       sort_()
                                     },
                                     pop = function(N = 1) {
                                       # 'Removes and returns head of queue
(or raises error if queue is empty).'
                                       if (N > size()) stop("insufficient
items in queue!")
                                       priorities <<-
priorities[-seq_len(N)]
                                       entries <<- entries[-seq_len(N)]
                                       callSuper(N)
                                     },
                                     initialize = function(prioritise =
NULL, ...) {
                                       'Creates a PriorityQueue object.'
                                       callSuper(...)
                                       #
                                       ## to enforce FIFO order
                                       count <<- 0
                                       if (is.null(prioritise))
                                         .self$prioritise = function(x) 0
                                       else
                                         .self$prioritise = prioritise
                                       #
                                       .self
                                     }
                                   )
)



igraph.watershed <- function(Gr, labelfield, unlabelled, vertexid, alltimes)
{
  Gres <- Gr
  ## Watershed, without marking boundary (Beucher)
  ## 1. find all marker nodes that have a background neighbour
  lablist <- which(vertex_attr(Gr, labelfield) != unlabelled)
  nlist <- ego(Gr, 1, lablist)
  uu <- which(map_lgl(nlist, ~any(vertex_attr(Gr, labelfield,
.x)==unlabelled)))
  ## uu indexes the labelled vertexes
  ## need indexes into all vertexes
  uu <- lablist[uu]
  ## create priority queue
  qq <- StablePriorityQueue$new()
  ## Insert the boundary markers
  kk <- lapply(uu, qq$push, priority=0)
  all.labels <- get.vertex.attribute(Gr, labelfield)
  all.ids <- get.vertex.attribute(Gr, vertexid)
  alltimes <- subset(alltimes, from %in% all.ids, select=c("from",
"Hospital", "minutes"))
  dd <- duplicated(alltimes[, c("from", "Hospital")])
  alltimes <- alltimes[!dd,]
  alltimes.wide <- spread_(alltimes, key="Hospital", value="minutes")
  ## Make the order the same as all.ids - so now we'll be able to index by
number
  rownames(alltimes.wide) <- alltimes.wide$from
  alltimes.wide <- alltimes.wide[all.ids, ]
  cc <- 1:ncol(alltimes.wide)
  names(cc) <- colnames(alltimes.wide)
  while (qq$size() > 0) {
    vid <- qq$pop()
    ## Get the neighbours
    nb <- neighborhood(Gr, 1, vid, mode="all", mindist=1)[[1]]
    nlabs <- all.labels[nb]
    ## Are any neighbours unknown?
    ul <- nlabs==unlabelled
    if (any(ul)) {
      this.label <- all.labels[vid]
      nbb <- nb[ul]
      all.labels[nbb] <- this.label
      this.label.idx <- cc[this.label]
      priorities <- alltimes.wide[[this.label.idx]][nbb]
      kk <- map2(nbb, priorities, ~qq$push(.x, priority = .y* -1))
    }
  }
  return(data.frame(PlaceID=all.ids, Hospital=all.labels, stringsAsFactors
= FALSE))
}




On Fri, Nov 24, 2017 at 10:26 PM, Grothausmann, Roman Dr. <
grothausmann.roman at mh-hannover.de> wrote:

> Dear mailing list members,
>
>
> I need to separate a mesh at "curved corners" (see attached PNG, using the
> colored labels from a facet analysis do not suffice but go in the right
> direction). So my current thought is to run vtkCurvature to get a Gaussian
> curvature value per point/vertex and then try to separate regions of
> positive values around local maxima. Just thresholding the result of
> vtkCurvature does not fully separate each local max from neighboring ones,
> but to my understanding a surface watershed would. I found two publications
> by Mangan and Whitaker on this:
>
> Partitioning 3D surface meshes using watershed:
> http://teacher.en.rmutt.ac.th/ktw/Resources/Full%20paper%20P
> DF/Partitioning%203D%20surface%20meshes%20using%20watershed%
> 20segmentation.pdf
>
> Surface Segmentation Using Morphological Watersheds:
> https://www.google.de/url?sa=t&rct=j&q=&esrc=s&source=web&cd
> =4&cad=rja&uact=8&ved=0ahUKEwjD0by1lafWAhVUGsAKHZ2MAbUQFgg_
> MAM&url=http%3A%2F%2Fciteseerx.ist.psu.edu%2Fviewdoc%
> 2Fdownload%3Fdoi%3D10.1.1.464.2788%26rep%3Drep1%26type%
> 3Dpdf&usg=AFQjCNGX-p9-ElQFcpsUyBRO0pCjBKCmNg
>
> Does anybody know about an implementation for this in VTK/ITK or another
> open-source library? If not, would it be possible to transfer the ITK
> watershed implementation for voxel data to mesh data, e.g. to crate a
> VTKmorphWatershedFilter?
>
> Thanks for any help or hints.
> Roman
>
>
> --
> Dr. Roman Grothausmann
>
> Tomographie und Digitale Bildverarbeitung
> Tomography and Digital Image Analysis
>
> Medizinische Hochschule Hannover
> Institut f?r Funktionelle und Angewandte Anatomie
> OE 4120, Carl-Neuberg-Str. 1, 30625 Hannover, Deutschland
>
> Tel. +49 511 532-2900
> grothausmann.roman at mh-hannover.de
> http://www.mh-hannover.de/anatomie.html
>
> The ITK community is transitioning from this mailing list to
> discourse.itk.org. Please join us there!
> ________________________________
> Powered by www.kitware.com
>
> Visit other Kitware open-source projects at
> http://www.kitware.com/opensource/opensource.html
>
> Kitware offers ITK Training Courses, for more information visit:
> http://www.kitware.com/products/protraining.php
>
> Please keep messages on-topic and check the ITK FAQ at:
> http://www.itk.org/Wiki/ITK_FAQ
>
> Follow this link to subscribe/unsubscribe:
> http://public.kitware.com/mailman/listinfo/insight-users
>
>
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From bakkari.abdelkhalek at hotmail.fr  Sat Nov 25 06:49:11 2017
From: bakkari.abdelkhalek at hotmail.fr (Abdelkhalek Bakkari)
Date: Sat, 25 Nov 2017 11:49:11 +0000
Subject: [ITK-users] U-Net: Convolutional Networks for image segmentation
Message-ID: <VI1PR0902MB204655751CE5A47AE540A14A83270@VI1PR0902MB2046.eurprd09.prod.outlook.com>

Dear ITK users,

I want to know if there is any ITK filter  or an example related to U-Net Convolutional Networks.

Thank you in advance.

Kind regards,
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From erin at computerhead.com.au  Sat Nov 25 19:34:04 2017
From: erin at computerhead.com.au (Erin McKay)
Date: Sun, 26 Nov 2017 11:34:04 +1100
Subject: [ITK-users] Insight-users Digest, Vol 163, Issue 10
In-Reply-To: <mailman.9.1511629239.23303.insight-users@itk.org>
References: <mailman.9.1511629239.23303.insight-users@itk.org>
Message-ID: <59024AB2-7D63-4301-9B1F-D54922F7E23A@computerhead.com.au>

Not without an adapter, but my Mac Pro might be able to

Erin McKay

> On 26 Nov 2017, at 04:00, insight-users-request at itk.org wrote:
> 
> Send Insight-users mailing list submissions to
>    insight-users at itk.org
> 
> To subscribe or unsubscribe via the World Wide Web, visit
>    http://public.kitware.com/mailman/listinfo/insight-users
> or, via email, send a message with subject or body 'help' to
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> 
> You can reach the person managing the list at
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> 
> When replying, please edit your Subject line so it is more specific
> than "Re: Contents of Insight-users digest..."
> 
> 
> Today's Topics:
> 
>   1. Re: watershed on surface meshs (Richard Beare)
>   2. Re: watershed on surface meshs (Richard Beare)
>   3. U-Net: Convolutional Networks for image segmentation
>      (Abdelkhalek Bakkari)
> 
> 
> ----------------------------------------------------------------------
> 
> Message: 1
> Date: Sat, 25 Nov 2017 07:53:49 +1100
> From: Richard Beare <richard.beare at gmail.com>
> To: "Grothausmann, Roman Dr." <grothausmann.roman at mh-hannover.de>
> Cc: ITK Mailing List <insight-users at itk.org>, VTK Mailing List
>    <vtkusers at vtk.org>
> Subject: Re: [ITK-users] watershed on surface meshs
> Message-ID:
>    <CA+V7QS9QiBXHtiyjNf107XZtt94G3-72bXHcpEpN51Z5m4R+YQ at mail.gmail.com>
> Content-Type: text/plain; charset="utf-8"
> 
> I don't recall an implementation of this anywhere. However you may be able
> to hack something together reasonably quickly. Watersheds are built around
> minimal paths, so depending on what complexity is available in the
> mesh-based shortest path tools. In the worst cast you could create a copy
> of the mesh for each seed region, compute the minimal distance to each non
> seed vertex, then do a vertex-wise min, tracking which mesh/seed region has
> the minimum, and that's your label. Not very efficient because you compute
> the entire mesh distance each time, and no obvious way to do a watershed
> line consistently, but perhaps that doesn't matter for testing the idea.
> 
> On Fri, Nov 24, 2017 at 10:26 PM, Grothausmann, Roman Dr. <
> grothausmann.roman at mh-hannover.de> wrote:
> 
>> Dear mailing list members,
>> 
>> 
>> I need to separate a mesh at "curved corners" (see attached PNG, using the
>> colored labels from a facet analysis do not suffice but go in the right
>> direction). So my current thought is to run vtkCurvature to get a Gaussian
>> curvature value per point/vertex and then try to separate regions of
>> positive values around local maxima. Just thresholding the result of
>> vtkCurvature does not fully separate each local max from neighboring ones,
>> but to my understanding a surface watershed would. I found two publications
>> by Mangan and Whitaker on this:
>> 
>> Partitioning 3D surface meshes using watershed:
>> http://teacher.en.rmutt.ac.th/ktw/Resources/Full%20paper%20P
>> DF/Partitioning%203D%20surface%20meshes%20using%20watershed%
>> 20segmentation.pdf
>> 
>> Surface Segmentation Using Morphological Watersheds:
>> https://www.google.de/url?sa=t&rct=j&q=&esrc=s&source=web&cd
>> =4&cad=rja&uact=8&ved=0ahUKEwjD0by1lafWAhVUGsAKHZ2MAbUQFgg_
>> MAM&url=http%3A%2F%2Fciteseerx.ist.psu.edu%2Fviewdoc%
>> 2Fdownload%3Fdoi%3D10.1.1.464.2788%26rep%3Drep1%26type%
>> 3Dpdf&usg=AFQjCNGX-p9-ElQFcpsUyBRO0pCjBKCmNg
>> 
>> Does anybody know about an implementation for this in VTK/ITK or another
>> open-source library? If not, would it be possible to transfer the ITK
>> watershed implementation for voxel data to mesh data, e.g. to crate a
>> VTKmorphWatershedFilter?
>> 
>> Thanks for any help or hints.
>> Roman
>> 
>> 
>> --
>> Dr. Roman Grothausmann
>> 
>> Tomographie und Digitale Bildverarbeitung
>> Tomography and Digital Image Analysis
>> 
>> Medizinische Hochschule Hannover
>> Institut f?r Funktionelle und Angewandte Anatomie
>> OE 4120, Carl-Neuberg-Str. 1, 30625 Hannover, Deutschland
>> 
>> Tel. +49 511 532-2900
>> grothausmann.roman at mh-hannover.de
>> http://www.mh-hannover.de/anatomie.html
>> 
>> The ITK community is transitioning from this mailing list to
>> discourse.itk.org. Please join us there!
>> ________________________________
>> Powered by www.kitware.com
>> 
>> Visit other Kitware open-source projects at
>> http://www.kitware.com/opensource/opensource.html
>> 
>> Kitware offers ITK Training Courses, for more information visit:
>> http://www.kitware.com/products/protraining.php
>> 
>> Please keep messages on-topic and check the ITK FAQ at:
>> http://www.itk.org/Wiki/ITK_FAQ
>> 
>> Follow this link to subscribe/unsubscribe:
>> http://public.kitware.com/mailman/listinfo/insight-users
>> 
>> 
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> ------------------------------
> 
> Message: 2
> Date: Sat, 25 Nov 2017 14:16:42 +1100
> From: Richard Beare <richard.beare at gmail.com>
> To: "Grothausmann, Roman Dr." <grothausmann.roman at mh-hannover.de>
> Cc: ITK Mailing List <insight-users at itk.org>
> Subject: Re: [ITK-users] watershed on surface meshs
> Message-ID:
>    <CA+V7QS9Xr0aWQ8MGD4s6zCSh+-qjUfXoLOLWWT5WhgbypexF_w at mail.gmail.com>
> Content-Type: text/plain; charset="utf-8"
> 
> Just remembered something that may be useful for testing. I wrote the
> following for doing watersheds on geospatial graphs using R/igraph.
> Certainly isn't efficient, but may be useful for testing if you can turn
> your mesh+curvature into something like a text file.
> 
> This was set up for allocating points on maps to destinations based on
> travel time. It performed a kind of smoothing to smooth non-sensical travel
> time estimates, but the basic algorithm is there. It will take some
> fiddling. You could probably do something equivalent with python, probably
> doing better than this priorty queue, but using much the same approach with
> igraph.
> 
> library(liqueueR)
> 
> ## Mostly a copy of PriorityQueue from liqueueR
> StablePriorityQueue <- setRefClass("StablePriorityQueue",
>                                   contains = "Queue",
>                                   fields = list(
>                                     count = "numeric",
>                                     entries = "numeric",
>                                     priorities = "numeric",
>                                     prioritise = "function"
>                                   ),
>                                   methods = list(
>                                     sort_ = function() {
>                                       order = order(priorities, entries,
> decreasing = TRUE, partial = size():1)
>                                       #
>                                       data <<- data[order]
>                                       priorities <<- priorities[order]
>                                       entries <<- entries[order]
>                                     },
>                                     push = function(item, priority = NULL)
> {
>                                       'Inserts element into the queue,
> reordering according to priority.'
>                                       callSuper(item)
>                                       #
>                                       if (is.null(priority)) priority =
> prioritise(item)
>                                       #
>                                       priorities <<- c(priorities,
> priority)
>                                       entries <<- c(entries, count)
>                                       count <<- count - 1
>                                       #
>                                       sort_()
>                                     },
>                                     pop = function(N = 1) {
>                                       # 'Removes and returns head of queue
> (or raises error if queue is empty).'
>                                       if (N > size()) stop("insufficient
> items in queue!")
>                                       priorities <<-
> priorities[-seq_len(N)]
>                                       entries <<- entries[-seq_len(N)]
>                                       callSuper(N)
>                                     },
>                                     initialize = function(prioritise =
> NULL, ...) {
>                                       'Creates a PriorityQueue object.'
>                                       callSuper(...)
>                                       #
>                                       ## to enforce FIFO order
>                                       count <<- 0
>                                       if (is.null(prioritise))
>                                         .self$prioritise = function(x) 0
>                                       else
>                                         .self$prioritise = prioritise
>                                       #
>                                       .self
>                                     }
>                                   )
> )
> 
> 
> 
> igraph.watershed <- function(Gr, labelfield, unlabelled, vertexid, alltimes)
> {
>  Gres <- Gr
>  ## Watershed, without marking boundary (Beucher)
>  ## 1. find all marker nodes that have a background neighbour
>  lablist <- which(vertex_attr(Gr, labelfield) != unlabelled)
>  nlist <- ego(Gr, 1, lablist)
>  uu <- which(map_lgl(nlist, ~any(vertex_attr(Gr, labelfield,
> .x)==unlabelled)))
>  ## uu indexes the labelled vertexes
>  ## need indexes into all vertexes
>  uu <- lablist[uu]
>  ## create priority queue
>  qq <- StablePriorityQueue$new()
>  ## Insert the boundary markers
>  kk <- lapply(uu, qq$push, priority=0)
>  all.labels <- get.vertex.attribute(Gr, labelfield)
>  all.ids <- get.vertex.attribute(Gr, vertexid)
>  alltimes <- subset(alltimes, from %in% all.ids, select=c("from",
> "Hospital", "minutes"))
>  dd <- duplicated(alltimes[, c("from", "Hospital")])
>  alltimes <- alltimes[!dd,]
>  alltimes.wide <- spread_(alltimes, key="Hospital", value="minutes")
>  ## Make the order the same as all.ids - so now we'll be able to index by
> number
>  rownames(alltimes.wide) <- alltimes.wide$from
>  alltimes.wide <- alltimes.wide[all.ids, ]
>  cc <- 1:ncol(alltimes.wide)
>  names(cc) <- colnames(alltimes.wide)
>  while (qq$size() > 0) {
>    vid <- qq$pop()
>    ## Get the neighbours
>    nb <- neighborhood(Gr, 1, vid, mode="all", mindist=1)[[1]]
>    nlabs <- all.labels[nb]
>    ## Are any neighbours unknown?
>    ul <- nlabs==unlabelled
>    if (any(ul)) {
>      this.label <- all.labels[vid]
>      nbb <- nb[ul]
>      all.labels[nbb] <- this.label
>      this.label.idx <- cc[this.label]
>      priorities <- alltimes.wide[[this.label.idx]][nbb]
>      kk <- map2(nbb, priorities, ~qq$push(.x, priority = .y* -1))
>    }
>  }
>  return(data.frame(PlaceID=all.ids, Hospital=all.labels, stringsAsFactors
> = FALSE))
> }
> 
> 
> 
> 
> On Fri, Nov 24, 2017 at 10:26 PM, Grothausmann, Roman Dr. <
> grothausmann.roman at mh-hannover.de> wrote:
> 
>> Dear mailing list members,
>> 
>> 
>> I need to separate a mesh at "curved corners" (see attached PNG, using the
>> colored labels from a facet analysis do not suffice but go in the right
>> direction). So my current thought is to run vtkCurvature to get a Gaussian
>> curvature value per point/vertex and then try to separate regions of
>> positive values around local maxima. Just thresholding the result of
>> vtkCurvature does not fully separate each local max from neighboring ones,
>> but to my understanding a surface watershed would. I found two publications
>> by Mangan and Whitaker on this:
>> 
>> Partitioning 3D surface meshes using watershed:
>> http://teacher.en.rmutt.ac.th/ktw/Resources/Full%20paper%20P
>> DF/Partitioning%203D%20surface%20meshes%20using%20watershed%
>> 20segmentation.pdf
>> 
>> Surface Segmentation Using Morphological Watersheds:
>> https://www.google.de/url?sa=t&rct=j&q=&esrc=s&source=web&cd
>> =4&cad=rja&uact=8&ved=0ahUKEwjD0by1lafWAhVUGsAKHZ2MAbUQFgg_
>> MAM&url=http%3A%2F%2Fciteseerx.ist.psu.edu%2Fviewdoc%
>> 2Fdownload%3Fdoi%3D10.1.1.464.2788%26rep%3Drep1%26type%
>> 3Dpdf&usg=AFQjCNGX-p9-ElQFcpsUyBRO0pCjBKCmNg
>> 
>> Does anybody know about an implementation for this in VTK/ITK or another
>> open-source library? If not, would it be possible to transfer the ITK
>> watershed implementation for voxel data to mesh data, e.g. to crate a
>> VTKmorphWatershedFilter?
>> 
>> Thanks for any help or hints.
>> Roman
>> 
>> 
>> --
>> Dr. Roman Grothausmann
>> 
>> Tomographie und Digitale Bildverarbeitung
>> Tomography and Digital Image Analysis
>> 
>> Medizinische Hochschule Hannover
>> Institut f?r Funktionelle und Angewandte Anatomie
>> OE 4120, Carl-Neuberg-Str. 1, 30625 Hannover, Deutschland
>> 
>> Tel. +49 511 532-2900
>> grothausmann.roman at mh-hannover.de
>> http://www.mh-hannover.de/anatomie.html
>> 
>> The ITK community is transitioning from this mailing list to
>> discourse.itk.org. Please join us there!
>> ________________________________
>> Powered by www.kitware.com
>> 
>> Visit other Kitware open-source projects at
>> http://www.kitware.com/opensource/opensource.html
>> 
>> Kitware offers ITK Training Courses, for more information visit:
>> http://www.kitware.com/products/protraining.php
>> 
>> Please keep messages on-topic and check the ITK FAQ at:
>> http://www.itk.org/Wiki/ITK_FAQ
>> 
>> Follow this link to subscribe/unsubscribe:
>> http://public.kitware.com/mailman/listinfo/insight-users
>> 
>> 
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> 
> ------------------------------
> 
> Message: 3
> Date: Sat, 25 Nov 2017 11:49:11 +0000
> From: Abdelkhalek Bakkari <bakkari.abdelkhalek at hotmail.fr>
> To: ITK Users <insight-users at public.kitware.com>, "dzenanz at gmail.com"
>    <dzenanz at gmail.com>
> Subject: [ITK-users] U-Net: Convolutional Networks for image
>    segmentation
> Message-ID:
>    <VI1PR0902MB204655751CE5A47AE540A14A83270 at VI1PR0902MB2046.eurprd09.prod.outlook.com>
>    
> Content-Type: text/plain; charset="iso-8859-1"
> 
> Dear ITK users,
> 
> I want to know if there is any ITK filter  or an example related to U-Net Convolutional Networks.
> 
> Thank you in advance.
> 
> Kind regards,
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> 
> ------------------------------
> 
> Subject: Digest Footer
> 
> The ITK community is transitioning from this mailing list to discourse.itk.org. Please join us there!
> ____________________________________
> Insight-users mailing list
> Insight-users at itk.org
> http://public.kitware.com/mailman/listinfo/insight-users
> 
> 
> ------------------------------
> 
> End of Insight-users Digest, Vol 163, Issue 10
> **********************************************

From dzenanz at gmail.com  Sun Nov 26 10:26:37 2017
From: dzenanz at gmail.com (=?UTF-8?B?RMW+ZW5hbiBadWtpxIc=?=)
Date: Sun, 26 Nov 2017 10:26:37 -0500
Subject: [ITK-users] U-Net: Convolutional Networks for image segmentation
In-Reply-To: <VI1PR0902MB204655751CE5A47AE540A14A83270@VI1PR0902MB2046.eurprd09.prod.outlook.com>
References: <VI1PR0902MB204655751CE5A47AE540A14A83270@VI1PR0902MB2046.eurprd09.prod.outlook.com>
Message-ID: <CAPf2UMTXZWfqXabY8=PuJaFBWSbz4TGk3wdyaH-nMZzXrraikw@mail.gmail.com>

Hi Abdelkhalek,

ITK has this group
<https://itk.org/Doxygen/html/group__ITKNeuralNetworks.html> of classes for
neural networks. But I don't think it has a convolutional NN.

Regards,
D?enan

On Sat, Nov 25, 2017 at 6:49 AM, Abdelkhalek Bakkari <
bakkari.abdelkhalek at hotmail.fr> wrote:

> Dear ITK users,
>
> I want to know if there is any ITK filter  or an example related
> to U-Net Convolutional Networks.
>
> Thank you in advance.
>
> Kind regards,
>
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From poyu_kao at ece.ucsb.edu  Tue Nov 28 21:32:54 2017
From: poyu_kao at ece.ucsb.edu (Po-Yu Kao)
Date: Tue, 28 Nov 2017 18:32:54 -0800
Subject: [ITK-users] How to using SimpleITK to change the voxel value
	without touch the metadata
Message-ID: <CA+pTWFT1kn2tq3bdOzsfeedGVetxoBX99MmOF9PuZ296nbk0jg@mail.gmail.com>

Hello,

I am using SimpleITK library in python 2.7.

I want to do some basic preprocessing on CT scans with nii.gz. format. For
example, I use img = sitk.ReadImage(ct_scan_path) to read the image, and
then use nda = sitk.GetArrayFromImage(ct_img) to access n-dimensional numpy
array. Then, I do some preprocessing steps on this n-dimensional numpy, and
save it back to the image format by using img_preprocessed =
sitk.GetImageFromArray(nda_preprocessed). However, when I check the
metadata of these two images, it gives me different values which are showed
below.

Does anyone know how to copy all the metadata from the original image to
another image? or Does anyone know how to access and change the voxel value
of the image without touching the metadata?

Original Image:
print img

Image (0x4237b40)
  RTTI typeinfo:   itk::Image<float, 3u>
  Reference Count: 1
  Modified Time: 3601
  Debug: Off
  Object Name:
  Observers:
    none
  Source: (none)
  Source output name: (none)
  Release Data: Off
  Data Released: False
  Global Release Data: Off
  PipelineMTime: 3578
  UpdateMTime: 3600
  RealTimeStamp: 0 seconds
  LargestPossibleRegion:
    Dimension: 3
    Index: [0, 0, 0]
    Size: [512, 512, 37]
  BufferedRegion:
    Dimension: 3
    Index: [0, 0, 0]
    Size: [512, 512, 37]
  RequestedRegion:
    Dimension: 3
    Index: [0, 0, 0]
    Size: [512, 512, 37]
  Spacing: [0.488281, 0.488281, 5]
  Origin: [-114, 294.012, 21.82]
  Direction:
1 0 0
0 -1 0
0 0 1

  IndexToPointMatrix:
0.488281 0 0
0 -0.488281 0
0 0 5

  PointToIndexMatrix:
2.048 0 0
0 -2.048 0
0 0 0.2

  Inverse Direction:
1 0 0
0 -1 0
0 0 1

  PixelContainer:
    ImportImageContainer (0x398e780)
      RTTI typeinfo:   itk::ImportImageContainer<unsigned long, float>
      Reference Count: 1
      Modified Time: 3597
      Debug: Off
      Object Name:
      Observers:
        none
      Pointer: 0x7f6ef9225010
      Container manages memory: true
      Size: 9699328
      Capacity: 9699328

Preprocessed Image:

Image (0x3857e60)
  RTTI typeinfo:   itk::Image<float, 3u>
  Reference Count: 1
  Modified Time: 3605
  Debug: Off
  Object Name:
  Observers:
    none
  Source: (none)
  Source output name: (none)
  Release Data: Off
  Data Released: False
  Global Release Data: Off
  PipelineMTime: 0
  UpdateMTime: 0
  RealTimeStamp: 0 seconds
  LargestPossibleRegion:
    Dimension: 3
    Index: [0, 0, 0]
    Size: [512, 512, 37]
  BufferedRegion:
    Dimension: 3
    Index: [0, 0, 0]
    Size: [512, 512, 37]
  RequestedRegion:
    Dimension: 3
    Index: [0, 0, 0]
    Size: [512, 512, 37]
  Spacing: [1, 1, 1]
  Origin: [0, 0, 0]
  Direction:
1 0 0
0 1 0
0 0 1

  IndexToPointMatrix:
1 0 0
0 1 0
0 0 1

  PointToIndexMatrix:
1 0 0
0 1 0
0 0 1

  Inverse Direction:
1 0 0
0 1 0
0 0 1

  PixelContainer:
    ImportImageContainer (0x39856c0)
      RTTI typeinfo:   itk::ImportImageContainer<unsigned long, float>
      Reference Count: 1
      Modified Time: 3606
      Debug: Off
      Object Name:
      Observers:
        none
      Pointer: 0x7f6ef4823010
      Container manages memory: true
      Size: 9699328
      Capacity: 9699328
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From poyu_kao at ece.ucsb.edu  Tue Nov 28 21:35:18 2017
From: poyu_kao at ece.ucsb.edu (Po-Yu Kao)
Date: Tue, 28 Nov 2017 18:35:18 -0800
Subject: [ITK-users] How to using SimpleITK to access and change the voxel
 value without touch the metadata
Message-ID: <CA+pTWFSv3S6FPcgO97LJ2AOjn_xV-tTnG3qGeqM4u4V-uptB5Q@mail.gmail.com>

Hello,

I am using SimpleITK library in python 2.7.

I want to do some basic preprocessing on CT scans with nii.gz. format. For
example, I use img = sitk.ReadImage(ct_scan_path) to read the image, and
then use nda = sitk.GetArrayFromImage(ct_img) to access n-dimensional numpy
array. Then, I do some preprocessing steps on this n-dimensional numpy, and
save it back to the image format by using img_preprocessed =
sitk.GetImageFromArray(nda_preprocessed). However, when I check the
metadata of these two images, it gives me different values which are showed
below.

Does anyone know how to copy all the metadata from the original image to
another image? or Does anyone know how to access and change the voxel value
of the image without touching the metadata?

Original Image:
print img

Image (0x4237b40)
  RTTI typeinfo:   itk::Image<float, 3u>
  Reference Count: 1
  Modified Time: 3601
  Debug: Off
  Object Name:
  Observers:
    none
  Source: (none)
  Source output name: (none)
  Release Data: Off
  Data Released: False
  Global Release Data: Off
  PipelineMTime: 3578
  UpdateMTime: 3600
  RealTimeStamp: 0 seconds
  LargestPossibleRegion:
    Dimension: 3
    Index: [0, 0, 0]
    Size: [512, 512, 37]
  BufferedRegion:
    Dimension: 3
    Index: [0, 0, 0]
    Size: [512, 512, 37]
  RequestedRegion:
    Dimension: 3
    Index: [0, 0, 0]
    Size: [512, 512, 37]
  Spacing: [0.488281, 0.488281, 5]
  Origin: [-114, 294.012, 21.82]
  Direction:
1 0 0
0 -1 0
0 0 1

  IndexToPointMatrix:
0.488281 0 0
0 -0.488281 0
0 0 5

  PointToIndexMatrix:
2.048 0 0
0 -2.048 0
0 0 0.2

  Inverse Direction:
1 0 0
0 -1 0
0 0 1

  PixelContainer:
    ImportImageContainer (0x398e780)
      RTTI typeinfo:   itk::ImportImageContainer<unsigned long, float>
      Reference Count: 1
      Modified Time: 3597
      Debug: Off
      Object Name:
      Observers:
        none
      Pointer: 0x7f6ef9225010
      Container manages memory: true
      Size: 9699328
      Capacity: 9699328

Preprocessed Image:

Image (0x3857e60)
  RTTI typeinfo:   itk::Image<float, 3u>
  Reference Count: 1
  Modified Time: 3605
  Debug: Off
  Object Name:
  Observers:
    none
  Source: (none)
  Source output name: (none)
  Release Data: Off
  Data Released: False
  Global Release Data: Off
  PipelineMTime: 0
  UpdateMTime: 0
  RealTimeStamp: 0 seconds
  LargestPossibleRegion:
    Dimension: 3
    Index: [0, 0, 0]
    Size: [512, 512, 37]
  BufferedRegion:
    Dimension: 3
    Index: [0, 0, 0]
    Size: [512, 512, 37]
  RequestedRegion:
    Dimension: 3
    Index: [0, 0, 0]
    Size: [512, 512, 37]
  Spacing: [1, 1, 1]
  Origin: [0, 0, 0]
  Direction:
1 0 0
0 1 0
0 0 1

  IndexToPointMatrix:
1 0 0
0 1 0
0 0 1

  PointToIndexMatrix:
1 0 0
0 1 0
0 0 1

  Inverse Direction:
1 0 0
0 1 0
0 0 1

  PixelContainer:
    ImportImageContainer (0x39856c0)
      RTTI typeinfo:   itk::ImportImageContainer<unsigned long, float>
      Reference Count: 1
      Modified Time: 3606
      Debug: Off
      Object Name:
      Observers:
        none
      Pointer: 0x7f6ef4823010
      Container manages memory: true
      Size: 9699328
      Capacity: 9699328
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