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] [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




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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] [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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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] [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?



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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] [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 c.metz at quantib.com  Thu Nov  9 03:36:02 2017
From: c.metz at quantib.com (Coert Metz)
Date: Thu, 9 Nov 2017 09:36:02 +0100
Subject: [ITK] GDCMImageIO
Message-ID: <CAAmKhgqF2MUMhmd_Jck3sPY1NXROBBO9r8WZVJsDmrt4gG65Og@mail.gmail.com>

Hi all,

GDCMImageIO seems to use GDCM's default for the transfer syntax, which is
an implicit one. Is there a way to make it use explicit transfer syntax?

Kind regards,
Coert Metz

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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] [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] [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:
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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] [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] [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 kenji.tsumura at neosoftmedical.com  Sat Nov 18 16:59:33 2017
From: kenji.tsumura at neosoftmedical.com (Kenji Tsumura)
Date: Sat, 18 Nov 2017 21:59:33 +0000
Subject: [ITK] Registration processing time comparison between V3 and V4
Message-ID: <10285631702C4D4CB5C4921DC143379501988346A1@neocoilexch01>

Hi,

I just started to learn ITK registration and noticed there is a difference in processing time between Registration V3 and V4. It took around 2.4 seconds to perform registration of 20 MRI images using V3, whereas it took around 7.2 seconds using V4. I have no idea where this difference comes from. It would be great if someone gives me an advice on how to make processing time using V4 equivalent of that of V3, as I want to use ObjectToObjectMultiMetricV4. In the past, there was a similar post, but no one gave a clear answer.

I posted the source code and image data in the following URL.
https://github.com/ktsumura/ITK-BSpline-Registration/tree/master

I followed the following examples.
https://itk.org/Wiki/ITK/Examples/Registration/ImageRegistrationMethodBSpline
DeformableRegistration4.cxx.

Thank you!

Kenji



Disclaimer: The information contained in this communication may be confidential, is intended only for the use of the recipient(s) named above, and may be legally privileged. If the reader of this message is not the intended recipient, you are hereby notified that any dissemination, distribution, or copying of this communication, or any of its contents, is strictly prohibited. If you have received this communication in error, please return it to the sender immediately and delete the original message and any copy of it from your computer system. If you have any questions concerning this message, please contact the sender.
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From dzenanz at gmail.com  Mon Nov 20 09:53:37 2017
From: dzenanz at gmail.com (=?UTF-8?B?RMW+ZW5hbiBadWtpxIc=?=)
Date: Mon, 20 Nov 2017 09:53:37 -0500
Subject: [ITK] Registration processing time comparison between V3 and V4
In-Reply-To: <10285631702C4D4CB5C4921DC143379501988346A1@neocoilexch01>
References: <10285631702C4D4CB5C4921DC143379501988346A1@neocoilexch01>
Message-ID: <CAPf2UMRwLRVRo30Z-xkgTsaLDfT_4U3iqcEHWWy7FsrjHmy9eQ@mail.gmail.com>

Hi Kenji,

on Friday we discussed
<https://docs.google.com/document/d/1I6DHtiGsA5sIPxr9ae683j-vyBpdfFeUpaLWyEVcSSg/view>
the need to make v4 registration faster and more flexible, partly due
to Brian Eastwood's question. The quick stopgap solution would be to
replace DiscreteGaussian by a faster but approximate Gaussian filter. The
long-term solution would be allowing users to implement their
own MultiScaleFilter which would allow them to override a number of
defaults, including smoothing and whether to force downsampling step
instead of doing resampling on the fly. But we haven't decided who should
implement it, or when.

Please post follow-up questions on Discourse <https://discourse.itk.org/>.

Regards,
D?enan

On Sat, Nov 18, 2017 at 4:59 PM, Kenji Tsumura <
kenji.tsumura at neosoftmedical.com> wrote:

> Hi,
>
>
>
> I just started to learn ITK registration and noticed there is a difference
> in processing time between Registration V3 and V4. It took around 2.4
> seconds to perform registration of 20 MRI images using V3, whereas it took
> around 7.2 seconds using V4. I have no idea where this difference comes
> from. It would be great if someone gives me an advice on how to make
> processing time using V4 equivalent of that of V3, as I want to use
> ObjectToObjectMultiMetricV4. In the past, there was a similar post, but no
> one gave a clear answer.
>
>
>
> I posted the source code and image data in the following URL.
>
> https://github.com/ktsumura/ITK-BSpline-Registration/tree/master
>
>
>
> I followed the following examples.
>
> https://itk.org/Wiki/ITK/Examples/Registration/
> ImageRegistrationMethodBSpline
>
> DeformableRegistration4.cxx.
>
>
>
> Thank you!
>
>
>
> Kenji
>
>
>
>
>
>
> Disclaimer: The information contained in this communication may be
> confidential, is intended only for the use of the recipient(s) named above,
> and may be legally privileged. If the reader of this message is not the
> intended recipient, you are hereby notified that any dissemination,
> distribution, or copying of this communication, or any of its contents, is
> strictly prohibited. If you have received this communication in error,
> please return it to the sender immediately and delete the original message
> and any copy of it from your computer system. If you have any questions
> concerning this message, please contact the sender.
>
> The ITK community is transitioning from this mailing list to
> discourse.itk.org. Please join us there!
> ________________________________________
> Community mailing list
> Community at itk.org
> http://public.kitware.com/mailman/listinfo/community
>
>
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From brian at mbfbioscience.com  Mon Nov 20 14:02:37 2017
From: brian at mbfbioscience.com (Brian Eastwood)
Date: Mon, 20 Nov 2017 19:02:37 +0000
Subject: [ITK] Registration processing time comparison between V3
Message-ID: <14D3864D0DE48E4994C435F2FE6034E5019481@exchange3.microbrightfield.com>

Hi Kenji,

As D?enan points out, I've seen similar speed differences. Sorry I missed the discussion on Friday!

There are two things I found to speed things up that you could try temporarily.
1) On your metric, call UseFixedImageGradientFilterOff() and UseMovingImageGradientFilterOff(). This means image gradients will be computed on a pixel-by-pixel basis rather than over the whole image with a filter. You'll probably want to combine this with setting a small value for SetMetricSamplingPercentage() on the registration method to limit how many sample points are evaluated in the image metric. Whether this offers a speed up will probably depend on your image sizes.
2) Replace the itk::DiscreteGaussianImageFilter with itk::SmoothingRecursiveGaussianImageFilter inside the registration method code. Note that these two filters have different interfaces (e.g. standard deviation vs. variance, normalization across scales). Yes, this requires modifying ITK source, but as it's in a header file I don't think you need to recompile ITK.

I found both of these options to speed up registration v4, but I think the approach D?enan outlined for the future will be much better.

Regards,
Brian

On Sat, Nov 18, 2017 at 4:59 PM, Kenji Tsumura < kenji.tsumura at neosoftmedical.com> wrote:

> Hi,
>
>
>
> I just started to learn ITK registration and noticed there is a 
> difference in processing time between Registration V3 and V4. It took 
> around 2.4 seconds to perform registration of 20 MRI images using V3, 
> whereas it took around 7.2 seconds using V4. I have no idea where this 
> difference comes from. It would be great if someone gives me an advice 
> on how to make processing time using V4 equivalent of that of V3, as I 
> want to use ObjectToObjectMultiMetricV4. In the past, there was a 
> similar post, but no one gave a clear answer.
>
>
>
> I posted the source code and image data in the following URL.
>
> https://github.com/ktsumura/ITK-BSpline-Registration/tree/master
>
>
>
> I followed the following examples.
>
> https://itk.org/Wiki/ITK/Examples/Registration/
> ImageRegistrationMethodBSpline
>
> DeformableRegistration4.cxx.
>
>
>
> Thank you!
>
>
>
> Kenji
>
>
>
>
>
>
> Disclaimer: The information contained in this communication may be 
> confidential, is intended only for the use of the recipient(s) named 
> above, and may be legally privileged. If the reader of this message is 
> not the intended recipient, you are hereby notified that any 
> dissemination, distribution, or copying of this communication, or any 
> of its contents, is strictly prohibited. If you have received this 
> communication in error, please return it to the sender immediately and 
> delete the original message and any copy of it from your computer 
> system. If you have any questions concerning this message, please contact the sender.
>
> The ITK community is transitioning from this mailing list to 
> discourse.itk.org. Please join us there!
> ________________________________________
> Community mailing list
> Community at itk.org
> http://public.kitware.com/mailman/listinfo/community
>
>
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****************************************



From kenji.tsumura at neosoftmedical.com  Mon Nov 20 15:38:33 2017
From: kenji.tsumura at neosoftmedical.com (Kenji Tsumura)
Date: Mon, 20 Nov 2017 20:38:33 +0000
Subject: [ITK] Registration processing time comparison between V3
In-Reply-To: <14D3864D0DE48E4994C435F2FE6034E5019481@exchange3.microbrightfield.com>
References: <14D3864D0DE48E4994C435F2FE6034E5019481@exchange3.microbrightfield.com>
Message-ID: <10285631702C4D4CB5C4921DC1433795019883472F@neocoilexch01>

Hi Brian and D?enan,

Thank you for the comments.
I will try Brian's suggestion.

Kenji

-----Original Message-----
From: Community [mailto:community-bounces at itk.org] On Behalf Of Brian Eastwood
Sent: Monday, November 20, 2017 1:03 PM
To: community at itk.org
Subject: Re: [ITK] Registration processing time comparison between V3

Hi Kenji,

As D?enan points out, I've seen similar speed differences. Sorry I missed the discussion on Friday!

There are two things I found to speed things up that you could try temporarily.
1) On your metric, call UseFixedImageGradientFilterOff() and UseMovingImageGradientFilterOff(). This means image gradients will be computed on a pixel-by-pixel basis rather than over the whole image with a filter. You'll probably want to combine this with setting a small value for SetMetricSamplingPercentage() on the registration method to limit how many sample points are evaluated in the image metric. Whether this offers a speed up will probably depend on your image sizes.
2) Replace the itk::DiscreteGaussianImageFilter with itk::SmoothingRecursiveGaussianImageFilter inside the registration method code. Note that these two filters have different interfaces (e.g. standard deviation vs. variance, normalization across scales). Yes, this requires modifying ITK source, but as it's in a header file I don't think you need to recompile ITK.

I found both of these options to speed up registration v4, but I think the approach D?enan outlined for the future will be much better.

Regards,
Brian

On Sat, Nov 18, 2017 at 4:59 PM, Kenji Tsumura < kenji.tsumura at neosoftmedical.com> wrote:

> Hi,
>
>
>
> I just started to learn ITK registration and noticed there is a
> difference in processing time between Registration V3 and V4. It took
> around 2.4 seconds to perform registration of 20 MRI images using V3,
> whereas it took around 7.2 seconds using V4. I have no idea where this
> difference comes from. It would be great if someone gives me an advice
> on how to make processing time using V4 equivalent of that of V3, as I
> want to use ObjectToObjectMultiMetricV4. In the past, there was a
> similar post, but no one gave a clear answer.
>
>
>
> I posted the source code and image data in the following URL.
>
> https://github.com/ktsumura/ITK-BSpline-Registration/tree/master
>
>
>
> I followed the following examples.
>
> https://itk.org/Wiki/ITK/Examples/Registration/
> ImageRegistrationMethodBSpline
>
> DeformableRegistration4.cxx.
>
>
>
> Thank you!
>
>
>
> Kenji
>
>
>
>
>
>
> Disclaimer: The information contained in this communication may be
> confidential, is intended only for the use of the recipient(s) named
> above, and may be legally privileged. If the reader of this message is
> not the intended recipient, you are hereby notified that any
> dissemination, distribution, or copying of this communication, or any
> of its contents, is strictly prohibited. If you have received this
> communication in error, please return it to the sender immediately and
> delete the original message and any copy of it from your computer
> system. If you have any questions concerning this message, please contact the sender.
>
> The ITK community is transitioning from this mailing list to
> discourse.itk.org. Please join us there!
> ________________________________________
> Community mailing list
> Community at itk.org
> http://public.kitware.com/mailman/listinfo/community
>
>
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****************************************


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________________________________________
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Disclaimer: The information contained in this communication may be confidential, is intended only for the use of the recipient(s) named above, and may be legally privileged. If the reader of this message is not the intended recipient, you are hereby notified that any dissemination, distribution, or copying of this communication, or any of its contents, is strictly prohibited. If you have received this communication in error, please return it to the sender immediately and delete the original message and any copy of it from your computer system. If you have any questions concerning this message, please contact the sender.

From tevain at telecom-paristech.fr  Mon Nov 20 17:18:09 2017
From: tevain at telecom-paristech.fr (Timothee Evain)
Date: Mon, 20 Nov 2017 23:18:09 +0100 (CET)
Subject: [ITK] Naming conflict ?
Message-ID: <841629828.5012894.1511216289559.JavaMail.zimbra@enst.fr>

Hi everyone,

I made some custom graph tools, that define classes like "Arc", "Node" and "Graph" into the global scope. The whole thing works well.
I was trying to integrate these tools with ITK, but including any ITK header leads to a failed compilation, with errors about "undeclared identifiers" about my custom classes.
The errors vanish when I put my code into a namespace, so I was thinking of a naming conflict with some variables or classes defined by ITK into the global scope, but I'm unable to find such structures in the ITK code.
Does anyone have encountered similar issues?

Tim

From dzenanz at gmail.com  Mon Nov 20 17:41:03 2017
From: dzenanz at gmail.com (=?UTF-8?B?RMW+ZW5hbiBadWtpxIc=?=)
Date: Mon, 20 Nov 2017 17:41:03 -0500
Subject: [ITK] Naming conflict ?
In-Reply-To: <841629828.5012894.1511216289559.JavaMail.zimbra@enst.fr>
References: <841629828.5012894.1511216289559.JavaMail.zimbra@enst.fr>
Message-ID: <CAPf2UMRFHfho9jW=rEcNkQUW6A5VkUrTVdpuTu30F_afGdHhFA@mail.gmail.com>

Hi Tim,

I don't remember encountering such a problem. Can you give a sample
declaration of your class, and the error message about it you get when
trying to include itkImage.h?

Regards,
D?enan

On Mon, Nov 20, 2017 at 5:18 PM, Timothee Evain <tevain at telecom-paristech.fr
> wrote:

> Hi everyone,
>
> I made some custom graph tools, that define classes like "Arc", "Node" and
> "Graph" into the global scope. The whole thing works well.
> I was trying to integrate these tools with ITK, but including any ITK
> header leads to a failed compilation, with errors about "undeclared
> identifiers" about my custom classes.
> The errors vanish when I put my code into a namespace, so I was thinking
> of a naming conflict with some variables or classes defined by ITK into the
> global scope, but I'm unable to find such structures in the ITK code.
> Does anyone have encountered similar issues?
>
> Tim
> The ITK community is transitioning from this mailing list to
> discourse.itk.org. Please join us there!
> ________________________________________
> Community mailing list
> Community at itk.org
> http://public.kitware.com/mailman/listinfo/community
>
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From tevain at telecom-paristech.fr  Tue Nov 21 05:36:50 2017
From: tevain at telecom-paristech.fr (Timothee Evain)
Date: Tue, 21 Nov 2017 11:36:50 +0100 (CET)
Subject: [ITK] Naming conflict ?
In-Reply-To: <CAPf2UMRFHfho9jW=rEcNkQUW6A5VkUrTVdpuTu30F_afGdHhFA@mail.gmail.com>
References: <841629828.5012894.1511216289559.JavaMail.zimbra@enst.fr>
 <CAPf2UMRFHfho9jW=rEcNkQUW6A5VkUrTVdpuTu30F_afGdHhFA@mail.gmail.com>
Message-ID: <586207980.5188156.1511260610191.JavaMail.zimbra@enst.fr>

Hi D?enan!

Sure, here you are :
error C2061: syntax error : identifier 'Arc'	27
error C2061: syntax error : identifier 'Arc'	31
error C2143: syntax error : missing ';' before '*'	30
error C2143: syntax error : missing ';' before '*'	49
error C4430: missing type specifier - int assumed. Note: C++ does not support default-int	30
error C4430: missing type specifier - int assumed. Note: C++ does not support default-int	49

given with the following code (I haven't included the definitions has they are useless to reproduce the bug). 
Comment out the #include <itkImage.h> and everything is good.

////////////////////////////////////////////////////////////////////////////
#include <string>
#include <itkImage.h>

   /* Forward declarations of Node and Arc classes since they are interdependant */
   class Node;
   class Arc;

   /* CLASS : Node
   Class that defines a node or summit for the graph
   */
   class Node
   {
   public:
      Node();
      Node(unsigned int NodeID);
      Node(unsigned int NodeID, int NodeLabel);
      Node(unsigned int NodeID, int NodeLabel, std::string NodeName);
      virtual ~Node();

      //Add an outgoing arc
(27)  void AddArc(Arc* OutwardArc);

      //Get/set the first outward arc
(30)  Arc* GetFirstOutwardArc();
(31)  void SetFirstOutwardArc(Arc* FirstArc);

      //Get/set the node ID
      unsigned int GetNodeID();
      void SetNodeID(unsigned int ID);

      //Get the number of arc that exit this node
      unsigned int GetArcCount();

      //Get/set the node name
      std::string GetNodeName();
      void SetNodeName(std::string InputName);

      //Get/set the node label
      float GetNodeLabel();
      void SetNodeLabel(float InputLabel);

   protected:
(49)  Arc* m_FirstOutwardArc;
      unsigned int m_ArcCount;
      unsigned int m_NodeID;
      std::string m_NodeName;
      float m_NodeLabel;
   };

   /* CLASS : Arc
   Defines a directionnal edge for graphs
   Each arc strictly have a starting and ending node
   */
   class Arc
   {
   public:
      Arc();
      Arc(Node* StartingNode, Node* EndingNode);
      virtual ~Arc();

      //Get/set the starting node
      Node* GetStartNode();
      void SetStartNode(Node* StartingNode);

      //Get/set the ending node
      Node* GetEndNode();
      void SetEndNode(Node* EndingNode);

      //Get/set the next arc originating from the same node
      virtual Arc* GetNextArc();
      virtual void SetNextArc(Arc* NextArc);

   protected:
      Node* m_StartNode;
      Node* m_EndNode;

   private:
      Arc* m_NextArcFromSameNode;

   };

Tim

From dzenanz at gmail.com  Tue Nov 21 09:51:39 2017
From: dzenanz at gmail.com (=?UTF-8?B?RMW+ZW5hbiBadWtpxIc=?=)
Date: Tue, 21 Nov 2017 09:51:39 -0500
Subject: [ITK] Naming conflict ?
In-Reply-To: <586207980.5188156.1511260610191.JavaMail.zimbra@enst.fr>
References: <841629828.5012894.1511216289559.JavaMail.zimbra@enst.fr>
 <CAPf2UMRFHfho9jW=rEcNkQUW6A5VkUrTVdpuTu30F_afGdHhFA@mail.gmail.com>
 <586207980.5188156.1511260610191.JavaMail.zimbra@enst.fr>
Message-ID: <CAPf2UMRZPsqkGWKLwwgs7c_fejfP2W2eSCAN66upH-hKgEKwhg@mail.gmail.com>

Hi Tim,

ITK indirectly includes windows headers, and your Arc class suffers a name
clash with

WINGDIAPI BOOL  WINAPI *Arc*( _In_ HDC hdc, _In_ int x1, _In_ int y1, _In_
int x2, _In_ int y2, _In_ int x3, _In_ int y3, _In_ int x4, _In_ int y4);

in c:\Program Files (x86)\Windows Kits\8.1\Include\um\wingdi.h, line 3612.
If your declarations are enclosed in a namespace ...

namespace Tim
{
    /* Forward declarations of Node and Arc classes since they are
interdependant */
    class Node;
    class Arc;
    ...
}

... the file compiles.

We are switching to discourse <https://discourse.itk.org/>, so please make
future posts there.

Regards,
D?enan

On Tue, Nov 21, 2017 at 5:36 AM, Timothee Evain <tevain at telecom-paristech.fr
> wrote:

> Hi D?enan!
>
> Sure, here you are :
> error C2061: syntax error : identifier 'Arc'    27
> error C2061: syntax error : identifier 'Arc'    31
> error C2143: syntax error : missing ';' before '*'      30
> error C2143: syntax error : missing ';' before '*'      49
> error C4430: missing type specifier - int assumed. Note: C++ does not
> support default-int       30
> error C4430: missing type specifier - int assumed. Note: C++ does not
> support default-int       49
>
> given with the following code (I haven't included the definitions has they
> are useless to reproduce the bug).
> Comment out the #include <itkImage.h> and everything is good.
>
> ////////////////////////////////////////////////////////////
> ////////////////
> #include <string>
> #include <itkImage.h>
>
>    /* Forward declarations of Node and Arc classes since they are
> interdependant */
>    class Node;
>    class Arc;
>
>    /* CLASS : Node
>    Class that defines a node or summit for the graph
>    */
>    class Node
>    {
>    public:
>       Node();
>       Node(unsigned int NodeID);
>       Node(unsigned int NodeID, int NodeLabel);
>       Node(unsigned int NodeID, int NodeLabel, std::string NodeName);
>       virtual ~Node();
>
>       //Add an outgoing arc
> (27)  void AddArc(Arc* OutwardArc);
>
>       //Get/set the first outward arc
> (30)  Arc* GetFirstOutwardArc();
> (31)  void SetFirstOutwardArc(Arc* FirstArc);
>
>       //Get/set the node ID
>       unsigned int GetNodeID();
>       void SetNodeID(unsigned int ID);
>
>       //Get the number of arc that exit this node
>       unsigned int GetArcCount();
>
>       //Get/set the node name
>       std::string GetNodeName();
>       void SetNodeName(std::string InputName);
>
>       //Get/set the node label
>       float GetNodeLabel();
>       void SetNodeLabel(float InputLabel);
>
>    protected:
> (49)  Arc* m_FirstOutwardArc;
>       unsigned int m_ArcCount;
>       unsigned int m_NodeID;
>       std::string m_NodeName;
>       float m_NodeLabel;
>    };
>
>    /* CLASS : Arc
>    Defines a directionnal edge for graphs
>    Each arc strictly have a starting and ending node
>    */
>    class Arc
>    {
>    public:
>       Arc();
>       Arc(Node* StartingNode, Node* EndingNode);
>       virtual ~Arc();
>
>       //Get/set the starting node
>       Node* GetStartNode();
>       void SetStartNode(Node* StartingNode);
>
>       //Get/set the ending node
>       Node* GetEndNode();
>       void SetEndNode(Node* EndingNode);
>
>       //Get/set the next arc originating from the same node
>       virtual Arc* GetNextArc();
>       virtual void SetNextArc(Arc* NextArc);
>
>    protected:
>       Node* m_StartNode;
>       Node* m_EndNode;
>
>    private:
>       Arc* m_NextArcFromSameNode;
>
>    };
>
> Tim
>
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From e.a.g.pfaehler at umcg.nl  Tue Nov 21 10:12:44 2017
From: e.a.g.pfaehler at umcg.nl (Pfaehler, EAG (ngmb))
Date: Tue, 21 Nov 2017 15:12:44 +0000
Subject: [ITK] [ITK-dev] Problem calculating oriented bounding box,
	itk::ShapeLabelObject
Message-ID: <FB00E28D0DFA214FB31273A13543E1AA315D5FCC@WPZKH0217.zkh.umcg.intra>

Dear all,

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

Thanks a lot for your answer.

Regards

Elli

My code:


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

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

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

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

Hi Elli,

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

Regards,
D?enan

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

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

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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] [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


The ITK community is transitioning from this mailing list to discourse.itk.org. Please join us there!
________________________________
Powered by www.kitware.com

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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] [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
    

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] [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
>      
>
>

The ITK community is transitioning from this mailing list to discourse.itk.org. Please join us there!
________________________________
Powered by www.kitware.com

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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] [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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________________________________
Powered by www.kitware.com

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Kitware offers ITK Training Courses, for more information visit:
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Please keep messages on-topic and check the ITK FAQ at:
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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] [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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________________________________
Powered by www.kitware.com

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Kitware offers ITK Training Courses, for more information visit:
http://www.kitware.com/products/protraining.php

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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] [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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________________________________
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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

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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] [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] [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] [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] [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] [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] [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] [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
>    insight-users-request at itk.org
> 
> You can reach the person managing the list at
>    insight-users-owner at itk.org
> 
> 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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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] [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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Kitware offers ITK Training Courses, for more information visit:
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From k3ops at free.fr  Mon Nov 27 08:13:01 2017
From: k3ops at free.fr (k3ops at free.fr)
Date: Mon, 27 Nov 2017 14:13:01 +0100 (CET)
Subject: [ITK] Levenberg Marquart optimization with bounds
Message-ID: <733652150.58739343.1511788381887.JavaMail.root@zimbra31-e6>

Hello all,

I would like to know if somebody has already used the Levenberg Marquart optimizer with parameter bounds?

I am trying to fit 6 values using the Levenberg Marquart optimizer with 3 parameters, it's working very well but it sometimes gets incorrect results (non optimal results) because I knwow that one of my parameter has a restricted range of value (e.g between 0 to 200). I looked for examples or other optimizer in ITK for adding this kind of restrictions but I found nothing.

I found this interesting website that explain what I need:
https://lmfit.github.io/lmfit-py/bounds.html

Thank you in advance,
Florent

From poyu_kao at ucsb.edu  Tue Nov 28 21:40:39 2017
From: poyu_kao at ucsb.edu (Po-Yu Kao)
Date: Tue, 28 Nov 2017 18:40:39 -0800
Subject: [ITK] How to using SimpleITK to access and change the voxel value
 without touch the metadata
Message-ID: <CA+pTWFSCbqT_jZNTikBzOkKLqT7b4ZScROfikr896O-jWidOCw@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 zivrafael.yaniv at nih.gov  Wed Nov 29 10:13:22 2017
From: zivrafael.yaniv at nih.gov (Yaniv, Ziv Rafael (NIH/NLM/LHC) [C])
Date: Wed, 29 Nov 2017 15:13:22 +0000
Subject: [ITK] How to using SimpleITK to access and change the voxel
 value without touch the metadata
In-Reply-To: <CA+pTWFSCbqT_jZNTikBzOkKLqT7b4ZScROfikr896O-jWidOCw@mail.gmail.com>
References: <CA+pTWFSCbqT_jZNTikBzOkKLqT7b4ZScROfikr896O-jWidOCw@mail.gmail.com>
Message-ID: <C06E922E-0D65-4E13-BDCD-D35E5E75B8D4@mail.nih.gov>

Hello Po-Yu Kao,

The step you are missing is that you need to explicitly copy the meta-data information from your original image, the function is CopyInformation(). This assumes that you did not change any spatial information (padded the numpy array as part of your processing which implies a change in the spatial region occupied by the image etc.).

Your code should look something like this:

ct_img = sitk.ReadImage(ct_scan_path)
nda = sitk.GetArrayFromImage(ct_img)

# Do some work on the numpy array nda

img_preprocessed = sitk.GetImageFromArray(nda_preprocessed)
img_preprocessed.CopyInformation(ct_img)

If you did change some spatial aspects of the image in your numpy code then you will need to set them manually:
img_preprocessed.SetSpacing(new_spacing)
img_preprocessed.SetOrigin(new_origin)
img_preprocessed.SetDirection(new_direction)

We are moving away from the mailing to a discourse forum: https://discourse.itk.org/
Please post future questions on that forum.

     regards
          Ziv


From: Po-Yu Kao <poyu_kao at ucsb.edu>
Date: Tuesday, November 28, 2017 at 9:41 PM
To: "community at itk.org" <community at itk.org>
Subject: [ITK] How to using SimpleITK to access and change the voxel value without touch the metadata

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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