void mitk::ContourUtils::FillContourInSlice( ContourModel* projectedContour, unsigned int timeStep, Image* sliceImage, int paintingPixelValue )
{
// 1. Use ipSegmentation to draw a filled(!) contour into a new 8 bit 2D image, which will later be copied back to the slice.
// We don't work on the "real" working data, because ipSegmentation would restrict us to 8 bit images
// convert the projected contour into a ipSegmentation format
mitkIpInt4_t* picContour = new mitkIpInt4_t[2 * projectedContour->GetNumberOfVertices(timeStep)];
unsigned int index(0);
ContourModel::VertexIterator iter = projectedContour->Begin(timeStep);
ContourModel::VertexIterator end = projectedContour->End(timeStep);
while( iter != end)
{
picContour[ 2 * index + 0 ] = static_cast<mitkIpInt4_t>( (*iter)->Coordinates[0] + 1.0 ); // +0.5 wahrscheinlich richtiger
picContour[ 2 * index + 1 ] = static_cast<mitkIpInt4_t>( (*iter)->Coordinates[1] + 1.0 );
//MITK_INFO << "mitk 2d [" << (*iter)[0] << ", " << (*iter)[1] << "] pic [" << picContour[ 2*index+0] << ", " << picContour[ 2*index+1] << "]";
iter++;
index++;
}
assert( sliceImage->GetSliceData() );
mitkIpPicDescriptor* originalPicSlice = mitkIpPicNew();
CastToIpPicDescriptor( sliceImage, originalPicSlice);
mitkIpPicDescriptor* picSlice = ipMITKSegmentationNew( originalPicSlice );
ipMITKSegmentationClear( picSlice );
assert( originalPicSlice && picSlice );
// here comes the actual contour filling algorithm (from ipSegmentation/Graphics Gems)
ipMITKSegmentationCombineRegion ( picSlice, picContour, projectedContour->GetNumberOfVertices(timeStep), NULL, IPSEGMENTATION_OR, 1); // set to 1
delete[] picContour;
// 2. Copy the filled contour to the working data slice
// copy all pixels that are non-zero to the original image (not caring for the actual type of the working image). perhaps make the replace value a parameter ( -> general painting tool ).
// make the pic slice an mitk/itk image (as little ipPic code as possible), call a templated method with accessbyitk, iterate over the original and the modified slice
Image::Pointer ipsegmentationModifiedSlice = Image::New();
ipsegmentationModifiedSlice->Initialize( CastToImageDescriptor( picSlice ) );
ipsegmentationModifiedSlice->SetSlice( picSlice->data );
AccessFixedDimensionByItk_2( sliceImage, ItkCopyFilledContourToSlice, 2, ipsegmentationModifiedSlice, paintingPixelValue );
ipsegmentationModifiedSlice = NULL; // free MITK header information
ipMITKSegmentationFree( picSlice ); // free actual memory
}
void ToFNrrdImageWriter::ConvertStreamToNrrdFormat( std::string fileName )
{
int CaptureWidth = 0;
int CaptureHeight = 0;
int PixelNumber = 0;
int ImageSizeInBytes = 0;
if (fileName==this->m_RGBImageFileName)
{
CaptureWidth = this->m_RGBCaptureWidth;
CaptureHeight = this->m_RGBCaptureHeight;
PixelNumber = this->m_RGBPixelNumber;
ImageSizeInBytes = this->m_RGBImageSizeInBytes;
} else
{
CaptureWidth = this->m_ToFCaptureWidth;
CaptureHeight = this->m_ToFCaptureHeight;
PixelNumber = this->m_ToFPixelNumber;
ImageSizeInBytes = this->m_ToFImageSizeInBytes;
}
Image::Pointer imageTemplate = Image::New();
int dimension ;
unsigned int* dimensions;
if(m_ToFImageType == ToFImageType2DPlusT)
{
dimension = 4;
dimensions = new unsigned int[dimension];
dimensions[0] = CaptureWidth;
dimensions[1] = CaptureHeight;
dimensions[2] = 1;
dimensions[3] = this->m_NumOfFrames;
}
else if( m_ToFImageType == ToFImageType3D)
{
dimension = 3;
dimensions = new unsigned int[dimension];
dimensions[0] = CaptureWidth;
dimensions[1] = CaptureHeight;
dimensions[2] = this->m_NumOfFrames;
}
else
{
throw std::logic_error("No image type set, please choose between 2D+t and 3D!");
}
float* floatData;
unsigned char* rgbData;
if (fileName==this->m_RGBImageFileName)
{
rgbData = new unsigned char[PixelNumber*3];
for(int i=0; i<PixelNumber*3; i++)
{
rgbData[i] = i + 0.0;
}
mitk::PixelType RGBType = MakePixelType<unsigned char, itk::RGBPixel<unsigned char>, 3>();
imageTemplate->Initialize( RGBType,dimension, dimensions, 1);
imageTemplate->SetSlice(rgbData, 0, 0, 0);
}
else
{
floatData = new float[PixelNumber];
for(int i=0; i<PixelNumber; i++)
{
floatData[i] = i + 0.0;
}
mitk::PixelType FloatType = MakeScalarPixelType<float>();
imageTemplate->Initialize( FloatType,dimension, dimensions, 1);
imageTemplate->SetSlice(floatData, 0, 0, 0);
}
itk::NrrdImageIO::Pointer nrrdWriter = itk::NrrdImageIO::New();
nrrdWriter->SetNumberOfDimensions(dimension);
nrrdWriter->SetPixelType( imageTemplate->GetPixelType().GetPixelType());
nrrdWriter->SetComponentType( (itk::ImageIOBase::IOComponentType) imageTemplate->GetPixelType().GetComponentType());
if(imageTemplate->GetPixelType().GetNumberOfComponents() > 1)
{
nrrdWriter->SetNumberOfComponents(imageTemplate->GetPixelType().GetNumberOfComponents());
}
itk::ImageIORegion ioRegion( dimension );
mitk::Vector3D spacing = imageTemplate->GetGeometry()->GetSpacing();
mitk::Point3D origin = imageTemplate->GetGeometry()->GetOrigin();
for(unsigned int i = 0; i < dimension; i++)
{
nrrdWriter->SetDimensions(i,dimensions[i]);
nrrdWriter->SetSpacing(i,spacing[i]);
nrrdWriter->SetOrigin(i,origin[i]);
mitk::Vector3D direction;
direction.Set_vnl_vector(imageTemplate->GetGeometry()->GetIndexToWorldTransform()->GetMatrix().GetVnlMatrix().get_column(i));
vnl_vector< double > axisDirection(dimension);
for(unsigned int j = 0; j < dimension; j++)
{
axisDirection[j] = direction[j]/spacing[i];
}
nrrdWriter->SetDirection( i, axisDirection );
ioRegion.SetSize(i, imageTemplate->GetLargestPossibleRegion().GetSize(i) );
ioRegion.SetIndex(i, imageTemplate->GetLargestPossibleRegion().GetIndex(i) );
}
nrrdWriter->SetIORegion(ioRegion);
nrrdWriter->SetFileName(fileName);
nrrdWriter->SetUseStreamedWriting(true);
std::ifstream stream(fileName.c_str(), std::ifstream::binary);
if (fileName==m_RGBImageFileName)
{
unsigned int size = PixelNumber*3 * this->m_NumOfFrames;
unsigned int sizeInBytes = size * sizeof(unsigned char);
unsigned char* data = new unsigned char[size];
stream.read((char*)data, sizeInBytes);
nrrdWriter->Write(data);
stream.close();
delete[] data;
}
else
{
unsigned int size = PixelNumber * this->m_NumOfFrames;
unsigned int sizeInBytes = size * sizeof(float);
float* data = new float[size];
stream.read((char*)data, sizeInBytes);
try
{
nrrdWriter->Write(data);
}
catch (itk::ExceptionObject* e)
{
MITK_ERROR<< e->what();
return;
}
stream.close();
delete[] data;
}
delete[] dimensions;
if (fileName==m_RGBImageFileName)
{
delete[] rgbData;
}
else
{
delete[] floatData;
}
}
