[Insight-users] Code to write back 2D image to 3D: Didnt work

Thu, 11 Dec 2003 13:01:02 -0800

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Hi Luiz,
Well, I decided to try the iterator approach to write back the 2D slice into
the 3D image into a user-defined slice location.
It didn't work. I have enclosed the code with this. Could somebody take a
look and let me know where I am going wrong.
Basically, I am writing back the 2D slice (which gets extracted correctly).
I am also writing the final 3D image which should contain
the 2D slice at the correct location. What I get back is a blank 3D image.

Radhika

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<div class=3DSection1>

<p class=3DMsoNormal><font size=3D2 face=3DArial><span =
style=3D'font-size:10.0pt;
font-family:Arial'>Hi <span =
class=3DSpellE>Luiz</span>,<o:p></o:p></span></font></p>

<p class=3DMsoNormal><font size=3D2 face=3DArial><span =
style=3D'font-size:10.0pt;
font-family:Arial'>Well, I decided to try the <span =
class=3DSpellE>iterator</span>
approach to write back the 2D slice into the 3D image into a =
user-defined slice
location.<o:p></o:p></span></font></p>

It didn't work. I have enclosed the code with this. =
Could
somebody take a look and let me know where I am going =
wrong.<o:p></o:p>

Basically, I am writing back the 2D slice (which =
gets
extracted correctly). I am also writing the final 3D image which should =
contain<o:p></o:p>

the<fo=
nt
size=3D2 face=3DArial> 2D slice at
the correct location. What I get back is a blank 3D image.<o:p></o:p></s=
pan>

<p class=3DMsoNormal><font size=3D2 face=3DArial><span =
style=3D'font-size:10.0pt;
font-family:Arial'><o:p>&nbsp;</o:p></span></font></p>

<p class=3DMsoNormal><font size=3D2 face=3DArial><span =
style=3D'font-size:10.0pt;
font-family:Arial'>Radhika<o:p></o:p></span></font></p>

<p class=3DMsoNormal><font size=3D2 face=3DArial><span =
style=3D'font-size:10.0pt;
font-family:Arial'><o:p>&nbsp;</o:p></span></font></p>

</div>

</body>

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	name="3D2D3D.cxx"
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	filename="3D2D3D.cxx"

// ITK include files

#include "itkImage.h"
#include "itkImageFileReader.h"
#include "itkImageFileWriter.h"
#include "itkImageRegionConstIteratorWithIndex.h"
#include "itkImageRegionIteratorWithIndex.h"
#include "itkExtractImageFilter.h"
#include "itkPasteImageFilter.h"

int main( int argc, char * argv[] )
{
    if( argc < 4 )
	{
		std::cerr << "Usage: " << std::endl;
		std::cerr << argv[0] << "  inputImageFile  ";
		std::cerr << " outputImageFileErosion  outputImageFileDilation";
		std::cerr << " lowerThreshold upperThreshold " << std::endl;
		return -1;
	}

	const unsigned int Dimension =3D 3;

	typedef unsigned char   PixelType;

	typedef itk::Image< PixelType,  Dimension >  ImageType;
	typedef itk::Image<PixelType,2> ImageType2D;
=09
	typedef itk::ImageRegionConstIteratorWithIndex< ImageType2D > =
ConstIteratorType2D;
	typedef itk::ImageRegionIteratorWithIndex< ImageType > IteratorType;
//	typedef itk::ImageRegionIteratorWithIndex< ImageType2D > =
IteratorType;

	// Software Guide : EndCodeSnippet

	typedef itk::ImageFileReader< ImageType  >  ReaderType;
	typedef itk::ImageFileWriter< ImageType >  WriterType;
	typedef itk::ImageFileWriter< ImageType2D >  WriterType2D;

	typedef itk::ExtractImageFilter< ImageType, ImageType2D> =
ExtractFilterType;
//	typedef itk::PasteImageFilter<ImageType,ImageType2D> =
PasteFilterType;
	 =20

  // Creation of Reader and Writer filters

  ReaderType::Pointer readervolume =3D ReaderType::New();
  WriterType::Pointer writervolume =3D WriterType::New();
  WriterType2D::Pointer writerimage =3D WriterType2D::New();

 // Creation of pointers to various filters =20

    ExtractFilterType::Pointer extracter2D =3D =
ExtractFilterType::New();
 //   PasteFilterType::Pointer paster2D =3D PasteFilterType::New();
  =20
// Reading all inputs=20
 =20
  readervolume->SetFileName( argv[1] );
  writervolume->SetFileName(argv[2]);
  readervolume->Update();
  writerimage->SetFileName(argv[3]);
  unsigned int s =3D ::atoi(argv[4]); // Reading in which slice to =
extract

// Setting an empty 3D image of same size, spacing and origin as input =
image=20

  ImageType::Pointer binimg3D =3D ImageType::New();
  =
binimg3D->SetRegions((readervolume->GetOutput())->GetRequestedRegion());=

  binimg3D->CopyInformation(readervolume->GetOutput());
  binimg3D->Allocate();

  // Setting up region in 3D image and setting size[2] =3D 0, so that a =
2D slice can be extracted

  ImageType::RegionType inputRegion =3D =
readervolume->GetOutput()->GetLargestPossibleRegion();
  ImageType::SizeType size =3D inputRegion.GetSize();
  size[2] =3D 0;
  ImageType::IndexType start =3D inputRegion.GetIndex();
  ImageType::RegionType desiredRegion;
  desiredRegion.SetSize(  size  );

=20
 // Extracting a 2D slice from 3D image and pasting back into a 3D =
image at the same slice location

    start[2] =3D s;   =20
    desiredRegion.SetIndex( start );
    extracter2D->SetExtractionRegion( desiredRegion );
    extracter2D->SetInput(readervolume->GetOutput());
    extracter2D->Update();
    ImageType2D::Pointer gs =3D extracter2D->GetOutput();
 /* paster2D->SetSourceImage(gs);
    paster2D->SetDestinationImage(binimg3D);
    paster2D->SetDestinationIndex(start);
    paster2D->SetSourceRegion(desiredRegion);=20
    writervolume->SetInput(paster2D->GetOutput()); */
    ImageType2D::RegionType newRegion=3Dgs->GetLargestPossibleRegion();
    ImageType2D::SizeType size2D;
    ImageType2D::IndexType index2D;
    size2D[0] =3D size[0];
    size2D[1] =3D size[1];
    index2D[0] =3D 0;
    index2D[1] =3D 0;
    ConstIteratorType2D it2D(gs,newRegion);
    inputRegion.SetSize(size);
    inputRegion.SetIndex(start);
    IteratorType it3D(binimg3D,desiredRegion);
    it3D.GoToBegin();
    it2D.GoToBegin();
    while (!it3D.IsAtEnd() && !it2D.IsAtEnd())
    {
	it3D.Set(it2D.Get());
	++it3D;
      ++it2D;
    }=20
  writervolume->SetInput(binimg3D);
  try=20
    {=20
    writervolume->Update();=20
    }=20
  catch( itk::ExceptionObject & err )=20
    {=20
    std::cout << "ExceptionObject caught !" << std::endl;=20
    std::cout << err << std::endl;=20
  return -1;
    }=20
 writerimage->SetInput(gs);
  try=20
    {=20
    writerimage->Update();=20
    }=20
  catch( itk::ExceptionObject & err )=20
    {=20
    std::cout << "ExceptionObject caught !" << std::endl;=20
    std::cout << err << std::endl;=20
  return -1;
    }=20

 =20

  return 0;
}

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