Esempio n. 1
0
  std::vector<itk::SmartPointer<BaseData> > NrrdTensorImageReader::Read()
  {
    std::vector<itk::SmartPointer<mitk::BaseData> > result;
    std::string location = GetInputLocation();

    if ( location == "")
    {
      throw itk::ImageFileReaderException(__FILE__, __LINE__, "Sorry, the filename is empty!");
    }
    else
    {
      try
      {
        mitk::LocaleSwitch localeSwitch("C");

        try
        {
          std::string fname3 = mitk::IOUtil::GetTempPath()+"/temp_dti.nii.gz";

          int c = 0;
          while( itksys::SystemTools::FileExists(fname3) )
          {
            fname3 = mitk::IOUtil::GetTempPath()+"/temp_dti_" + boost::lexical_cast<std::string>(c) + ".nii.gz";
            ++c;
          }

          itksys::SystemTools::CopyAFile(location.c_str(), fname3.c_str());

          typedef itk::VectorImage<float,3> ImageType;
          itk::NiftiImageIO::Pointer io = itk::NiftiImageIO::New();
          typedef itk::ImageFileReader<ImageType> FileReaderType;
          FileReaderType::Pointer reader = FileReaderType::New();
          reader->SetImageIO(io);
          reader->SetFileName(fname3);
          reader->Update();
          ImageType::Pointer img = reader->GetOutput();

          TensorImage::ItkTensorImageType::Pointer vecImg = TensorImage::ItkTensorImageType::New();
          vecImg->SetSpacing( img->GetSpacing() );   // Set the image spacing
          vecImg->SetOrigin( img->GetOrigin() );     // Set the image origin
          vecImg->SetDirection( img->GetDirection() );  // Set the image direction
          vecImg->SetRegions( img->GetLargestPossibleRegion());
          vecImg->Allocate();

          itk::ImageRegionIterator<TensorImage::ItkTensorImageType> ot (vecImg, vecImg->GetLargestPossibleRegion() );
          ot.GoToBegin();

          itk::ImageRegionIterator<ImageType> it (img, img->GetLargestPossibleRegion() );
          it.GoToBegin();

          typedef ImageType::PixelType  VarPixType;
          typedef TensorImage::PixelType FixPixType;
          int numComponents = img->GetNumberOfComponentsPerPixel();

          if (numComponents==6)
          {
            MITK_INFO << "Trying to load dti as 6-comp nifti ...";
            while (!it.IsAtEnd())
            {
              VarPixType vec = it.Get();
              FixPixType fixVec(vec.GetDataPointer());

              TensorImage::PixelType tensor;
              tensor.SetElement(0, vec.GetElement(0));
              tensor.SetElement(1, vec.GetElement(1));
              tensor.SetElement(2, vec.GetElement(2));
              tensor.SetElement(3, vec.GetElement(3));
              tensor.SetElement(4, vec.GetElement(4));
              tensor.SetElement(5, vec.GetElement(5));

              fixVec = tensor;

              ot.Set(fixVec);
              ++ot;
              ++it;
            }
          }
          else if(numComponents==9)
          {
            MITK_INFO << "Trying to load dti as 9-comp nifti ...";
            while (!it.IsAtEnd())
            {
              VarPixType vec = it.Get();
              TensorImage::PixelType tensor;
              tensor.SetElement(0, vec.GetElement(0));
              tensor.SetElement(1, vec.GetElement(1));
              tensor.SetElement(2, vec.GetElement(2));
              tensor.SetElement(3, vec.GetElement(4));
              tensor.SetElement(4, vec.GetElement(5));
              tensor.SetElement(5, vec.GetElement(8));

              FixPixType fixVec(tensor);
              ot.Set(fixVec);
              ++ot;
              ++it;
            }
          }
          else if (numComponents==1)
          {
            MITK_INFO << "Trying to load dti as 4D nifti ...";
            typedef itk::Image<float,4> ImageType;
            typedef itk::ImageFileReader<ImageType> FileReaderType;
            FileReaderType::Pointer reader = FileReaderType::New();
            reader->SetImageIO(io);
            reader->SetFileName(fname3);
            reader->Update();
            ImageType::Pointer img = reader->GetOutput();

            itk::Size<4> size = img->GetLargestPossibleRegion().GetSize();

            while (!ot.IsAtEnd())
            {
              TensorImage::PixelType tensor;
              ImageType::IndexType idx;
              idx[0] = ot.GetIndex()[0]; idx[1] = ot.GetIndex()[1]; idx[2] = ot.GetIndex()[2];

              if (size[3]==6)
              {
                for (unsigned int te=0; te<size[3]; te++)
                {
                  idx[3] = te;
                  tensor.SetElement(te, img->GetPixel(idx));
                }
              }
              else if (size[3]==9)
              {
                idx[3] = 0;
                tensor.SetElement(0, img->GetPixel(idx));
                idx[3] = 1;
                tensor.SetElement(1, img->GetPixel(idx));
                idx[3] = 2;
                tensor.SetElement(2, img->GetPixel(idx));
                idx[3] = 4;
                tensor.SetElement(3, img->GetPixel(idx));
                idx[3] = 5;
                tensor.SetElement(4, img->GetPixel(idx));
                idx[3] = 8;
                tensor.SetElement(5, img->GetPixel(idx));
              }
              else
                throw itk::ImageFileReaderException(__FILE__, __LINE__, "Unknown number of components for DTI file. Should be 6 or 9!");

              FixPixType fixVec(tensor);
              ot.Set(fixVec);
              ++ot;
            }
          }
          OutputType::Pointer resultImage = OutputType::New();
          resultImage->InitializeByItk( vecImg.GetPointer() );
          resultImage->SetVolume( vecImg->GetBufferPointer() );
          result.push_back( resultImage.GetPointer() );
        }
        catch(...)
        {
          MITK_INFO << "Trying to load dti as nrrd ...";

          typedef itk::VectorImage<float,3> ImageType;
          itk::NrrdImageIO::Pointer io = itk::NrrdImageIO::New();
          typedef itk::ImageFileReader<ImageType> FileReaderType;
          FileReaderType::Pointer reader = FileReaderType::New();
          reader->SetImageIO(io);
          reader->SetFileName(location);
          reader->Update();
          ImageType::Pointer img = reader->GetOutput();

          TensorImage::ItkTensorImageType::Pointer vecImg = TensorImage::ItkTensorImageType::New();
          vecImg->SetSpacing( img->GetSpacing() );   // Set the image spacing
          vecImg->SetOrigin( img->GetOrigin() );     // Set the image origin
          vecImg->SetDirection( img->GetDirection() );  // Set the image direction
          vecImg->SetRegions( img->GetLargestPossibleRegion());
          vecImg->Allocate();

          itk::ImageRegionIterator<TensorImage::ItkTensorImageType> ot (vecImg, vecImg->GetLargestPossibleRegion() );
          ot.GoToBegin();

          itk::ImageRegionIterator<ImageType> it (img, img->GetLargestPossibleRegion() );
          it.GoToBegin();

          typedef ImageType::PixelType  VarPixType;
          typedef TensorImage::PixelType FixPixType;
          int numComponents = img->GetNumberOfComponentsPerPixel();

          itk::MetaDataDictionary imgMetaDictionary = img->GetMetaDataDictionary();
          std::vector<std::string> imgMetaKeys = imgMetaDictionary.GetKeys();
          std::vector<std::string>::const_iterator itKey = imgMetaKeys.begin();
          std::string metaString;

          bool readFrame = false;
          double xx, xy, xz, yx, yy, yz, zx, zy, zz;
          MeasurementFrameType measFrame;
          measFrame.SetIdentity();
          MeasurementFrameType measFrameTransp;
          measFrameTransp.SetIdentity();

          for (; itKey != imgMetaKeys.end(); itKey ++)
          {
            itk::ExposeMetaData<std::string> (imgMetaDictionary, *itKey, metaString);
            if (itKey->find("measurement frame") != std::string::npos)
            {
              sscanf(metaString.c_str(), " ( %lf , %lf , %lf ) ( %lf , %lf , %lf ) ( %lf , %lf , %lf ) \n", &xx, &xy, &xz, &yx, &yy, &yz, &zx, &zy, &zz);

              if (xx>10e-10 || xy>10e-10 || xz>10e-10 ||
                yx>10e-10 || yy>10e-10 || yz>10e-10 ||
                zx>10e-10 || zy>10e-10 || zz>10e-10 )
              {
                readFrame = true;

                measFrame(0,0) = xx;
                measFrame(0,1) = xy;
                measFrame(0,2) = xz;
                measFrame(1,0) = yx;
                measFrame(1,1) = yy;
                measFrame(1,2) = yz;
                measFrame(2,0) = zx;
                measFrame(2,1) = zy;
                measFrame(2,2) = zz;

                measFrameTransp = measFrame.GetTranspose();
              }
            }
          }

          if (numComponents==6)
          {
            while (!it.IsAtEnd())
            {
              // T'=RTR'
              VarPixType vec = it.Get();
              FixPixType fixVec(vec.GetDataPointer());

              if(readFrame)
              {
                TensorImage::PixelType tensor;
                tensor.SetElement(0, vec.GetElement(0));
                tensor.SetElement(1, vec.GetElement(1));
                tensor.SetElement(2, vec.GetElement(2));
                tensor.SetElement(3, vec.GetElement(3));
                tensor.SetElement(4, vec.GetElement(4));
                tensor.SetElement(5, vec.GetElement(5));

                tensor = ConvertMatrixTypeToFixedArrayType(tensor.PreMultiply(measFrame));
                tensor = ConvertMatrixTypeToFixedArrayType(tensor.PostMultiply(measFrameTransp));
                fixVec = tensor;
              }

              ot.Set(fixVec);
              ++ot;
              ++it;
            }
          }
          else if(numComponents==9)
          {
            while (!it.IsAtEnd())
            {
              VarPixType vec = it.Get();
              TensorImage::PixelType tensor;
              tensor.SetElement(0, vec.GetElement(0));
              tensor.SetElement(1, vec.GetElement(1));
              tensor.SetElement(2, vec.GetElement(2));
              tensor.SetElement(3, vec.GetElement(4));
              tensor.SetElement(4, vec.GetElement(5));
              tensor.SetElement(5, vec.GetElement(8));

              if(readFrame)
              {
                tensor = ConvertMatrixTypeToFixedArrayType(tensor.PreMultiply(measFrame));
                tensor = ConvertMatrixTypeToFixedArrayType(tensor.PostMultiply(measFrameTransp));
              }

              FixPixType fixVec(tensor);
              ot.Set(fixVec);
              ++ot;
              ++it;
            }
          }
          else if (numComponents==1)
          {
            typedef itk::Image<float,4> ImageType;
            itk::NrrdImageIO::Pointer io = itk::NrrdImageIO::New();
            typedef itk::ImageFileReader<ImageType> FileReaderType;
            FileReaderType::Pointer reader = FileReaderType::New();
            reader->SetImageIO(io);
            reader->SetFileName(location);
            reader->Update();
            ImageType::Pointer img = reader->GetOutput();

            itk::Size<4> size = img->GetLargestPossibleRegion().GetSize();

            while (!ot.IsAtEnd())
            {
              TensorImage::PixelType tensor;
              ImageType::IndexType idx;
              idx[0] = ot.GetIndex()[0]; idx[1] = ot.GetIndex()[1]; idx[2] = ot.GetIndex()[2];

              if (size[3]==6)
              {
                for (unsigned int te=0; te<size[3]; te++)
                {
                  idx[3] = te;
                  tensor.SetElement(te, img->GetPixel(idx));
                }
              }
              else if (size[3]==9)
              {
                idx[3] = 0;
                tensor.SetElement(0, img->GetPixel(idx));
                idx[3] = 1;
                tensor.SetElement(1, img->GetPixel(idx));
                idx[3] = 2;
                tensor.SetElement(2, img->GetPixel(idx));
                idx[3] = 4;
                tensor.SetElement(3, img->GetPixel(idx));
                idx[3] = 5;
                tensor.SetElement(4, img->GetPixel(idx));
                idx[3] = 8;
                tensor.SetElement(5, img->GetPixel(idx));
              }
              else
                throw itk::ImageFileReaderException(__FILE__, __LINE__, "Unknown number of komponents for DTI file. Should be 6 or 9!");

              if(readFrame)
              {
                tensor = ConvertMatrixTypeToFixedArrayType(tensor.PreMultiply(measFrame));
                tensor = ConvertMatrixTypeToFixedArrayType(tensor.PostMultiply(measFrameTransp));
              }
              FixPixType fixVec(tensor);
              ot.Set(fixVec);
              ++ot;
            }
          }
          else
          {
            throw itk::ImageFileReaderException(__FILE__, __LINE__, "Image has wrong number of pixel components!");
          }

          OutputType::Pointer resultImage = OutputType::New();
          resultImage->InitializeByItk( vecImg.GetPointer() );
          resultImage->SetVolume( vecImg->GetBufferPointer() );
          result.push_back( resultImage.GetPointer() );
        }

      }
      catch(std::exception& e)
      {
        throw itk::ImageFileReaderException(__FILE__, __LINE__, e.what());
      }
      catch(...)
      {
        throw itk::ImageFileReaderException(__FILE__, __LINE__, "Sorry, an error occurred while reading the requested DTI file!");
      }
    }

    return result;
  }
Esempio n. 2
0
  std::vector<itk::SmartPointer<BaseData> > NrrdQBallImageReader::Read()
  {
    std::vector<itk::SmartPointer<mitk::BaseData> > result;
    std::string location = GetInputLocation();

    if ( location == "")
    {
      throw itk::ImageFileReaderException(__FILE__, __LINE__, "Sorry, the filename of the vessel tree to be read is empty!");
    }
    else
    {
      try
      {
        const std::string& locale = "C";
        const std::string& currLocale = setlocale( LC_ALL, NULL );

        if ( locale.compare(currLocale)!=0 )
        {
          try
          {
            setlocale(LC_ALL, locale.c_str());
          }
          catch(...)
          {
            MITK_INFO << "Could not set locale " << locale;
          }
        }

        typedef itk::VectorImage<float,3> ImageType;
        itk::NrrdImageIO::Pointer io = itk::NrrdImageIO::New();
        typedef itk::ImageFileReader<ImageType> FileReaderType;
        FileReaderType::Pointer reader = FileReaderType::New();
        reader->SetImageIO(io);
        reader->SetFileName(location);
        reader->Update();
        ImageType::Pointer img = reader->GetOutput();

        typedef itk::Image<itk::Vector<float,QBALL_ODFSIZE>,3> VecImgType;
        VecImgType::Pointer vecImg = VecImgType::New();
        vecImg->SetSpacing( img->GetSpacing() );   // Set the image spacing
        vecImg->SetOrigin( img->GetOrigin() );     // Set the image origin
        vecImg->SetDirection( img->GetDirection() );  // Set the image direction
        vecImg->SetLargestPossibleRegion( img->GetLargestPossibleRegion());
        vecImg->SetBufferedRegion( img->GetLargestPossibleRegion() );
        vecImg->Allocate();

        itk::ImageRegionIterator<VecImgType> ot (vecImg, vecImg->GetLargestPossibleRegion() );
        ot.GoToBegin();

        itk::ImageRegionIterator<ImageType> it (img, img->GetLargestPossibleRegion() );

        typedef ImageType::PixelType  VarPixType;
        typedef VecImgType::PixelType FixPixType;

        for (it.GoToBegin(); !it.IsAtEnd(); ++it)
        {
          VarPixType vec = it.Get();
          FixPixType fixVec(vec.GetDataPointer());
          ot.Set(fixVec);
          ++ot;
        }

        OutputType::Pointer resultImage = OutputType::New();
        resultImage->InitializeByItk( vecImg.GetPointer() );
        resultImage->SetVolume( vecImg->GetBufferPointer() );
        result.push_back( resultImage.GetPointer() );

        try
        {
          setlocale(LC_ALL, currLocale.c_str());
        }
        catch(...)
        {
          MITK_INFO << "Could not reset locale " << currLocale;
        }
      }
      catch(std::exception& e)
      {
        throw itk::ImageFileReaderException(__FILE__, __LINE__, e.what());
      }
      catch(...)
      {
        throw itk::ImageFileReaderException(__FILE__, __LINE__, "Sorry, an error occurred while reading the requested vessel tree file!");
      }
    }
    return result;
  }