From kjwjj627 at gmail.com  Wed Oct  3 11:30:04 2018
From: kjwjj627 at gmail.com (wonnybro)
Date: Wed, 3 Oct 2018 08:30:04 -0700 (MST)
Subject: [ITK-users] DVFs interpolation by BSpline
Message-ID: <1538580604795-0.post@n7.nabble.com>

Hi, ITK users

I really really need your help, please help me...
I am trying to do BSpline interpolation of DVFs obtained by image
registrations of 10 images. 
I'm trying to modify the BSplineScatteredDataPointSetToImageFilter from the
Insight Journal. However,
I am having trouble to find the correct parameter in order to make the
filter work. 
I'll have scattered 3-D points of several DVFs over time and I want to fit
these DVFs by a 4-D Bspline. Afterwards I want to evaluate output DVF to one
time step.

Here you can find the code, unfortunately it crashes.

Please help me...please.

Thanks in advance.

#include "itkBSplineScatteredDataPointSetToImageFilter.h"
#include "itkPointSet.h"
#include "itkImage.h"
#include "itkVectorImage.h"
#include "itkImageFileReader.h"
#include "itkImageFileWriter.h"

int main (int argc, char* argv[])
{
  const unsigned int ImageDimension = 3;

  using VectorType = itk::Vector<float, ImageDimension>;
  using InputImageType = itk::Image<VectorType, ImageDimension>;
  using InputPointType = InputImageType::PointType;
  using OutputImageType = itk::Image<VectorType, ImageDimension + 1>;
  using PointSetType = itk::PointSet<VectorType, ImageDimension + 1>;
  using OutputPointType = PointSetType::PointType;
  using ReaderType = itk::ImageFileReader<InputImageType>;
  using WriterType = itk::ImageFileWriter<OutputImageType>;

  PointSetType::Pointer pointSet = PointSetType::New();
  unsigned long pointId = 0;
  InputImageType::PointType origin;
  InputImageType::SpacingType spacing;
  InputImageType::SizeType size;
  for (int i = 1; i < argc; ++i)
  {
    ReaderType::Pointer reader = ReaderType::New();
    std::cout << "Reading file " << argv[i] << std::endl;
    reader->SetFileName(argv[i]);
    try
    {
      reader->Update();
    }
    catch (itk::ExceptionObject & err)
    {
      std::cout << "ExceptionObject caught !" << std::endl;
      std::cout << err << std::endl;
      return EXIT_FAILURE;
    }
    using IteratorType = itk::ImageRegionConstIterator<InputImageType>;
    const InputImageType * image = reader->GetOutput();
    IteratorType it(image, image->GetBufferedRegion());
    it.GoToBegin();
    InputPointType inPoint;
    OutputPointType outPoint;
    int iCount = 0;
    while (!it.IsAtEnd())
    {
      inPoint = image->GetPixel(it.GetIndex());
      for (int j = 0; j < ImageDimension; ++j)
        outPoint[j] = inPoint[i];
      outPoint[ImageDimension] = i - 1;
      pointSet->SetPoint(pointId, outPoint);
      // Transfer the pixel data to the value associated with the point.
      pointSet->SetPointData(pointId, it.Get());
      ++it;
      ++pointId;
      ++iCount;
    }
    std::cout << "Number of points in " << argv[i] << " = " << iCount <<
std::endl;
    std::cout << "Total number of points = " <<
pointSet->GetNumberOfPoints() << std::endl;
    origin = image->GetOrigin();
    spacing = image->GetSpacing();
    size = image->GetLargestPossibleRegion().GetSize();
  }

  typedef itk::BSplineScatteredDataPointSetToImageFilter < PointSetType,
OutputImageType > SplineFilterType;
  SplineFilterType::Pointer splineFilter = SplineFilterType::New();

  int splineorder=3; // complexity of the spline

  SplineFilterType::ArrayType ncontrol;
  ncontrol[0]=splineorder + 1;
  SplineFilterType::ArrayType closedim;
  closedim[0]= 0;

  OutputImageType::PointType parametricDomainOrigin;
  OutputImageType::SpacingType parametricDomainSpacing;
  OutputImageType::SizeType parametricDomainSize;
  for (int i = 0; i < ImageDimension; ++i)
  {
    parametricDomainOrigin[i] = origin[i];
    parametricDomainSpacing[i] = spacing[i];
    parametricDomainSize[i] = size[i];
  }
  parametricDomainOrigin[ImageDimension] = 0;
  parametricDomainSize[ImageDimension] = argc - 2;
  parametricDomainSpacing[ImageDimension] = 10.0;

  splineFilter->SetGenerateOutputImage( true );   // the only reason to turn
this off is if one only wants to use the control point lattice for further
processing
  splineFilter->SetInput ( pointSet );
  splineFilter->SetSplineOrder ( splineorder );
  splineFilter->SetNumberOfControlPoints ( ncontrol );
  splineFilter->SetNumberOfLevels( 3 );
  splineFilter->SetCloseDimension ( closedim );
  splineFilter->SetSize( parametricDomainSize );
  splineFilter->SetSpacing( parametricDomainSpacing );
  splineFilter->SetOrigin( parametricDomainOrigin );
  std::cout << "Before update spline filter" << std::endl;
  splineFilter->Update();
  std::cout << "After update spline filter" << std::endl;

  WriterType::Pointer writer = WriterType::New();
  writer->SetInput(splineFilter->GetOutput());
  writer->SetFileName("Output.mhd");
  writer->Update();
  std::cout << "After write image filter" << std::endl;

  return EXIT_SUCCESS;
};



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

From dzenanz at gmail.com  Wed Oct  3 14:10:44 2018
From: dzenanz at gmail.com (=?UTF-8?B?RMW+ZW5hbiBadWtpxIc=?=)
Date: Wed, 3 Oct 2018 14:10:44 -0400
Subject: [ITK-users] DVFs interpolation by BSpline
In-Reply-To: <1538580604795-0.post@n7.nabble.com>
References: <1538580604795-0.post@n7.nabble.com>
Message-ID: <CAPf2UMS9gEwOP1BWnu5ctuFG_MdJYFA6JMWLH1zhmEYYPGwc8w@mail.gmail.com>

Hi JongWon,

welcome to ITK! To reproduce your problem we will need the input file too.
If it crashes with different input files, please provide the smallest one.
Also, we have migrated to the forum <https://discourse.itk.org/>, so please
post the updated question there.

Regards,
D?enan

On Wed, Oct 3, 2018 at 11:30 AM wonnybro <kjwjj627 at gmail.com> wrote:

> Hi, ITK users
>
> I really really need your help, please help me...
> I am trying to do BSpline interpolation of DVFs obtained by image
> registrations of 10 images.
> I'm trying to modify the BSplineScatteredDataPointSetToImageFilter from the
> Insight Journal. However,
> I am having trouble to find the correct parameter in order to make the
> filter work.
> I'll have scattered 3-D points of several DVFs over time and I want to fit
> these DVFs by a 4-D Bspline. Afterwards I want to evaluate output DVF to
> one
> time step.
>
> Here you can find the code, unfortunately it crashes.
>
> Please help me...please.
>
> Thanks in advance.
>
> #include "itkBSplineScatteredDataPointSetToImageFilter.h"
> #include "itkPointSet.h"
> #include "itkImage.h"
> #include "itkVectorImage.h"
> #include "itkImageFileReader.h"
> #include "itkImageFileWriter.h"
>
> int main (int argc, char* argv[])
> {
>   const unsigned int ImageDimension = 3;
>
>   using VectorType = itk::Vector<float, ImageDimension>;
>   using InputImageType = itk::Image<VectorType, ImageDimension>;
>   using InputPointType = InputImageType::PointType;
>   using OutputImageType = itk::Image<VectorType, ImageDimension + 1>;
>   using PointSetType = itk::PointSet<VectorType, ImageDimension + 1>;
>   using OutputPointType = PointSetType::PointType;
>   using ReaderType = itk::ImageFileReader<InputImageType>;
>   using WriterType = itk::ImageFileWriter<OutputImageType>;
>
>   PointSetType::Pointer pointSet = PointSetType::New();
>   unsigned long pointId = 0;
>   InputImageType::PointType origin;
>   InputImageType::SpacingType spacing;
>   InputImageType::SizeType size;
>   for (int i = 1; i < argc; ++i)
>   {
>     ReaderType::Pointer reader = ReaderType::New();
>     std::cout << "Reading file " << argv[i] << std::endl;
>     reader->SetFileName(argv[i]);
>     try
>     {
>       reader->Update();
>     }
>     catch (itk::ExceptionObject & err)
>     {
>       std::cout << "ExceptionObject caught !" << std::endl;
>       std::cout << err << std::endl;
>       return EXIT_FAILURE;
>     }
>     using IteratorType = itk::ImageRegionConstIterator<InputImageType>;
>     const InputImageType * image = reader->GetOutput();
>     IteratorType it(image, image->GetBufferedRegion());
>     it.GoToBegin();
>     InputPointType inPoint;
>     OutputPointType outPoint;
>     int iCount = 0;
>     while (!it.IsAtEnd())
>     {
>       inPoint = image->GetPixel(it.GetIndex());
>       for (int j = 0; j < ImageDimension; ++j)
>         outPoint[j] = inPoint[i];
>       outPoint[ImageDimension] = i - 1;
>       pointSet->SetPoint(pointId, outPoint);
>       // Transfer the pixel data to the value associated with the point.
>       pointSet->SetPointData(pointId, it.Get());
>       ++it;
>       ++pointId;
>       ++iCount;
>     }
>     std::cout << "Number of points in " << argv[i] << " = " << iCount <<
> std::endl;
>     std::cout << "Total number of points = " <<
> pointSet->GetNumberOfPoints() << std::endl;
>     origin = image->GetOrigin();
>     spacing = image->GetSpacing();
>     size = image->GetLargestPossibleRegion().GetSize();
>   }
>
>   typedef itk::BSplineScatteredDataPointSetToImageFilter < PointSetType,
> OutputImageType > SplineFilterType;
>   SplineFilterType::Pointer splineFilter = SplineFilterType::New();
>
>   int splineorder=3; // complexity of the spline
>
>   SplineFilterType::ArrayType ncontrol;
>   ncontrol[0]=splineorder + 1;
>   SplineFilterType::ArrayType closedim;
>   closedim[0]= 0;
>
>   OutputImageType::PointType parametricDomainOrigin;
>   OutputImageType::SpacingType parametricDomainSpacing;
>   OutputImageType::SizeType parametricDomainSize;
>   for (int i = 0; i < ImageDimension; ++i)
>   {
>     parametricDomainOrigin[i] = origin[i];
>     parametricDomainSpacing[i] = spacing[i];
>     parametricDomainSize[i] = size[i];
>   }
>   parametricDomainOrigin[ImageDimension] = 0;
>   parametricDomainSize[ImageDimension] = argc - 2;
>   parametricDomainSpacing[ImageDimension] = 10.0;
>
>   splineFilter->SetGenerateOutputImage( true );   // the only reason to
> turn
> this off is if one only wants to use the control point lattice for further
> processing
>   splineFilter->SetInput ( pointSet );
>   splineFilter->SetSplineOrder ( splineorder );
>   splineFilter->SetNumberOfControlPoints ( ncontrol );
>   splineFilter->SetNumberOfLevels( 3 );
>   splineFilter->SetCloseDimension ( closedim );
>   splineFilter->SetSize( parametricDomainSize );
>   splineFilter->SetSpacing( parametricDomainSpacing );
>   splineFilter->SetOrigin( parametricDomainOrigin );
>   std::cout << "Before update spline filter" << std::endl;
>   splineFilter->Update();
>   std::cout << "After update spline filter" << std::endl;
>
>   WriterType::Pointer writer = WriterType::New();
>   writer->SetInput(splineFilter->GetOutput());
>   writer->SetFileName("Output.mhd");
>   writer->Update();
>   std::cout << "After write image filter" << std::endl;
>
>   return EXIT_SUCCESS;
> };
>
>
>
> --
> Sent from: http://itk-users.7.n7.nabble.com/
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> discourse.itk.org. Please join us there!
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From vrnova at gmail.com  Thu Oct  4 09:33:33 2018
From: vrnova at gmail.com (Yanling Liu)
Date: Thu, 4 Oct 2018 09:33:33 -0400
Subject: [ITK-users] Imaging analysis PostDoc position (NCI/FNLCR)
Message-ID: <CACNiyLCMPAuO+x0ocWPWtn5Pf_Pfa_P5YHzRnD6L-w1Qhpu1tw@mail.gmail.com>

Dear ITK users,

The Advanced Biomedical and Computational Science group at the NCI
Frederick National Laboratory for Cancer Research (FNLCR) seeks a post doc
fellow with image analysis background to work on tissue toxicity study from
radiation treatment. The post doc will support the collaboration between
FNLCR and University of Maryland School of Medicine.

To apply:
https://careers.leidos.com/jobs/3071866-postdoctoral-fellow-nci/apply

Thank you
Yanling
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