[Insight-users] [vtkusers] Watershed (Volume Rendering) Cropping Problem
Luis Ibanez
luis.ibanez at kitware.com
Mon Mar 29 18:39:09 EDT 2010
Hi Yusuf,
Please note that the output image of the Watershed filter is an image
of labels, and as such, it is not a well suited input for a Volume
Rendering visualization, given that the actual values of the labels
are irrelevant.
For example, one region will have a value of 27345, while another
region will have a value of 15, and that simply means that they are
"different" regions, not that the first region should be less transparent
than the second one.
You should use the same kind of visualization that you would use
for presenting the output of a connected components filter.
In order to visualize the output of the watershed algorithm you may
want to use simple color encoding,
as illustrated in the ITK Software Guide:
http://www.itk.org/ItkSoftwareGuide.pdf
or may want to first extract the regions that you consider relevant,
and then perform a surface-rendering visualization of them.
This approach is illustrated in the applications:
InsightApplications/
SegmentationEditor/
SegmentationEditorFltkGui/
Regards,
Luis
----------------------------------------------------------------------------------
On Mon, Mar 29, 2010 at 6:07 AM, Yusuf OEZBEK <nasil122002 at yahoo.de> wrote:
> Hello All.
>
> I have a problem with to cut (cropping) a 3D object, which I produced by the
> segmentation-method “watershed”. In the beginning I read the DICOM (. dcm)
> images with itkImageSeriesReader then I run watershed algorithm, in order to
> connect itk with vtk and a 3D object produce, I use ImageToVTKImageFilter
> and volume rendering (ray casting). And after segmentation of cutting the
> images I give below vtkFixedPointVolumeRayCastMapper
> (SetCroppingRegionPlanes) the Xmin, Xmax, Ymin, Ymax, Zmin and Zmax
> coordinates, but the result is a black screen. But when I read the images
> with vtkDICOMImageReader and then segmented with volume rendering, then it
> works completely well. The problem arises only for watershed -algorithm.
> Where is my mistake in the code? What should I do?
>
> Thank you.
>
>
>
>
>
> My Code for Volume Rendering:
>
> int levelForVolumeRendering =
> (int)this->sliderRangeMin->value()-(int)this->sliderRangeMax->value()/2;
>
> int widhtForVolumeRendering =
> (int)this->sliderRangeMin->value()+(int)this->sliderRangeMax->value()/2;
>
>
>
>
>
> mode3D = vtkInteractorStyleTrackballCamera::New();
>
>
>
> renderer3D = vtkRenderer::New();
>
>
>
> renderWindow3D = vtkRenderWindow::New();
>
> renderWindow3D->AddRenderer(renderer3D);
>
>
>
> displayImage3D->SetRenderWindow(renderWindow3D);
>
> displayImage3D->SetInteractorStyle(mode3D);
>
> displayImage3D->Initialize();
>
>
>
>
>
> vtkPiecewiseFunction *oTFun = vtkPiecewiseFunction::New();
>
> oTFun->AddPoint((double)levelForVolumeRendering, 0);
>
> oTFun->AddPoint((double)widhtForVolumeRendering, 1.0);
>
>
>
>
>
> vtkPiecewiseFunction* gradOpacity = vtkPiecewiseFunction::New();
>
> gradOpacity->AddPoint(0, 0.0);
>
> gradOpacity->AddPoint((int)this->changeLevelInput->value(), 1.0);
>
> gradOpacity->AddPoint((int)this->changeWidthInput->value(), 1.0);
>
>
>
>
>
> volumeColor = vtkColorTransferFunction::New();
>
> volumeColor->AddRGBPoint((double)levelForVolumeRendering, .62, .36, .18 );
>
> volumeColor->AddRGBPoint((double)widhtForVolumeRendering, .83, .66, 1);
>
>
>
>
>
> volumeProperty = vtkVolumeProperty::New();
>
> volumeProperty->SetShade(0);
>
> volumeProperty->SetAmbient(0.3);
>
> volumeProperty->SetDiffuse(1.0);
>
> volumeProperty->SetSpecular(0.2);
>
> volumeProperty->SetSpecularPower(50.0);
>
> volumeProperty->SetColor(volumeColor);
>
> volumeProperty->SetScalarOpacity(oTFun);
>
> volumeProperty->ShadeOn();
>
> volumeProperty->SetInterpolationTypeToLinear();
>
>
>
> //read with vtkDICOMImageReader and give 6 coordinates for cropping
>
> volumeRayCastMapper = vtkFixedPointVolumeRayCastMapper::New();
>
> volumeRayCastMapper->SetInputConnection(reader2D->GetOutputPort());
>
> volumeRayCastMapper->CroppingOn();
>
> volumeRayCastMapper->SetCroppingRegionPlanes(minpoint4[0], maxpoint4[0],
> minpoint4[1], maxpoint4[1],minpoint4[2], maxpoint4[2]);
>
> volumeRayCastMapper->SetCroppingRegionFlagsToSubVolume();
>
>
>
>
>
> volume = vtkVolume::New();
>
> volume->SetProperty(volumeProperty);
>
> volume->SetMapper(volumeRayCastMapper);
>
>
>
> camera3D = vtkCamera::New();
>
> camera3D->SetViewUp(0, 0, -1);
>
> camera3D->SetPosition(0, 1, 0);
>
> camera3D->SetFocalPoint(0, 0, 0);
>
> camera3D->ComputeViewPlaneNormal();
>
> camera3D->Azimuth(20);
>
>
>
> renderer3D->AddViewProp(volume);
>
> renderer3D->SetActiveCamera(camera3D);
>
> renderer3D->ResetCamera();
>
> camera3D->Dolly(1.3);
>
> renderer3D->ResetCameraClippingRange();
>
>
>
>
>
> Watershed Segmentation:
>
>
>
> typedef float InternalPixelType;
>
> const unsigned int Dimension = 3;
>
>
>
> typedef itk::OrientedImage<InternalPixelType, Dimension> ImageType;
>
> typedef itk::ImageSeriesReader<ImageType> ReaderType;
>
> typedef itk::GDCMImageIO ImageIOType;
>
> typedef itk::GDCMSeriesFileNames NamesGeneratorType;
>
> typedef std::vector<std::string> SeriesIdContainer;
>
> typedef std::vector<std::string> FileNamesContainer;
>
>
>
> ImageIOType::Pointer dicomIO = ImageIOType::New();
>
>
>
> ReaderType::Pointer reader = ReaderType::New();
>
> reader->SetImageIO(dicomIO);
>
>
>
> NamesGeneratorType::Pointer nameGenerator = NamesGeneratorType::New();
>
> nameGenerator->SetUseSeriesDetails(true);
>
> nameGenerator->AddSeriesRestriction("0008|0021");
>
> nameGenerator->SetDirectory(selectedDirectory);
>
>
>
> const SeriesIdContainer & seriesUID = nameGenerator->GetSeriesUIDs();
>
> SeriesIdContainer::const_iterator seriesItr = seriesUID.begin();
>
> SeriesIdContainer::const_iterator seriesEnd = seriesUID.end();
>
>
>
> while( seriesItr != seriesEnd )
>
> {
>
> seriesItr++;
>
> }
>
>
>
> std::string seriesIdentifier;
>
> seriesIdentifier = seriesUID.begin()->c_str();
>
>
>
> FileNamesContainer fileNames;
>
> fileNames = nameGenerator->GetFileNames(seriesIdentifier);
>
>
>
> reader->SetFileNames(fileNames);
>
> reader->Update();
>
>
>
>
>
> typedef itk::RGBPixel<unsigned char> RGBPixelType;
>
> typedef itk::Image<RGBPixelType,3> RGBImageType;
>
> typedef itk::Image< InternalPixelType, 3 > InternalImageType;
>
> typedef
> itk::GradientMagnitudeRecursiveGaussianImageFilter<InternalImageType,InternalImageType>
> GradientMagnitudeFilterType;
>
> GradientMagnitudeFilterType::Pointer gradienMagnitudeFilter =
> GradientMagnitudeFilterType::New();
>
> gradienMagnitudeFilter->SetInput( reader->GetOutput() );
>
> gradienMagnitudeFilter->SetSigma( 1.0 );
>
>
>
> typedef itk::WatershedImageFilter<InternalImageType> WatershedFilterType;
>
> WatershedFilterType::Pointer watershedFilter = WatershedFilterType::New();
>
> watershedFilter->SetInput(gradienMagnitudeFilter->GetOutput());
>
> watershedFilter->SetThreshold(this->sliderThresholdWatershed->value());
>
> watershedFilter->SetLevel(this->sliderLevelWatershed->value());
>
>
>
> typedef itk::Functor::ScalarToRGBPixelFunctor<unsigned long>
> ColorMapFunctorType;
>
> typedef WatershedFilterType::OutputImageType LabeledImageType;
>
>
>
>
>
> connector = ConnectorType::New();
>
> connector->SetInput( watershedFilter->GetOutput());
>
>
>
> shiftWatershed = vtkImageShiftScale::New();
>
> shiftWatershed->SetInput(connector->GetOutput());
>
> shiftWatershed->SetOutputScalarTypeToUnsignedChar();
>
>
>
>
>
> mode3D = vtkInteractorStyleTrackballCamera::New();
>
>
>
> renderer3D = vtkRenderer::New();
>
>
>
> renderWindow3D = vtkRenderWindow::New();
>
> renderWindow3D->AddRenderer(renderer3D);
>
>
>
> displayImage3D->SetRenderWindow(renderWindow3D);
>
> displayImage3D->SetInteractorStyle(mode3D);
>
> displayImage3D->Initialize();
>
>
>
>
>
> piecewiseWatershed = vtkPiecewiseFunction::New();
>
> piecewiseWatershed->AddPoint(0, 0.0);
>
> piecewiseWatershed->AddPoint(64, 0.0);
>
> piecewiseWatershed->AddPoint(128, 0.5);
>
> piecewiseWatershed->AddPoint(192, 1.0);
>
> piecewiseWatershed->AddPoint(255, 1.0);
>
>
>
>
>
> volumeColorWatershed = vtkColorTransferFunction::New();
>
> volumeColorWatershed->AddRGBPoint(0, 0.0, 0.0, 0.0);
>
> volumeColorWatershed->AddRGBPoint(64, 1.0, 0.0, 0.0);
>
> volumeColorWatershed->AddRGBPoint(128, 0.0, 0.0, 1.0);
>
> volumeColorWatershed->AddRGBPoint(192, 0.0, 1.0, 0.0);
>
> volumeColorWatershed->AddRGBPoint(255, 0.0, 0.0, 0.0);
>
>
>
> volumePropertyWatershed = vtkVolumeProperty::New();
>
> volumePropertyWatershed->SetShade(0);
>
> volumePropertyWatershed->SetAmbient(0.3);
>
> volumePropertyWatershed->SetDiffuse(1.0);
>
> volumePropertyWatershed->SetSpecular(0.2);
>
> volumePropertyWatershed->SetSpecularPower(50.0);
>
> volumePropertyWatershed->SetColor(volumeColorWatershed);
>
> volumePropertyWatershed->SetScalarOpacity(piecewiseWatershed);
>
> volumePropertyWatershed->ShadeOn();
>
> volumePropertyWatershed->SetInterpolationTypeToLinear();
>
>
>
> volumeRayCastMapperWatershed = vtkFixedPointVolumeRayCastMapper::New();
>
> volumeRayCastMapperWatershed->SetInputConnection(shiftWatershed->GetOutputPort());
>
> volumeRayCastMapperWatershed->CroppingOn();
>
> volumeRayCastMapperWatershed->SetCroppingRegionPlanes(minpoint4[0],
> maxpoint4[0], minpoint4[1], maxpoint4[1], minpoint4[2], maxpoint4[2]);
>
> volumeRayCastMapperWatershed->SetCroppingRegionFlagsToSubVolume();
>
>
>
>
>
> volumeWatershed = vtkVolume::New();
>
> volumeWatershed->SetProperty(volumePropertyWatershed);
>
> volumeWatershed->SetMapper(volumeRayCastMapperWatershed);
>
>
>
> camera3D = vtkCamera::New();
>
> camera3D->SetViewUp(0, 0, -1);
>
> camera3D->SetPosition(0, 1, 0);
>
> camera3D->SetFocalPoint(0, 0, 0);
>
> camera3D->ComputeViewPlaneNormal();
>
> camera3D->Azimuth(20);
>
>
>
> renderer3D->AddViewProp(volumeWatershed);
>
> renderer3D->SetActiveCamera(camera3D);
>
> renderer3D->ResetCamera();
>
> camera3D->Dolly(1.3);
>
> renderer3D->ResetCameraClippingRange();
>
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