[Insight-users] Unable to display segmented images properly using itk-vtk

Sun, 22 Feb 2004 15:49:57 -0800 (PST)

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Hi all,

I have the segmented visible human data in Analyze format.  In a separate file type called knowledgeframe file, i have the offsets for each of the segmented volumes.  I am trying to load the data in ITK and use the SetOrigin method to set the offset for each of the segmented volume.  Then i connect ITK and VTK and try to display the images.  Even though each of the segmented images shows up correctly, its world coordinates are not correct which i expect to be correct after i do a setorigin(). 

My code follows and is also attached.  If you can find an obvious issue with it, please do let me know:

void visibleHuman()

{

ofstream fout("debug.txt");

const unsigned int dim = 3; 

string testdir = "..\\common\\data\\VisibleHuman\\Analyze\\";

string inputFile = "analyze.txt";

itksys::SystemTools::ChangeDirectory(testdir.c_str());

Reader::Pointer analyzeReader = Reader::New();

AnalyzeBinaryBitmapImageIO::Pointer Analyzeio;

Analyzeio = AnalyzeBinaryBitmapImageIO::New();

Analyzeio->SetByteOrder(itk::AnalyzeImageIO::LittleEndian);

analyzeReader->SetImageIO(Analyzeio); 

//Load filenames

vector <string> files; 

fstream fin(inputFile.c_str());

while(!fin.eof())

{

char str[100];

fin.getline(str, 79, '\n');

if (strlen(str) > 0) { 

files.push_back(str);

}

}

fin.close();

//Initialize VTK Stuff.

vtkRenderer* ren = vtkRenderer::New();

vtkRenderWindow* renwin = vtkRenderWindow::New();

vtkRenderWindowInteractor* iren = vtkRenderWindowInteractor::New();

renwin->AddRenderer( ren ); 

ren->SetBackground(0.4392,0.5020,0.5647);

vtkProgressCallback * cbc;

cbc = vtkProgressCallback::New();

renwin->SetSize(350,350);

iren->SetRenderWindow(renwin); 

iren->GetInteractorStyle()->GetInteractor()->AddObserver(vtkCommand::EndPickEvent,cbc);

cbc->iren = iren;

float factor;

cout << "\nImage Shrinking Factor? "; 

factor = 4; 

cin >> factor;

cout << factor;

vtkClipVolume* clip[15];

vtkDataSetMapper* mapper1[15];

vtkTransformFilter * transFilter[16];

vtkActor* actors[20];

int k;

for(k =0; k < files.size();++k)

{

//Read the segmented image file in analyze format

string filename = "DS101" + files[k] + ".hdr";

analyzeReader->SetFileName(filename.c_str()); 

//Read additional header info including offsets of the segmented file

string kfffilename = "..\\kff\\" + files[k] + "01697.kff";

KffFileReader kffReader(kfffilename.c_str());

KnowledgeFrame kff = kffReader.GetOutput();

try

{

analyzeReader->Update(); 

}

catch(itk::ExceptionObject & err) 

{

std::cout << "Exception: " << std::endl;

std::cout << err << std::endl;

continue;

}

typedef itk::ShrinkImageFilter <ImageType,RealImageType> ShrinkFilterType;

ShrinkFilterType::Pointer pShrinkFilter = ShrinkFilterType::New();

analyzeReader->GetOutput()->Print(fout);

float spacing[]={0.144,0.144,1};

double origin[ImageType::ImageDimension];

origin[0] = kff.m_volumeOfInterest.m_VoiBoundaryX;

origin[1] = kff.m_volumeOfInterest.m_VoiBoundaryY;

origin[2] = kff.m_volumeOfInterest.m_VoiBoundaryZ;

analyzeReader->GetOutput()->SetOrigin(origin);

analyzeReader->GetOutput()->SetSpacing(spacing);

pShrinkFilter->SetInput(analyzeReader->GetOutput());

pShrinkFilter->SetNumberOfThreads(4); 

unsigned int dfactors[3] = { factor, factor, factor };

pShrinkFilter->SetShrinkFactors(dfactors);

pShrinkFilter->UpdateLargestPossibleRegion();

//Give to VTK for rendering

typedef itk::VTKImageExport< RealImageType > VTKExportType; 

VTKExportType::Pointer exporter = VTKExportType::New();

exporter->SetInput( pShrinkFilter->GetOutput() );

vtkImageImport* importer = vtkImageImport::New();

ConnectPipelines(exporter, importer);

importer->Update();

vtkImageData* image = importer->GetOutput();

//VTK convert image to unstructured grid i.e. tetrahedrons.

cout << "\nClipping Volume"; 

clip[k] = vtkClipVolume::New();

clip[k]->SetInput(image); 

clip[k]->SetValue(254);

cout << "\nMapping Data";

mapper1[k] = vtkDataSetMapper::New(); 

mapper1[k]->SetInput(dynamic_cast<vtkDataSet*>(clip[k]->GetOutput())); 

mapper1[k]->ScalarVisibilityOff();

//vtkActor* actor = vtkGenerateActorFromImageData(0,1,importer->GetOutput());

actors[k] = vtkActor::New();

actors[k]->SetMapper(mapper1[k]); 

vtkTransform* transform = vtkTransform::New();

cbc->ren = ren;

cbc->renwin = renwin;

actors[k]->GetProperty()->SetRepresentationToWireframe();

ren->AddActor( actors[k]); 

pShrinkFilter->Delete(); 

}

renwin->Render();

iren->Start(); 

// Clean up after VTK

iren->Delete();

renwin->Delete();

ren->Delete(); 

fout.close();

}

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<DIV>
<DIV>Hi all,</DIV>
<DIV>&nbsp;</DIV>
<DIV>I have the segmented visible human data in Analyze format.&nbsp; In a separate file type called knowledgeframe file, i have the offsets for each of the segmented volumes.&nbsp; I am trying to load the data in ITK and use the SetOrigin method to set the offset for each of the segmented volume.&nbsp; Then i connect ITK and VTK and try to display the images.&nbsp; Even though each of the segmented images shows up correctly, its world coordinates are not correct which i expect to be correct after i do a setorigin(). </DIV>
<DIV>&nbsp;</DIV>
<DIV>My code follows and is also attached.&nbsp; If you can find an obvious issue with it, please do let me know:</DIV>
<DIV>&nbsp;</DIV>
<DIV><FONT color=#0000ff size=2>
<P>void</FONT><FONT size=2> visibleHuman()</P>
<P>{</P>
<P>ofstream fout("debug.txt");</P>
<P></FONT><FONT color=#0000ff size=2>const</FONT><FONT size=2> </FONT><FONT color=#0000ff size=2>unsigned</FONT><FONT size=2> </FONT><FONT color=#0000ff size=2>int</FONT><FONT size=2> dim = 3; </P>
<P>string testdir = "..\\common\\data\\VisibleHuman\\Analyze\\";</P>
<P>string inputFile = "analyze.txt";</P>
<P>itksys::SystemTools::ChangeDirectory(testdir.c_str());</P>
<P>Reader::Pointer analyzeReader = Reader::New();</P>
<P>AnalyzeBinaryBitmapImageIO::Pointer Analyzeio;</P>
<P>Analyzeio = AnalyzeBinaryBitmapImageIO::New();</P>
<P>Analyzeio-&gt;SetByteOrder(itk::AnalyzeImageIO::LittleEndian);</P>
<P>analyzeReader-&gt;SetImageIO(Analyzeio); </P>
<P></P>
<P></FONT><FONT color=#008000 size=2>//Load filenames</P></FONT><FONT size=2>
<P>vector &lt;string&gt; files; </P>
<P>fstream fin(inputFile.c_str());</P>
<P></FONT><FONT color=#0000ff size=2>while</FONT><FONT size=2>(!fin.eof())</P>
<P>{</P>
<P></FONT><FONT color=#0000ff size=2>char</FONT><FONT size=2> str[100];</P>
<P>fin.getline(str, 79, '\n');</P>
<P></FONT><FONT color=#0000ff size=2>if</FONT><FONT size=2> (strlen(str) &gt; 0) { </P>
<P>files.push_back(str);</P>
<P>}</P>
<P>}</P>
<P>fin.close();</P>
<P>&nbsp;</P>
<P></FONT><FONT color=#008000 size=2>//Initialize VTK Stuff.</P></FONT><FONT size=2>
<P>vtkRenderer* ren = vtkRenderer::New();</P>
<P>vtkRenderWindow* renwin = vtkRenderWindow::New();</P>
<P>vtkRenderWindowInteractor* iren = vtkRenderWindowInteractor::New();</P>
<P>renwin-&gt;AddRenderer( ren ); </P>
<P>ren-&gt;SetBackground(0.4392,0.5020,0.5647);</P>
<P>vtkProgressCallback * cbc;</P>
<P>cbc = vtkProgressCallback::New();</P>
<P>renwin-&gt;SetSize(350,350);</P>
<P>iren-&gt;SetRenderWindow(renwin); </P>
<P>iren-&gt;GetInteractorStyle()-&gt;GetInteractor()-&gt;AddObserver(vtkCommand::EndPickEvent,cbc);</P>
<P>cbc-&gt;iren = iren;</P>
<P></P>
<P></FONT><FONT color=#0000ff size=2>float</FONT><FONT size=2> factor;</P>
<P>cout &lt;&lt; "\nImage Shrinking Factor? "; </P>
<P>factor = 4; </P>
<P>cin &gt;&gt; factor;</P>
<P>cout &lt;&lt; factor;</P>
<P>vtkClipVolume* clip[15];</P>
<P>vtkDataSetMapper* mapper1[15];</P>
<P>vtkTransformFilter * transFilter[16];</P>
<P>vtkActor* actors[20];</P>
<P></FONT><FONT color=#0000ff size=2>int</FONT><FONT size=2> k;</P>
<P>&nbsp;</P>
<P></FONT><FONT color=#0000ff size=2>for</FONT><FONT size=2>(k =0; k &lt; files.size();++k)</P>
<P>{</P>
<P></FONT><FONT color=#008000 size=2>//Read the segmented image file in analyze format</P></FONT><FONT size=2>
<P>string filename = "DS101" + files[k] + ".hdr";</P>
<P>analyzeReader-&gt;SetFileName(filename.c_str()); </P>
<P></FONT><FONT color=#008000 size=2>//Read additional header info including offsets of the segmented file</P></FONT><FONT size=2>
<P>string kfffilename = "..\\kff\\" + files[k] + "01697.kff";</P>
<P>KffFileReader kffReader(kfffilename.c_str());</P>
<P>KnowledgeFrame kff = kffReader.GetOutput();</P>
<P></FONT><FONT color=#0000ff size=2>try</P></FONT><FONT size=2>
<P>{</P>
<P>analyzeReader-&gt;Update(); </P>
<P>}</P>
<P></FONT><FONT color=#0000ff size=2>catch</FONT><FONT size=2>(itk::ExceptionObject &amp; err) </P>
<P>{</P>
<P>std::cout &lt;&lt; "Exception: " &lt;&lt; std::endl;</P>
<P>std::cout &lt;&lt; err &lt;&lt; std::endl;</P>
<P></FONT><FONT color=#0000ff size=2>continue</FONT><FONT size=2>;</P>
<P>}</P>
<P></FONT><FONT color=#0000ff size=2>typedef</FONT><FONT size=2> itk::ShrinkImageFilter &lt;ImageType,RealImageType&gt; ShrinkFilterType;</P>
<P>ShrinkFilterType::Pointer pShrinkFilter = ShrinkFilterType::New();</P>
<P>analyzeReader-&gt;GetOutput()-&gt;Print(fout);</P>
<P></P>
<P></FONT><FONT color=#0000ff size=2>float</FONT><FONT size=2> spacing[]={0.144,0.144,1};</P>
<P></FONT><FONT color=#0000ff size=2>double</FONT><FONT size=2> origin[ImageType::ImageDimension];</P>
<P>origin[0] = kff.m_volumeOfInterest.m_VoiBoundaryX;</P>
<P>origin[1] = kff.m_volumeOfInterest.m_VoiBoundaryY;</P>
<P>origin[2] = kff.m_volumeOfInterest.m_VoiBoundaryZ;</P>
<P>analyzeReader-&gt;GetOutput()-&gt;SetOrigin(origin);</P>
<P>analyzeReader-&gt;GetOutput()-&gt;SetSpacing(spacing);</P>
<P>pShrinkFilter-&gt;SetInput(analyzeReader-&gt;GetOutput());</P>
<P>pShrinkFilter-&gt;SetNumberOfThreads(4); </P>
<P></FONT><FONT color=#0000ff size=2>unsigned</FONT><FONT size=2> </FONT><FONT color=#0000ff size=2>int</FONT><FONT size=2> dfactors[3] = { factor, factor, factor };</P>
<P>pShrinkFilter-&gt;SetShrinkFactors(dfactors);</P>
<P>pShrinkFilter-&gt;UpdateLargestPossibleRegion();</P>
<P></P>
<P></FONT><FONT color=#008000 size=2>//Give to VTK for rendering</P></FONT><FONT size=2>
<P></FONT><FONT color=#0000ff size=2>typedef</FONT><FONT size=2> itk::VTKImageExport&lt; RealImageType &gt; VTKExportType; </P>
<P>VTKExportType::Pointer exporter = VTKExportType::New();</P>
<P>exporter-&gt;SetInput( pShrinkFilter-&gt;GetOutput() );</P>
<P>vtkImageImport* importer = vtkImageImport::New();</P>
<P>ConnectPipelines(exporter, importer);</P>
<P>importer-&gt;Update();</P>
<P>vtkImageData* image = importer-&gt;GetOutput();</P>
<P>&nbsp;</P>
<P>&nbsp;</P>
<P></FONT><FONT color=#008000 size=2>//VTK convert image to unstructured grid i.e. tetrahedrons.</P></FONT><FONT size=2>
<P>cout &lt;&lt; "\nClipping Volume"; </P>
<P>clip[k] = vtkClipVolume::New();</P>
<P>clip[k]-&gt;SetInput(image); </P>
<P>clip[k]-&gt;SetValue(254);</P>
<P>cout &lt;&lt; "\nMapping Data";</P>
<P>mapper1[k] = vtkDataSetMapper::New(); </P>
<P>mapper1[k]-&gt;SetInput(</FONT><FONT color=#0000ff size=2>dynamic_cast</FONT><FONT size=2>&lt;vtkDataSet*&gt;(clip[k]-&gt;GetOutput())); </P>
<P>mapper1[k]-&gt;ScalarVisibilityOff();</P>
<P></FONT><FONT color=#008000 size=2>//vtkActor* actor = vtkGenerateActorFromImageData(0,1,importer-&gt;GetOutput());</P></FONT><FONT size=2>
<P>actors[k] = vtkActor::New();</P>
<P>actors[k]-&gt;SetMapper(mapper1[k]); </P>
<P>vtkTransform* transform = vtkTransform::New();</P>
<P>cbc-&gt;ren = ren;</P>
<P>cbc-&gt;renwin = renwin;</P>
<P>actors[k]-&gt;GetProperty()-&gt;SetRepresentationToWireframe();</P>
<P>ren-&gt;AddActor( actors[k]); </P>
<P>pShrinkFilter-&gt;Delete(); </P>
<P>}</P>
<P>renwin-&gt;Render();</P>
<P>iren-&gt;Start(); </P>
<P></FONT><FONT color=#008000 size=2>// Clean up after VTK</P></FONT><FONT size=2>
<P>iren-&gt;Delete();</P>
<P>renwin-&gt;Delete();</P>
<P>ren-&gt;Delete(); </P>
<P>fout.close();</P>
<P>}</P></FONT></DIV></DIV><p><hr SIZE=1>
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Content-Type: text/plain; name="source1.cpp"
Content-Description: source1.cpp
Content-Disposition: inline; filename="source1.cpp"

void visibleHuman()
{

	ofstream fout("debug.txt");
	const unsigned int dim = 3;	
	string testdir = "..\\common\\data\\VisibleHuman\\Analyze\\";
	string inputFile = "analyze.txt";

	itksys::SystemTools::ChangeDirectory(testdir.c_str());
	Reader::Pointer analyzeReader = Reader::New();
	AnalyzeBinaryBitmapImageIO::Pointer Analyzeio;
	Analyzeio = AnalyzeBinaryBitmapImageIO::New();
	Analyzeio->SetByteOrder(itk::AnalyzeImageIO::LittleEndian);
	analyzeReader->SetImageIO(Analyzeio);		

	//Load filenames
	vector <string> files;	
	fstream fin(inputFile.c_str());
	while(!fin.eof())
	{
		char str[100];
		fin.getline(str, 79, '\n');
		if (strlen(str) > 0) {			
			files.push_back(str);
		}
	}
	fin.close();

	//Initialize VTK Stuff.
	vtkRenderer* ren = vtkRenderer::New();
	vtkRenderWindow* renwin = vtkRenderWindow::New();
	vtkRenderWindowInteractor* iren = vtkRenderWindowInteractor::New();
	renwin->AddRenderer( ren );	
	ren->SetBackground(0.4392,0.5020,0.5647);
	vtkProgressCallback * cbc;
	cbc = vtkProgressCallback::New();
	renwin->SetSize(350,350);
	iren->SetRenderWindow(renwin);	
	iren->GetInteractorStyle()->GetInteractor()->AddObserver(vtkCommand::EndPickEvent,cbc);
	cbc->iren = iren;

	float factor;
	cout << "\nImage Shrinking Factor? ";	
	factor = 4;	
	cin >> factor;
	cout << factor;
	vtkClipVolume* clip[15];
	vtkDataSetMapper* mapper1[15];
	vtkTransformFilter * transFilter[16];
	vtkActor* actors[20];
	int k;

	for(k =0; k < files.size();++k)
	{
		//Read the segmented image file in analyze format
		string filename = "DS101" + files[k] + ".hdr";
		analyzeReader->SetFileName(filename.c_str());			

		//Read additional header info including offsets of the segmented file
		string kfffilename = "..\\kff\\" + files[k] + "01697.kff";
		KffFileReader kffReader(kfffilename.c_str());
		KnowledgeFrame kff = kffReader.GetOutput();
		try
		{
			analyzeReader->Update();					
		}
		catch(itk::ExceptionObject & err) 
		{
			std::cout << "Exception: " << std::endl;
			std::cout << err << std::endl;
			continue;
		}

		typedef itk::ShrinkImageFilter  <ImageType,RealImageType> ShrinkFilterType;
		ShrinkFilterType::Pointer pShrinkFilter = ShrinkFilterType::New();
		analyzeReader->GetOutput()->Print(fout);

		float spacing[]={0.144,0.144,1};
		double origin[ImageType::ImageDimension];
		origin[0] = kff.m_volumeOfInterest.m_VoiBoundaryX;
		origin[1] = kff.m_volumeOfInterest.m_VoiBoundaryY;
		origin[2] = kff.m_volumeOfInterest.m_VoiBoundaryZ;

		analyzeReader->GetOutput()->SetOrigin(origin);
		analyzeReader->GetOutput()->SetSpacing(spacing);
		pShrinkFilter->SetInput(analyzeReader->GetOutput());
		pShrinkFilter->SetNumberOfThreads(4);		

		unsigned int dfactors[3] = { factor, factor, factor };
		pShrinkFilter->SetShrinkFactors(dfactors);
		pShrinkFilter->UpdateLargestPossibleRegion();

		//Give to VTK for rendering
		typedef itk::VTKImageExport< RealImageType >  VTKExportType;		
		VTKExportType::Pointer exporter = VTKExportType::New();
		exporter->SetInput( pShrinkFilter->GetOutput() );

		vtkImageImport* importer = vtkImageImport::New();
		ConnectPipelines(exporter, importer);
		importer->Update();

		vtkImageData* image = importer->GetOutput();

		//VTK convert image to unstructured grid i.e. tetrahedrons.
		cout << "\nClipping Volume";		
		clip[k] = vtkClipVolume::New();
		clip[k]->SetInput(image);						
		clip[k]->SetValue(254);

		cout << "\nMapping Data";
		mapper1[k] = vtkDataSetMapper::New();		
		mapper1[k]->SetInput(dynamic_cast<vtkDataSet*>(clip[k]->GetOutput()));		
		mapper1[k]->ScalarVisibilityOff();

		//vtkActor* actor = vtkGenerateActorFromImageData(0,1,importer->GetOutput());
		actors[k] = vtkActor::New();
		actors[k]->SetMapper(mapper1[k]);		
		vtkTransform* transform = vtkTransform::New();

		cbc->ren = ren;
		cbc->renwin = renwin;

		actors[k]->GetProperty()->SetRepresentationToWireframe();

		ren->AddActor(	actors[k]);		
		pShrinkFilter->Delete();		
	}
	renwin->Render();
	iren->Start();		

	// Clean up after VTK
	iren->Delete();
	renwin->Delete();
	ren->Delete();	
	fout.close();

}
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