mitk::DataNode::Pointer mitk::Tool::CreateEmptySegmentationNode( Image* original, const std::string& organName, const mitk::Color& color )
{
// we NEED a reference image for size etc.
if (!original) return NULL;
// actually create a new empty segmentation
PixelType pixelType(mitk::MakeScalarPixelType<DefaultSegmentationDataType>() );
Image::Pointer segmentation = Image::New();
if (original->GetDimension() == 2)
{
const unsigned int dimensions[] = { original->GetDimension(0), original->GetDimension(1), 1 };
segmentation->Initialize(pixelType, 3, dimensions);
}
else
{
segmentation->Initialize(pixelType, original->GetDimension(), original->GetDimensions());
}
unsigned int byteSize = sizeof(DefaultSegmentationDataType);
if(segmentation->GetDimension() < 4)
{
for (unsigned int dim = 0; dim < segmentation->GetDimension(); ++dim)
{
byteSize *= segmentation->GetDimension(dim);
}
mitk::ImageWriteAccessor writeAccess(segmentation, segmentation->GetVolumeData(0));
memset( writeAccess.GetData(), 0, byteSize );
}
else
{//if we have a time-resolved image we need to set memory to 0 for each time step
for (unsigned int dim = 0; dim < 3; ++dim)
{
byteSize *= segmentation->GetDimension(dim);
}
for( unsigned int volumeNumber = 0; volumeNumber < segmentation->GetDimension(3); volumeNumber++)
{
mitk::ImageWriteAccessor writeAccess(segmentation, segmentation->GetVolumeData(volumeNumber));
memset( writeAccess.GetData(), 0, byteSize );
}
}
if (original->GetTimeGeometry() )
{
TimeGeometry::Pointer originalGeometry = original->GetTimeGeometry()->Clone();
segmentation->SetTimeGeometry( originalGeometry );
}
else
{
Tool::ErrorMessage("Original image does not have a 'Time sliced geometry'! Cannot create a segmentation.");
return NULL;
}
return CreateSegmentationNode( segmentation, organName, color );
}
mitk::DataNode::Pointer mitk::Tool::CreateEmptySegmentationNode( Image* original, const std::string& organName, const mitk::Color& color )
{
// we NEED a reference image for size etc.
if (!original) return NULL;
// actually create a new empty segmentation
PixelType pixelType(mitk::MakeScalarPixelType<DefaultSegmentationDataType>() );
Image::Pointer segmentation = Image::New();
if (original->GetDimension() == 2)
{
const unsigned int dimensions[] = { original->GetDimension(0), original->GetDimension(1), 1 };
segmentation->Initialize(pixelType, 3, dimensions);
}
else
{
segmentation->Initialize(pixelType, original->GetDimension(), original->GetDimensions());
}
unsigned int byteSize = sizeof(DefaultSegmentationDataType);
for (unsigned int dim = 0; dim < segmentation->GetDimension(); ++dim)
{
byteSize *= segmentation->GetDimension(dim);
}
memset( segmentation->GetData(), 0, byteSize );
if (original->GetTimeSlicedGeometry() )
{
AffineGeometryFrame3D::Pointer originalGeometryAGF = original->GetTimeSlicedGeometry()->Clone();
TimeSlicedGeometry::Pointer originalGeometry = dynamic_cast<TimeSlicedGeometry*>( originalGeometryAGF.GetPointer() );
segmentation->SetGeometry( originalGeometry );
}
else
{
Tool::ErrorMessage("Original image does not have a 'Time sliced geometry'! Cannot create a segmentation.");
return NULL;
}
return CreateSegmentationNode( segmentation, organName, color );
}
mitk::DataNode::Pointer mitk::Tool::CreateEmptySegmentationNode(Image *original,
const std::string &organName,
const mitk::Color &color)
{
// we NEED a reference image for size etc.
if (!original)
return nullptr;
// actually create a new empty segmentation
PixelType pixelType(mitk::MakeScalarPixelType<DefaultSegmentationDataType>());
LabelSetImage::Pointer segmentation = LabelSetImage::New();
if (original->GetDimension() == 2)
{
const unsigned int dimensions[] = {original->GetDimension(0), original->GetDimension(1), 1};
segmentation->Initialize(pixelType, 3, dimensions);
segmentation->AddLayer();
}
else
{
segmentation->Initialize(original);
}
mitk::Label::Pointer label = mitk::Label::New();
label->SetName(organName);
label->SetColor(color);
label->SetValue(1);
segmentation->GetActiveLabelSet()->AddLabel(label);
segmentation->GetActiveLabelSet()->SetActiveLabel(1);
unsigned int byteSize = sizeof(mitk::Label::PixelType);
if (segmentation->GetDimension() < 4)
{
for (unsigned int dim = 0; dim < segmentation->GetDimension(); ++dim)
{
byteSize *= segmentation->GetDimension(dim);
}
mitk::ImageWriteAccessor writeAccess(segmentation.GetPointer(), segmentation->GetVolumeData(0));
memset(writeAccess.GetData(), 0, byteSize);
}
else
{
// if we have a time-resolved image we need to set memory to 0 for each time step
for (unsigned int dim = 0; dim < 3; ++dim)
{
byteSize *= segmentation->GetDimension(dim);
}
for (unsigned int volumeNumber = 0; volumeNumber < segmentation->GetDimension(3); volumeNumber++)
{
mitk::ImageWriteAccessor writeAccess(segmentation.GetPointer(), segmentation->GetVolumeData(volumeNumber));
memset(writeAccess.GetData(), 0, byteSize);
}
}
if (original->GetTimeGeometry())
{
TimeGeometry::Pointer originalGeometry = original->GetTimeGeometry()->Clone();
segmentation->SetTimeGeometry(originalGeometry);
}
else
{
Tool::ErrorMessage("Original image does not have a 'Time sliced geometry'! Cannot create a segmentation.");
return nullptr;
}
// Add some DICOM Tags as properties to segmentation image
PropertyList::Pointer dicomSegPropertyList = mitk::DICOMSegmentationPropertyHandler::GetDICOMSegmentationProperties(original->GetPropertyList());
segmentation->GetPropertyList()->ConcatenatePropertyList(dicomSegPropertyList);
mitk::DICOMSegmentationPropertyHandler::GetDICOMSegmentProperties(segmentation->GetActiveLabel(segmentation->GetActiveLayer()));
return CreateSegmentationNode(segmentation, organName, color);
}