C++ image::Pointer类代码示例

void mitk::BinaryThresholdULTool::CreateNewSegmentationFromThreshold(DataNode* node)
{
  if (node)
  {
    Image::Pointer feedBackImage = dynamic_cast<Image*>( m_ThresholdFeedbackNode->GetData() );
    if (feedBackImage.IsNotNull())
    {
      // create a new image of the same dimensions and smallest possible pixel type
      DataNode::Pointer emptySegmentation = GetTargetSegmentationNode();

      if (emptySegmentation)
      {
        // actually perform a thresholding and ask for an organ type
        for (unsigned int timeStep = 0; timeStep < feedBackImage->GetTimeSteps(); ++timeStep)
        {
          try
          {
            ImageTimeSelector::Pointer timeSelector = ImageTimeSelector::New();
            timeSelector->SetInput( feedBackImage );
            timeSelector->SetTimeNr( timeStep );
            timeSelector->UpdateLargestPossibleRegion();
            Image::Pointer feedBackImage3D = timeSelector->GetOutput();

            if (feedBackImage3D->GetDimension() == 2)
            {
              AccessFixedDimensionByItk_2( feedBackImage3D, ITKSetVolume, 2, dynamic_cast<Image*>(emptySegmentation->GetData()), timeStep );
            }
            else
            {
              AccessFixedDimensionByItk_2( feedBackImage3D, ITKSetVolume, 3, dynamic_cast<Image*>(emptySegmentation->GetData()), timeStep );
            }

          }
          catch(...)
          {
            Tool::ErrorMessage("Error accessing single time steps of the original image. Cannot create segmentation.");
          }
        }

        //since we are maybe working on a smaller image, pad it to the size of the original image
        if (m_OriginalImageNode.GetPointer() != m_NodeForThresholding.GetPointer())
        {
          mitk::PadImageFilter::Pointer padFilter = mitk::PadImageFilter::New();

          padFilter->SetInput(0, dynamic_cast<mitk::Image*> (emptySegmentation->GetData()));
          padFilter->SetInput(1, dynamic_cast<mitk::Image*> (m_OriginalImageNode->GetData()));
          padFilter->SetBinaryFilter(true);
          padFilter->SetUpperThreshold(1);
          padFilter->SetLowerThreshold(1);
          padFilter->Update();

          emptySegmentation->SetData(padFilter->GetOutput());
        }

        m_ToolManager->SetWorkingData( emptySegmentation );
        m_ToolManager->GetWorkingData(0)->Modified();
      }
    }
  }
}

void job_test()
{
	typedef itk::Image<int,3> Image;
	typedef itk::ImageFileReader<Image> Reader;

	// Read in the image (when debugging in VC++, it may be necessary to set the working directory to "$(TargetDir)").
	std::cout << "Loading input image...\n";
	Reader::Pointer reader = Reader::New();
	reader->SetFileName("../resources/test.bmp");
	reader->Update();
	Image::Pointer image = reader->GetOutput();

	// Create a DICOM volume (obviously not a proper one, as the image being read in is actually a greyscale one).
	DICOMVolume_Ptr volume(new DICOMVolume(image));

	// Set the segmentation options.
	itk::Size<3> size = image->GetLargestPossibleRegion().GetSize();
	WindowSettings windowSettings(40, 400);	// dummy window settings
	CTSegmentationOptions options(30, CTSegmentationOptions::INPUTTYPE_HOUNSFIELD, size, 10, windowSettings);

	// Build the IPF.
	std::cout << "Building IPF...\n";
	typedef CTIPFBuilder::IPF_Ptr IPF_Ptr;
	IPF_Ptr ipf;
	Job_Ptr job(new CTIPFBuilder(volume, options, ipf));
	Job::execute_in_thread(job);
	while(!job->is_finished());

	// Output the mosaic images for each of the partition forest layers.
	std::cout << "Outputting mosaic images...\n";
	for(int i=0; i<=ipf->highest_layer(); ++i)
	{
		output_mosaic_image(ipf, i, size[0], size[1]);
	}
}

//#################### HELPER FUNCTIONS ####################
itk::Image<unsigned char,2>::Pointer make_mosaic_image(const boost::shared_ptr<const PartitionForest<CTImageLeafLayer,CTImageBranchLayer> >& ipf, int layerIndex,
													   int width, int height)
{
	typedef itk::Image<unsigned char,2> Image;
	typedef PartitionForest<CTImageLeafLayer,CTImageBranchLayer> IPF;

	Image::Pointer image = ITKImageUtil::make_image<unsigned char>(width, height);

	Image::IndexType index;
	int n = 0;
	for(index[1]=0; index[1]<height; ++index[1])
		for(index[0]=0; index[0]<width; ++index[0])
		{
			unsigned char mosaicValue;
			if(layerIndex > 0)
			{
				PFNodeID ancestor = ipf->ancestor_of(PFNodeID(0, n), layerIndex);
				mosaicValue = static_cast<unsigned char>(ipf->branch_properties(ancestor).mean_grey_value());
			}
			else mosaicValue = ipf->leaf_properties(n).grey_value();

			image->SetPixel(index, mosaicValue);
			++n;
		}

	return image;
}

  bool CalculateSegmentationVolume::ReadyToRun()
  {
    Image::Pointer image;
    GetPointerParameter("Input", image);

    return image.IsNotNull() && GetGroupNode();
  }

void mitk::SegTool2D::WriteBackSegmentationResult(std::vector<mitk::SegTool2D::SliceInformation> sliceList, bool writeSliceToVolume)
{
  std::vector<mitk::Surface::Pointer> contourList;
  contourList.reserve(sliceList.size());
  ImageToContourFilter::Pointer contourExtractor = ImageToContourFilter::New();

  DataNode* workingNode( m_ToolManager->GetWorkingData(0) );
  Image* image = dynamic_cast<Image*>(workingNode->GetData());

  mitk::ImageTimeSelector::Pointer timeSelector = mitk::ImageTimeSelector::New();
  timeSelector->SetInput( image );
  timeSelector->SetTimeNr( 0 );
  timeSelector->SetChannelNr( 0 );
  timeSelector->Update();
  Image::Pointer dimRefImg = timeSelector->GetOutput();

  for (unsigned int i = 0; i < sliceList.size(); ++i)
  {
    SliceInformation currentSliceInfo = sliceList.at(i);
    if(writeSliceToVolume)
      this->WriteSliceToVolume(currentSliceInfo);
    if (m_SurfaceInterpolationEnabled && dimRefImg->GetDimension() == 3)
    {
      currentSliceInfo.slice->DisconnectPipeline();
      contourExtractor->SetInput(currentSliceInfo.slice);
      contourExtractor->Update();
      mitk::Surface::Pointer contour = contourExtractor->GetOutput();
      contour->DisconnectPipeline();

      contourList.push_back(contour);
    }
  }
  mitk::SurfaceInterpolationController::GetInstance()->AddNewContours(contourList);
  mitk::RenderingManager::GetInstance()->RequestUpdateAll();
}

  bool CalculateSegmentationVolume::ThreadedUpdateFunction()
  {
    // get image
    Image::Pointer image;
    GetPointerParameter("Input", image);

    AccessFixedDimensionByItk(image.GetPointer(),
                              ItkImageProcessing,
                              3); // some magic to call the correctly templated function (we only do 3D images here!)

    // consider single voxel volume
    Vector3D spacing = image->GetSlicedGeometry()->GetSpacing();                           // spacing in mm
    float volumeML = (ScalarType)m_Volume * spacing[0] * spacing[1] * spacing[2] / 1000.0; // convert to ml

    DataNode *groupNode = GetGroupNode();
    if (groupNode)
    {
      groupNode->SetProperty("volume", FloatProperty::New(volumeML));
      groupNode->SetProperty("centerOfMass", Vector3DProperty::New(m_CenterOfMass));
      groupNode->SetProperty("boundingBoxMinimum", Vector3DProperty::New(m_MinIndexOfBoundingBox));
      groupNode->SetProperty("boundingBoxMaximum", Vector3DProperty::New(m_MaxIndexOfBoundingBox));
      groupNode->SetProperty("showVolume", BoolProperty::New(true));
    }

    return true;
  }

/*
 * What is the input requested region that is required to produce the output
 * requested region? By default, the largest possible region is always
 * required but this is overridden in many subclasses. For instance, for an
 * image processing filter where an output pixel is a simple function of an
 * input pixel, the input requested region will be set to the output
 * requested region. For an image processing filter where an output pixel is
 * a function of the pixels in a neighborhood of an input pixel, then the
 * input requested region will need to be larger than the output requested
 * region (to avoid introducing artificial boundary conditions). This
 * function should never request an input region that is outside the the
 * input largest possible region (i.e. implementations of this method should
 * crop the input requested region at the boundaries of the input largest
 * possible region). 
 */
void mitk::ExtractImageFilter::GenerateInputRequestedRegion()
{
  Superclass::GenerateInputRequestedRegion();

  ImageToImageFilter::InputImagePointer input = const_cast< ImageToImageFilter::InputImageType* > ( this->GetInput() );
  Image::Pointer output = this->GetOutput();

  if (input->GetDimension() == 2)
  {
    input->SetRequestedRegionToLargestPossibleRegion();
    return;
  }

  Image::RegionType requestedRegion;
  requestedRegion = output->GetRequestedRegion();
  requestedRegion.SetIndex(0, 0);
  requestedRegion.SetIndex(1, 0);
  requestedRegion.SetIndex(2, 0);
  requestedRegion.SetSize(0, input->GetDimension(0));
  requestedRegion.SetSize(1, input->GetDimension(1));
  requestedRegion.SetSize(2, input->GetDimension(2));

  requestedRegion.SetIndex( m_SliceDimension, m_SliceIndex ); // only one slice needed
  requestedRegion.SetSize( m_SliceDimension, 1 );

  input->SetRequestedRegion( &requestedRegion );
}

void mitk::GeometryClipImageFilter::GenerateData()
{
  Image::ConstPointer input = this->GetInput();
  Image::Pointer output = this->GetOutput();

  if((output->IsInitialized()==false) || (m_ClippingGeometry.IsNull()))
    return;

  const Geometry2D * clippingGeometryOfCurrentTimeStep = NULL;

  if(m_TimeSlicedClippingGeometry.IsNull())
  {
    clippingGeometryOfCurrentTimeStep = dynamic_cast<const Geometry2D*>(m_ClippingGeometry.GetPointer());
  }
  else
  {
    clippingGeometryOfCurrentTimeStep = dynamic_cast<const Geometry2D*>(m_TimeSlicedClippingGeometry->GetGeometry3D(0));
  }

  if(clippingGeometryOfCurrentTimeStep == NULL)
    return;

  m_InputTimeSelector->SetInput(input);
  m_OutputTimeSelector->SetInput(this->GetOutput());

  mitk::Image::RegionType outputRegion = output->GetRequestedRegion();
  const mitk::TimeSlicedGeometry *outputTimeGeometry = output->GetTimeSlicedGeometry();
  const mitk::TimeSlicedGeometry *inputTimeGeometry = input->GetTimeSlicedGeometry();
  ScalarType timeInMS;

  int timestep=0;
  int tstart=outputRegion.GetIndex(3);
  int tmax=tstart+outputRegion.GetSize(3);

  int t;
  for(t=tstart;t<tmax;++t)
  {
    timeInMS = outputTimeGeometry->TimeStepToMS( t );

    timestep = inputTimeGeometry->MSToTimeStep( timeInMS );

    m_InputTimeSelector->SetTimeNr(timestep);
    m_InputTimeSelector->UpdateLargestPossibleRegion();
    m_OutputTimeSelector->SetTimeNr(t);
    m_OutputTimeSelector->UpdateLargestPossibleRegion();

    if(m_TimeSlicedClippingGeometry.IsNotNull())
    {
      timestep = m_TimeSlicedClippingGeometry->MSToTimeStep( timeInMS );
      if(m_TimeSlicedClippingGeometry->IsValidTime(timestep) == false)
        continue;

      clippingGeometryOfCurrentTimeStep = dynamic_cast<const Geometry2D*>(m_TimeSlicedClippingGeometry->GetGeometry3D(timestep));
    }

    AccessByItk_2(m_InputTimeSelector->GetOutput(),_InternalComputeClippedImage,this,clippingGeometryOfCurrentTimeStep);
  }

  m_TimeOfHeaderInitialization.Modified();
}

static IntensityProfile::Pointer ComputeIntensityProfile(Image::Pointer image, itk::PolyLineParametricPath<3>::Pointer path)
{
  IntensityProfile::Pointer intensityProfile = IntensityProfile::New();
  itk::PolyLineParametricPath<3>::InputType input = path->StartOfInput();
  BaseGeometry* imageGeometry = image->GetGeometry();
  const PixelType pixelType = image->GetPixelType();

  IntensityProfile::MeasurementVectorType measurementVector;
  itk::PolyLineParametricPath<3>::OffsetType offset;
  Point3D worldPoint;
  itk::Index<3> index;

  do
  {
    imageGeometry->IndexToWorld(path->Evaluate(input), worldPoint);
    imageGeometry->WorldToIndex(worldPoint, index);

    mitkPixelTypeMultiplex3(ReadPixel, pixelType, image, index, measurementVector.GetDataPointer());
    intensityProfile->PushBack(measurementVector);

    offset = path->IncrementInput(input);
  } while ((offset[0] | offset[1] | offset[2]) != 0);

  return intensityProfile;
}

ImageBinary::Pointer label2mask(Image::Pointer label, unsigned int element)
{
	ImageBinary::Pointer mask = ImageBinary::New();
	Image::RegionType region = label->GetLargestPossibleRegion();
	mask->SetRegions(region);
	mask->Allocate();
	mask->FillBuffer(0);


	ConstIterator iterator_label(label, label->GetLargestPossibleRegion());
	IteratorBinary iterator_mask(mask, mask->GetLargestPossibleRegion());	

	try
	{
		while(!iterator_label.IsAtEnd())
		{
			if(iterator_label.Get() == element && element || iterator_label.Get() != 0 && !element)
				iterator_mask.Set(1);
			++iterator_label; ++iterator_mask;
		}
	}
	catch(itk::ExceptionObject & err)
	{
		std::cerr<<"Exception caught, outside bounds using iterators"<<std::endl;
		std::cerr<<err<<std::endl;
	}

	return mask;
}

void mitk::SegTool2D::UpdateSurfaceInterpolation(const Image *slice,
                                                 const Image *workingImage,
                                                 const PlaneGeometry *plane,
                                                 bool detectIntersection)
{
  if (!m_SurfaceInterpolationEnabled)
    return;

  ImageToContourFilter::Pointer contourExtractor = ImageToContourFilter::New();
  mitk::Surface::Pointer contour;

  if (detectIntersection)
  {
    // Test whether there is something to extract or whether the slice just contains intersections of others
    mitk::Image::Pointer slice2 = slice->Clone();
    mitk::MorphologicalOperations::Erode(slice2, 2, mitk::MorphologicalOperations::Ball);

    contourExtractor->SetInput(slice2);
    contourExtractor->Update();
    contour = contourExtractor->GetOutput();

    if (contour->GetVtkPolyData()->GetNumberOfPoints() == 0)
    {
      // Remove contour!
      mitk::SurfaceInterpolationController::ContourPositionInformation contourInfo;
      contourInfo.contourNormal = plane->GetNormal();
      contourInfo.contourPoint = plane->GetOrigin();
      mitk::SurfaceInterpolationController::GetInstance()->RemoveContour(contourInfo);
      return;
    }
  }

  contourExtractor->SetInput(slice);
  contourExtractor->Update();
  contour = contourExtractor->GetOutput();

  mitk::ImageTimeSelector::Pointer timeSelector = mitk::ImageTimeSelector::New();
  timeSelector->SetInput(workingImage);
  timeSelector->SetTimeNr(0);
  timeSelector->SetChannelNr(0);
  timeSelector->Update();
  Image::Pointer dimRefImg = timeSelector->GetOutput();

  if (contour->GetVtkPolyData()->GetNumberOfPoints() != 0 && dimRefImg->GetDimension() == 3)
  {
    mitk::SurfaceInterpolationController::GetInstance()->AddNewContour(contour);
    contour->DisconnectPipeline();
  }
  else
  {
    // Remove contour!
    mitk::SurfaceInterpolationController::ContourPositionInformation contourInfo;
    contourInfo.contourNormal = plane->GetNormal();
    contourInfo.contourPoint = plane->GetOrigin();
    mitk::SurfaceInterpolationController::GetInstance()->RemoveContour(contourInfo);
  }
}

void mitk::BinaryThresholdULTool::CreateNewSegmentationFromThreshold(DataNode* node, const std::string& organName, const Color& color)
{
  if (node)
  {
    Image::Pointer image = dynamic_cast<Image*>( m_NodeForThresholding->GetData() );
    if (image.IsNotNull())
    {
      // create a new image of the same dimensions and smallest possible pixel type
      DataNode::Pointer emptySegmentation = Tool::CreateEmptySegmentationNode( image, organName, color );

      if (emptySegmentation)
      {
        // actually perform a thresholding and ask for an organ type
        for (unsigned int timeStep = 0; timeStep < image->GetTimeSteps(); ++timeStep)
        {
          try
          {
            ImageTimeSelector::Pointer timeSelector = ImageTimeSelector::New();
            timeSelector->SetInput( image );
            timeSelector->SetTimeNr( timeStep );
            timeSelector->UpdateLargestPossibleRegion();
            Image::Pointer image3D = timeSelector->GetOutput();

            AccessFixedDimensionByItk_2( image3D, ITKThresholding, 3, dynamic_cast<Image*>(emptySegmentation->GetData()), timeStep );
          }
          catch(...)
          {
            Tool::ErrorMessage("Error accessing single time steps of the original image. Cannot create segmentation.");
          }
        }

        //since we are maybe working on a smaller image, pad it to the size of the original image
        if (m_OriginalImageNode.GetPointer() != m_NodeForThresholding.GetPointer())
        {
          mitk::PadImageFilter::Pointer padFilter = mitk::PadImageFilter::New();

          padFilter->SetInput(0, dynamic_cast<mitk::Image*> (emptySegmentation->GetData()));
          padFilter->SetInput(1, dynamic_cast<mitk::Image*> (m_OriginalImageNode->GetData()));
          padFilter->SetBinaryFilter(true);
          padFilter->SetUpperThreshold(1);
          padFilter->SetLowerThreshold(1);
          padFilter->Update();

          emptySegmentation->SetData(padFilter->GetOutput());
        }

        if (DataStorage* ds = m_ToolManager->GetDataStorage())
        {
          ds->Add( emptySegmentation, m_OriginalImageNode );
        }

        m_ToolManager->SetWorkingData( emptySegmentation );
      }
    }
  }
}

  bool SegmentationSink::ReadyToRun()
  {
    Image::Pointer image;
    GetPointerParameter("Input", image);

    DataNode::Pointer groupNode;
    GetPointerParameter("Group node", groupNode);

    return image.IsNotNull() && groupNode.IsNotNull();
  }

mitk::Image::Pointer mitk::CompressedImageContainer::GetImage()
{
  if (m_ByteBuffers.empty())
    return nullptr;

  // uncompress image data, create an Image
  Image::Pointer image = Image::New();
  unsigned int dims[20]; // more than 20 dimensions and bang
  for (unsigned int dim = 0; dim < m_ImageDimension; ++dim)
    dims[dim] = m_ImageDimensions[dim];

  image->Initialize(*m_PixelType, m_ImageDimension, dims); // this IS needed, right ?? But it does allocate memory ->
                                                           // does create one big lump of memory (also in windows)

  unsigned int timeStep(0);
  for (auto iter = m_ByteBuffers.begin(); iter != m_ByteBuffers.end(); ++iter, ++timeStep)
  {
    ImageReadAccessor imgAcc(image, image->GetVolumeData(timeStep));
    auto *dest((unsigned char *)imgAcc.GetData());
    ::uLongf destLen(m_OneTimeStepImageSizeInBytes);
    ::Bytef *source(iter->first);
    ::uLongf sourceLen(iter->second);
    int zlibRetVal = ::uncompress(dest, &destLen, source, sourceLen);
    if (itk::Object::GetDebug())
    {
      if (zlibRetVal == Z_OK)
      {
        MITK_INFO << "Success, destLen now " << destLen << " bytes" << std::endl;
      }
      else
      {
        switch (zlibRetVal)
        {
          case Z_DATA_ERROR:
            MITK_ERROR << "compressed data corrupted" << std::endl;
            break;
          case Z_MEM_ERROR:
            MITK_ERROR << "not enough memory" << std::endl;
            break;
          case Z_BUF_ERROR:
            MITK_ERROR << "output buffer too small" << std::endl;
            break;
          default:
            MITK_ERROR << "other, unspecified error" << std::endl;
            break;
        }
      }
    }
  }

  image->SetGeometry(m_ImageGeometry);
  image->Modified();

  return image;
}

/*
 * Generate the information decribing the output data. The default
 * implementation of this method will copy information from the input to the
 * output. A filter may override this method if its output will have different
 * information than its input. For instance, a filter that shrinks an image will
 * need to provide an implementation for this method that changes the spacing of
 * the pixels. Such filters should call their superclass' implementation of this
 * method prior to changing the information values they need (i.e.
 * GenerateOutputInformation() should call
 * Superclass::GenerateOutputInformation() prior to changing the information.
 */
void mitk::ExtractImageFilter::GenerateOutputInformation()
{
 Image::Pointer output = this->GetOutput();
 Image::ConstPointer input = this->GetInput();
 if (input.IsNull()) return;

 if ( m_SliceDimension >= input->GetDimension() && input->GetDimension() != 2 )
 {
   MITK_ERROR << "mitk::ExtractImageFilter:GenerateOutputInformation  m_SliceDimension == " << m_SliceDimension << " makes no sense with an " << input->GetDimension() << "D image." << std::endl;
   itkExceptionMacro("This is not a sensible value for m_SliceDimension.");
   return;
 }

 unsigned int sliceDimension( m_SliceDimension );
 if ( input->GetDimension() == 2)
 {
   sliceDimension = 2;
 }

  unsigned int tmpDimensions[2];

  switch ( sliceDimension )
  {
    default:
    case 2: 
      // orientation = PlaneGeometry::Axial;
      tmpDimensions[0] = input->GetDimension(0);
      tmpDimensions[1] = input->GetDimension(1);
      break;
    case 1: 
      // orientation = PlaneGeometry::Frontal;
      tmpDimensions[0] = input->GetDimension(0);
      tmpDimensions[1] = input->GetDimension(2);
      break;
    case 0: 
      // orientation = PlaneGeometry::Sagittal;
      tmpDimensions[0] = input->GetDimension(1);
      tmpDimensions[1] = input->GetDimension(2);
      break;
  }

  output->Initialize(input->GetPixelType(), 2, tmpDimensions, 1 /*input->GetNumberOfChannels()*/);

  // initialize the spacing of the output
/*
  Vector3D spacing = input->GetSlicedGeometry()->GetSpacing();
  if(input->GetDimension()>=2)
    spacing[2]=spacing[1];
  else
    spacing[2] = 1.0;
  output->GetSlicedGeometry()->SetSpacing(spacing);
*/

  output->SetPropertyList(input->GetPropertyList()->Clone());
}