void itk::ConnectomicsNetworkToConnectivityMatrixImageFilter::GenerateData()
{

  this->AllocateOutputs();

  OutputImageType::Pointer output = this->GetOutput();

  if(m_InputNetwork.IsNull())
  {
    MITK_ERROR << "Failed to generate data, no valid network was set.";
    return;
  }

  typedef mitk::ConnectomicsNetwork::NetworkType NetworkType;
  typedef boost::graph_traits< NetworkType >::vertex_descriptor DescriptorType;
  typedef boost::graph_traits< NetworkType >::vertex_iterator IteratorType;

  // prepare connectivity matrix for data
  std::vector< std::vector< int > > connectivityMatrix;
  int numberOfVertices = m_InputNetwork->GetNumberOfVertices();

  connectivityMatrix.resize( numberOfVertices );
  for( int index(0); index < numberOfVertices; index++ )
  {
    connectivityMatrix[ index ].resize( numberOfVertices );
  }

  // Create LabelToIndex translation
  std::map< std::string, DescriptorType > labelToIndexMap;

  NetworkType boostGraph = *(m_InputNetwork->GetBoostGraph());

  // translate index to label
  IteratorType iterator, end;
  boost::tie(iterator, end) = boost::vertices( boostGraph );

  for ( ; iterator != end; ++iterator)
  {
    labelToIndexMap.insert(
      std::pair< std::string, DescriptorType >(
      boostGraph[ *iterator ].label, *iterator )
      );
  }

  std::vector< std::string > indexToLabel;

  // translate index to label
  indexToLabel.resize( numberOfVertices );

  boost::tie(iterator, end) = boost::vertices( boostGraph );

  for ( ; iterator != end; ++iterator)
  {
    indexToLabel[ *iterator ] = boostGraph[ *iterator ].label;
  }

  //translate label to position
  std::vector< std::string > positionToLabelVector;
  positionToLabelVector = indexToLabel;

  std::sort ( positionToLabelVector.begin(), positionToLabelVector.end() );

  for( int outerLoop( 0 ); outerLoop < numberOfVertices; outerLoop++  )
  {
    DescriptorType fromVertexDescriptor = labelToIndexMap.find( positionToLabelVector[ outerLoop ] )->second;
    for( int innerLoop( outerLoop + 1 ); innerLoop < numberOfVertices; innerLoop++  )
    {
      DescriptorType toVertexDescriptor = labelToIndexMap.find( positionToLabelVector[ innerLoop ] )->second;


      int weight( 0 );

      if( boost::edge(toVertexDescriptor, fromVertexDescriptor, boostGraph ).second )
      {
        weight = m_InputNetwork->GetEdge( fromVertexDescriptor , toVertexDescriptor ).weight;;
      }
      connectivityMatrix[outerLoop][innerLoop] = weight;
      connectivityMatrix[innerLoop][outerLoop] = weight;
    }
  }


  OutputImageType::SpacingType spacing;
  spacing[0] = 1.0;
  spacing[1] = 1.0;
  OutputImageType::PointType origin;
  origin[0] = 0.0;
  origin[1] = 0.0;
  OutputImageType::IndexType index;
  index[0] = 0.0;
  index[1] = 0.0;
  OutputImageType::SizeType size;
  size[0] = numberOfVertices;
  size[1] = numberOfVertices;
  OutputImageType::RegionType region;
  region.SetIndex( index );
  region.SetSize( size );

  output->SetSpacing( spacing );   // Set the image spacing
  output->SetOrigin( origin );     // Set the image origin
  output->SetRegions( region );
  output->Allocate();
  output->FillBuffer(0);


  itk::ImageRegionIterator< OutputImageType > it_connect(output, output->GetLargestPossibleRegion());

  int counter( 0 );

  double rescaleFactor( 1.0 );
  double rescaleMax( 255.0 );

  if( m_RescaleConnectivity )
  {
    rescaleFactor = rescaleMax / m_InputNetwork->GetMaximumWeight();
  }

  // Colour pixels according to connectivity
  if(  m_BinaryConnectivity )
  {
    // binary connectivity
    while( !it_connect.IsAtEnd() )
    {
      if( connectivityMatrix[ ( counter - counter % numberOfVertices ) / numberOfVertices][ counter % numberOfVertices ] )
      {
        it_connect.Set( 1 );
      }
      else
      {
        it_connect.Set( 0 );
      }
      ++it_connect;
      counter++;
    }
  }
  else
  {
    // if desired rescale to the 0-255 range
    while( !it_connect.IsAtEnd() )
    {
      it_connect.Set( ( unsigned short ) rescaleFactor *
        connectivityMatrix[ ( counter - counter % numberOfVertices ) / numberOfVertices][ counter % numberOfVertices ]
      );
      ++it_connect;
      counter++;
    }
  }

}
Example #2
0
int runGrAnisDiff(unsigned char* imgIn, int r, int c, int z, int iter, int timeStep, int comductance)
{
	
	//pixel types
	typedef unsigned char InputPixelType;
	typedef float OutputPixelType;
	typedef itk::Image< InputPixelType, 3 > InputImageType;
	typedef itk::Image< OutputPixelType, 3 > OutputImageType;
	
	//create an ITK image from the input image
	OutputImageType::Pointer im;
	im = OutputImageType::New();
	OutputImageType::PointType origin;
    origin[0] = 0.; 
    origin[1] = 0.;    
	origin[2] = 0.;    
    im->SetOrigin( origin );

    OutputImageType::IndexType start;
    start[0] =   0;  // first index on X
    start[1] =   0;  // first index on Y    
	start[2] =   0;  // first index on Z    
    OutputImageType::SizeType  size;
    size[0]  = c;  // size along X
    size[1]  = r;  // size along Y
	size[2]  = z;  // size along Z
  
    OutputImageType::RegionType region;
    region.SetSize( size );
    region.SetIndex( start );
    
 //   double spacing[3];
	//spacing[0] = 1; //spacing along x
	//spacing[1] = 1; //spacing along y
	//spacing[2] = sampl_ratio; //spacing along z

    im->SetRegions( region );
	//im->SetSpacing(spacing);
    im->Allocate();
    im->FillBuffer(0);
	im->Update();	
	
	//copy the input image into the ITK image
	typedef itk::ImageRegionIteratorWithIndex< OutputImageType > IteratorType;
	IteratorType iterator1(im,im->GetRequestedRegion());
	
	for(int i=0; i<r*c*z; i++)
	{					
		iterator1.Set((float)imgIn[i]);
		++iterator1;		
	}

	//apply gradient anisotropic diffusion
	typedef itk::GradientAnisotropicDiffusionImageFilter< OutputImageType, OutputImageType > FilterType;
	FilterType::Pointer filter = FilterType::New();
	filter->SetInput( im );

	filter->SetNumberOfIterations( iter );
	filter->SetTimeStep( timeStep );
	filter->SetConductanceParameter( comductance );

	try
	{
		filter->Update();
	}
	catch( itk::ExceptionObject & err ) 
    { 
		std::cerr << err << std::endl;
		return 0;
	}

	typedef itk::RescaleIntensityImageFilter< OutputImageType, InputImageType > RescaleFilterType;

	RescaleFilterType::Pointer rescaler = RescaleFilterType::New();
	rescaler->SetOutputMinimum(   0 );
	rescaler->SetOutputMaximum( 255 );
	rescaler->SetInput( filter->GetOutput() );
	rescaler->Update();

	//overwrite the input image for now in order to save space
	typedef itk::ImageRegionIteratorWithIndex< InputImageType > IteratorType2;
	IteratorType2 iterator2(rescaler->GetOutput(),rescaler->GetOutput()->GetRequestedRegion());
	
	for(int i=0; i<r*c*z; i++)
	{					
		imgIn[i] = iterator2.Get();
		++iterator2;		
	}

	return 1;
}
Example #3
0
void segmentation::on_abnormalRegionSegButton_clicked()
{
    fstream fin11, fin12; 
    char* s11Txt = ("../data/ped/txt/15715_11.txt");//s11.txt
    char* s12Txt = ("../data/ped/txt/15715_12.txt");
    int (*s11)[512] = new int[64][512];
    int (*s12)[512] = new int[64][512];
    int (*p)[512] = new int[64][512];
    //read TXT
    fin11.open(s11Txt, ios::in); 
    fin12.open(s12Txt, ios::in);
    //get the p matrix
    for(int z = 0; z < 64; z++)
    {
        for(int x = 0; x < 512; x++)
        {
            fin11>>s11[z][x];
            fin12>>s12[z][x];
            if(s12[z][x] - s11[z][x] > 5)  //5 threshold  
                p[z][x] = 1;
            else 
                p[z][x] = 0;
        }
    }
    fin11.close();
    fin12.close();
    //read filtered MHD data
    typedef itk::Image<unsigned short, 3>InputImageType; 
    typedef itk::Image<unsigned short, 3>OutputImageType;
    typedef itk::Image<unsigned char, 3>InitOutputImageType;
    InputImageType::Pointer inputImage = InputImageType::New();
    OutputImageType::Pointer outputImage = OutputImageType::New();
    InitOutputImageType::Pointer initOutputImage = InitOutputImageType::New();
    typedef itk::ImageFileReader<InputImageType>ReaderType;
    ReaderType::Pointer reader = ReaderType::New();
    reader->SetFileName(inputFileName);//读入原图像
    reader->Update();
    inputImage = reader->GetOutput();
    InputImageType::IndexType voxelIndex;
    InitOutputImageType::IndexType initvoxelIndex;
    OutputImageType::IndexType newvoxelIndex;
    InputImageType::SizeType imgSize = inputImage->GetLargestPossibleRegion().GetSize();
    OutputImageType::IndexType index;
    index[0] = 0;
    index[1] = 0;
    index[2] = 0;
    OutputImageType::SizeType size;
    size[0] = imgSize[0];
    size[1] = imgSize[1];
    size[2] = imgSize[2];
    //create a region for initial result
    InitOutputImageType::RegionType initRegion;
    initRegion.SetIndex(index);
    initRegion.SetSize(size);
    initOutputImage->SetRegions( initRegion);
    initOutputImage->Allocate();
    //create a region for enhance result
    OutputImageType::RegionType region;
    region.SetIndex(index);
    region.SetSize(size);
    outputImage->SetRegions(region);
    outputImage->Allocate();
    //Initial result for PED segmentation  (a binary image)
    for(int z = 0; z < imgSize[2]; z++)
        for(int x = 0; x < imgSize[0]; x++)
        {
            initvoxelIndex[0] = x;
            initvoxelIndex[2] = z;
            for(int y = 0; y < imgSize[1]; y++)
            {
                //set all background a black region
                initvoxelIndex[1] = y;
                initOutputImage->SetPixel(initvoxelIndex, 0);
            }
            //set the same intensity for all PED region (empirical value)
            if(p[z][x] == 1)
            {
                for(int y = s11[z][x]; y <= s12[z][x]; y++) 
                {
                    initvoxelIndex[1] = y;
                    initOutputImage->SetPixel(initvoxelIndex, 255);//亮区域
                }
            }
        }
        //输出中间分割结果
        //文件前缀名
        filePrefix = inputFileName;//char* to string
        filePrefix = filePrefix.substr(0, filePrefix.length() - 4);
        string strInitFileName;
        strInitFileName = filePrefix + "_initBinaryImg.mhd";
        strcpy(initFileName, strInitFileName.c_str());//string to char*
        typedef itk::ImageFileWriter<InitOutputImageType>InitWriterType;
        InitWriterType::Pointer initWriter = InitWriterType::New();
        initWriter->SetFileName(initFileName);//生成二值图
        initWriter->SetInput(initOutputImage);
        initWriter->Update();
        //Enhance PED region and overlay it on the original image
        for(int z = 0; z < imgSize[2]; z++)
            for(int x = 0; x < imgSize[0]; x++)
            {
                voxelIndex[0] = x;
                voxelIndex[2] = z;
                newvoxelIndex[0] = x;
                newvoxelIndex[2] = z;
                for(int y = 0; y < imgSize[1]; y++)
                {
                    voxelIndex[1] = y;
                    newvoxelIndex[1] = y;
                    outputImage->SetPixel(newvoxelIndex, inputImage->GetPixel(voxelIndex));
                }
                //set the same intensity for all PED region (empirical value)
                if(p[z][x] == 1)
                {
                    for(int y = s11[z][x]; y <= s12[z][x]; y++) 
                    {
                        newvoxelIndex[1] = y;
                        outputImage->SetPixel(newvoxelIndex, 65535);//亮区域
                    }
                }
            }
            //释放内存不能缺省
            delete[]s11;
            delete[]s12;
            delete[]p;

            typedef itk::ImageFileWriter<OutputImageType>WriterType;
            WriterType::Pointer writer = WriterType::New();
            filePrefix = filePrefix + "_initResult.mhd";
            strcpy(outputFileName, filePrefix.c_str());//string to char*
            initResultFileName = outputFileName;//输出初始分割结果,二值图重叠在原图像上面
            writer->SetFileName(outputFileName);
            writer->SetInput(outputImage);
            writer->Update();

            emit returnOutputFileName(outputFileName);//发出信号
}
int main(int argc, char** argv) {

    if (argc < 5) {
        std::cerr << "From the 3 images representing fiber orientation estimate angles and calculate angle homogeneity in the neighborhoods." << std::endl;
        std::cerr << "Usage: CalculateEntropyFiberAngles coordx_image coordy_image coordz_image out_image neigborhood_radius" << std::endl;
        return EXIT_FAILURE;
    }

    //parsing parameters
    int c = 1;
    const char* imagex_filename = argv[c++];
    const char* imagey_filename = argv[c++];
    const char* imagez_filename = argv[c++];
    const char* output_filename = argv[c++];
    int neighborhood_radius = atoi(argv[c++]);


    const unsigned int Dimension = 3;

    std::cout << "Input x: " << imagex_filename << std::endl;
    std::cout << "Input y: " << imagey_filename << std::endl;
    std::cout << "Input z: " << imagez_filename << std::endl;
    std::cout << "Output: " << output_filename << std::endl;
    std::cout << "Neighborhood radius: " << neighborhood_radius << std::endl;



    //main program
    typedef float InputPixelType;
    typedef float OutputPixelType;
    typedef itk::Image< InputPixelType, Dimension > InputImageType;
    typedef itk::Image< OutputPixelType, Dimension > OutputImageType;
    typedef itk::ImageFileReader< InputImageType > ReaderType;
    typedef itk::ImageFileWriter< OutputImageType > WriterType;
    ReaderType::Pointer readerx = ReaderType::New();
    ReaderType::Pointer readery = ReaderType::New();
    ReaderType::Pointer readerz = ReaderType::New();
    WriterType::Pointer writer = WriterType::New();
    readerx->SetFileName(imagex_filename);
    readery->SetFileName(imagex_filename);
    readerz->SetFileName(imagex_filename);
    writer->SetFileName(output_filename);



    std::cout<<"Reading X"<<std::endl;
    readerx->Update();
    std::cout<<"Reading Y"<<std::endl;
    readery->Update();
    std::cout<<"Reading Z"<<std::endl;
    readerz->Update();

    
    const InputImageType * inputx = readerx->GetOutput();
    const InputImageType * inputy = readery->GetOutput();
    const InputImageType * inputz = readerz->GetOutput();


    //create the output image
    OutputImageType::Pointer image = OutputImageType::New();
    image->SetRegions(inputx->GetLargestPossibleRegion());
    image->SetSpacing(inputx->GetSpacing());
    image->SetOrigin(inputx->GetOrigin());
    image->Allocate();
    image->FillBuffer(0);

    
    InputImageType::SizeType radius;
    radius[0] = neighborhood_radius;
    radius[1] = neighborhood_radius;
    radius[2] = neighborhood_radius;
    
    itk::ConstNeighborhoodIterator<InputImageType> 
            iteratorx(radius, inputx, image->GetRequestedRegion());
    itk::ConstNeighborhoodIterator<InputImageType> 
            iteratory(radius, inputy, image->GetRequestedRegion());
    itk::ConstNeighborhoodIterator<InputImageType> 
            iteratorz(radius, inputz, image->GetRequestedRegion());

    itk::ImageRegionIterator<OutputImageType>  it( image, image->GetRequestedRegion() );
    
    iteratorx.GoToBegin();
    iteratory.GoToBegin();
    iteratorz.GoToBegin();
    it.GoToBegin();
  
    const unsigned int nneighbors = (neighborhood_radius*2+1)*(neighborhood_radius*2+1)*(neighborhood_radius*2+1);
    Eigen::MatrixXf neighbors( nneighbors-1, 3 ); //to store the vectors
    Eigen::Vector3f central_vector;
    
    int c_id = (int) (nneighbors / 2); // get offset of center pixel
    
    
    //check image size for the progress indicator
    OutputImageType::RegionType region = image->GetLargestPossibleRegion();
    OutputImageType::SizeType size = region.GetSize();
    const unsigned long int npixels = size[0]*size[1]*size[2];
    
    unsigned long int k = 0;
    while ( ! iteratorx.IsAtEnd() )
    {
        if(k%10000 == 0)
        {
            std::cout<<"Processed "<<k<<"/"<<npixels<<"\r"<<std::flush;
        }
            
        k++;
            
        unsigned int j = 0;
        for (unsigned int i = 0; i < nneighbors; ++i)
        {    
            if(i!=c_id) //exclude the center
            {
                neighbors(j, 0) = iteratorx.GetPixel(i);  
                neighbors(j, 1) = iteratory.GetPixel(i);  
                neighbors(j, 2) = iteratorz.GetPixel(i);  
                j++;
            }
            else
            {
                central_vector(0) = iteratorx.GetPixel(i);  
                central_vector(1) = iteratory.GetPixel(i);  
                central_vector(2) = iteratorz.GetPixel(i);                  
            }
        }
        
        // calculate the angles 
        Eigen::VectorXf dp = neighbors*central_vector;
        
        const float variance = ((dp.array()-dp.mean()).pow(2)).mean();
        it.Set(variance);        
        
        ++iteratorx;
        ++iteratory;
        ++iteratorz;
        ++it;
    }    
    std::cout<<std::endl;
    
    //  The output of the resampling filter is connected to a writer and the
    //  execution of the pipeline is triggered by a writer update.
    try {
        writer->SetInput(image);
        writer->Update();
    } catch (itk::ExceptionObject & excep) {
        std::cerr << "Exception caught !" << std::endl;
        std::cerr << excep << std::endl;
    }

    

    
    return EXIT_SUCCESS;
}
void IntrinsicFeatureCalculator::GetDistanceToSurfaceMeasures(vtkSmartPointer<vtkTable> table, std::vector< ftk::Object::Point > surfacePoints)
{
	typedef itk::Image< IPixelT, 3 > InputImageType;
	typedef itk::Image< LPixelT, 3 > OutputImageType;
	typedef itk::DanielssonDistanceMapImageFilter< OutputImageType, OutputImageType > DanielssonFilterType;
	typedef itk::RescaleIntensityImageFilter< OutputImageType, OutputImageType > RescalerType;
	typedef itk::ImageFileReader< InputImageType  >  ReaderType;
	typedef itk::ImageFileWriter< InputImageType >  InputWriterType;
	typedef itk::ImageFileWriter< OutputImageType >  WriterType;
	typedef itk::LineIterator< OutputImageType > LineIteratorType;

	vtkSmartPointer<vtkDoubleArray> column = vtkSmartPointer<vtkDoubleArray>::New();
	column->SetName( "Dist_To_Surface" );
	column->SetNumberOfValues( table->GetNumberOfRows() );
	table->AddColumn(column);	

	OutputImageType::Pointer im;
	im = OutputImageType::New();
	OutputImageType::PointType origin;
    origin[0] = 0; 
    origin[1] = 0;    
	origin[2] = 0;    
    im->SetOrigin( origin );

    OutputImageType::IndexType start;
    start[0] =   0;  // first index on X
    start[1] =   0;  // first index on Y    
	start[2] =   0;  // first index on Z    
    
	OutputImageType::Pointer temp_image = labelImage->GetItkPtr< LPixelT >(0,0);
	itk::Size<3> im_size = temp_image->GetBufferedRegion().GetSize();
	im_size[2] = 1;
  
    InputImageType::RegionType region;
    region.SetSize( im_size );
    region.SetIndex( start );
    
    im->SetRegions( region );
    im->Allocate();
    im->FillBuffer(0);
	im->Update();
	
	//copy the input image into the ITK image
	for(int p = 1; p < (int)surfacePoints.size(); ++p)
	{
		itk::Index<3> indx,indy;
		indx[0] = surfacePoints[p-1].x;
		indx[1] = surfacePoints[p-1].y;
		indx[2] = 0;
		indy[0] = surfacePoints[p].x;
		indy[1] = surfacePoints[p].y;
		indy[2] = 0;
		LineIteratorType it( im, indx, indy );
		//it.GoToBegin();
		//while(!it.IsAtEnd())
		for(it.GoToBegin(); !it.IsAtEnd(); ++it)
		{
			it.Set(255);			
		}
	}

	DanielssonFilterType::Pointer danielssonFilter = DanielssonFilterType::New();	
	WriterType::Pointer writer = WriterType::New();	
	danielssonFilter->SetInput( im );
	writer->SetFileName( "DistanceMap.tif" );
	danielssonFilter->InputIsBinaryOn();
	danielssonFilter->Update();
	OutputImageType::Pointer distMap = danielssonFilter->GetOutput();
	writer->SetInput( distMap );
	writer->Update();
	
	for(int row=0; row<(int)table->GetNumberOfRows(); ++row)
	{
		OutputImageType::IndexType indx;
		indx[0] = table->GetValue(row, 1).ToInt();
		indx[1] = table->GetValue(row, 2).ToInt();
		indx[2] = 0;
		int dist = distMap->GetPixel(indx);
		table->SetValueByName(row, "Dist_To_Surface", vtkVariant(dist));
	}



}