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();
}
}
}
}
bool CalculateSegmentationVolume::ReadyToRun()
{
Image::Pointer image;
GetPointerParameter("Input", image);
return image.IsNotNull() && GetGroupNode();
}
void mitk::BinaryThresholdTool::SetupPreviewNode()
{
if (m_NodeForThresholding.IsNotNull())
{
Image::Pointer image = dynamic_cast<Image*>(m_NodeForThresholding->GetData());
Image::Pointer originalImage = dynamic_cast<Image*> (m_OriginalImageNode->GetData());
if (image.IsNotNull())
{
mitk::Image* workingimage = dynamic_cast<mitk::Image*>(m_ToolManager->GetWorkingData(0)->GetData());
if (workingimage)
{
m_ThresholdFeedbackNode->SetData(workingimage->Clone());
//Let's paint the feedback node green...
mitk::LabelSetImage::Pointer previewImage = dynamic_cast<mitk::LabelSetImage*> (m_ThresholdFeedbackNode->GetData());
itk::RGBPixel<float> pixel;
pixel[0] = 0.0f;
pixel[1] = 1.0f;
pixel[2] = 0.0f;
previewImage->GetActiveLabel()->SetColor(pixel);
previewImage->GetActiveLabelSet()->UpdateLookupTable(previewImage->GetActiveLabel()->GetValue());
}
else
m_ThresholdFeedbackNode->SetData(mitk::Image::New());
int layer(50);
m_NodeForThresholding->GetIntProperty("layer", layer);
m_ThresholdFeedbackNode->SetIntProperty("layer", layer + 1);
if (DataStorage* ds = m_ToolManager->GetDataStorage())
{
if (!ds->Exists(m_ThresholdFeedbackNode))
ds->Add(m_ThresholdFeedbackNode, m_OriginalImageNode);
}
if (image.GetPointer() == originalImage.GetPointer())
{
Image::StatisticsHolderPointer statistics = originalImage->GetStatistics();
m_SensibleMinimumThresholdValue = static_cast<double>(statistics->GetScalarValueMin());
m_SensibleMaximumThresholdValue = static_cast<double>(statistics->GetScalarValueMax());
}
if ((originalImage->GetPixelType().GetPixelType() == itk::ImageIOBase::SCALAR)
&& (originalImage->GetPixelType().GetComponentType() == itk::ImageIOBase::FLOAT || originalImage->GetPixelType().GetComponentType() == itk::ImageIOBase::DOUBLE))
m_IsFloatImage = true;
else
m_IsFloatImage = false;
m_CurrentThresholdValue = (m_SensibleMaximumThresholdValue + m_SensibleMinimumThresholdValue) / 2.0;
IntervalBordersChanged.Send(m_SensibleMinimumThresholdValue, m_SensibleMaximumThresholdValue, m_IsFloatImage);
ThresholdingValueChanged.Send(m_CurrentThresholdValue);
}
}
}
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();
}
bool ShowSegmentationAsSurface::ReadyToRun()
{
try
{
Image::Pointer image;
GetPointerParameter("Input", image);
return image.IsNotNull() && GetGroupNode();
}
catch (std::invalid_argument &)
{
return false;
}
}
void mitk::BinaryThresholdULTool::SetupPreviewNode()
{
if (m_NodeForThresholding.IsNotNull())
{
Image::Pointer image = dynamic_cast<Image*>( m_NodeForThresholding->GetData() );
Image::Pointer originalImage = dynamic_cast<Image*> (m_OriginalImageNode->GetData());
if (image.IsNotNull())
{
mitk::Image* workingimage = dynamic_cast<mitk::Image*>(m_ToolManager->GetWorkingData(0)->GetData());
if(workingimage)
m_ThresholdFeedbackNode->SetData( workingimage->Clone() );
else
m_ThresholdFeedbackNode->SetData( mitk::Image::New() );
int layer(50);
m_NodeForThresholding->GetIntProperty("layer", layer);
m_ThresholdFeedbackNode->SetIntProperty("layer", layer+1);
if (DataStorage* ds = m_ToolManager->GetDataStorage())
{
if (!ds->Exists(m_ThresholdFeedbackNode))
ds->Add( m_ThresholdFeedbackNode, m_OriginalImageNode );
}
if (image.GetPointer() == originalImage.GetPointer())
{
m_SensibleMinimumThresholdValue = static_cast<double>( originalImage->GetScalarValueMin() );
m_SensibleMaximumThresholdValue = static_cast<double>( originalImage->GetScalarValueMax() );
}
m_CurrentLowerThresholdValue = (m_SensibleMaximumThresholdValue + m_SensibleMinimumThresholdValue) / 3.0;
m_CurrentUpperThresholdValue = 2.0 * m_CurrentLowerThresholdValue;
IntervalBordersChanged.Send(m_SensibleMinimumThresholdValue, m_SensibleMaximumThresholdValue);
ThresholdingValuesChanged.Send(m_CurrentLowerThresholdValue, m_CurrentUpperThresholdValue);
}
}
}
bool mitk::AutoCropTool::ProcessOneWorkingData( DataNode* node )
{
if (node)
{
Image::Pointer image = dynamic_cast<Image*>( node->GetData() );
if (image.IsNull()) return false;
// if (image->GetDimension() == 4)
// {
// Tool::ErrorMessage.Send("Cropping 3D+t segmentations is not implemented. Sorry. Bug #1281");
// return false;
// }
AutoCropImageFilter::Pointer cropFilter = AutoCropImageFilter::New();
cropFilter->SetInput( image );
cropFilter->SetBackgroundValue( 0 );
try
{
cropFilter->Update();
image = cropFilter->GetOutput();
if (image.IsNotNull())
{
node->SetData( image );
}
else
{
return false;
}
}
catch(...)
{
return false;
}
}
return true;
}
void mitk::RegionGrow3DTool::SetupPreviewNodeFor( DataNode* nodeToProceed)
{
if (nodeToProceed)
{
Image::Pointer image = dynamic_cast<Image*>( nodeToProceed->GetData() );
if (image.IsNotNull())
{
m_FeedbackNode->SetData( image );
int layer(50);
nodeToProceed->GetIntProperty("layer", layer);
m_FeedbackNode->SetIntProperty("layer", layer+1);
m_FeedbackNode->SetLevelWindow(NULL);
if (DataStorage* storage = m_ToolManager->GetDataStorage())
{
if (storage->Exists(m_FeedbackNode))
storage->Remove(m_FeedbackNode);
storage->Add( m_FeedbackNode, nodeToProceed );
}
}
}
mitk::RenderingManager::GetInstance()->RequestUpdateAll();
}
void mitk::BinaryThresholdULTool::SetupPreviewNode()
{
if (m_NodeForThresholding.IsNotNull())
{
Image::Pointer image = dynamic_cast<Image*>( m_NodeForThresholding->GetData() );
Image::Pointer originalImage = dynamic_cast<Image*> (m_OriginalImageNode->GetData());
if (image.IsNotNull())
{
// initialize and a new node with the same image as our reference image
// use the level window property of this image copy to display the result of a thresholding operation
m_ThresholdFeedbackNode->SetData( image );
int layer(50);
m_NodeForThresholding->GetIntProperty("layer", layer);
m_ThresholdFeedbackNode->SetIntProperty("layer", layer+1);
if (DataStorage* ds = m_ToolManager->GetDataStorage())
{
if (!ds->Exists(m_ThresholdFeedbackNode))
ds->Add( m_ThresholdFeedbackNode, m_OriginalImageNode );
}
if (image.GetPointer() == originalImage.GetPointer())
{
m_SensibleMinimumThresholdValue = static_cast<int>( originalImage->GetScalarValueMin() );
m_SensibleMaximumThresholdValue = static_cast<int>( originalImage->GetScalarValueMax() );
}
m_CurrentLowerThresholdValue = (m_SensibleMaximumThresholdValue + m_SensibleMinimumThresholdValue) / 3;
m_CurrentUpperThresholdValue = 2*m_CurrentLowerThresholdValue;
IntervalBordersChanged.Send(m_SensibleMinimumThresholdValue, m_SensibleMaximumThresholdValue);
ThresholdingValuesChanged.Send(m_CurrentLowerThresholdValue, m_CurrentUpperThresholdValue);
}
}
}
/**Documentation
* Test for gibbs tracking filter
*/
int mitkGibbsTrackingTest(int argc, char* argv[])
{
MITK_TEST_BEGIN("mitkGibbsTrackingTest");
MITK_TEST_CONDITION_REQUIRED(argc>4,"check for input data")
QBallImage::Pointer mitkQballImage;
Image::Pointer mitkMaskImage;
mitk::FiberBundleX::Pointer fib1;
try{
MITK_INFO << "Q-Ball image: " << argv[1];
MITK_INFO << "Mask image: " << argv[2];
MITK_INFO << "Parameter file: " << argv[3];
MITK_INFO << "Reference bundle: " << argv[4];
RegisterDiffusionCoreObjectFactory();
RegisterFiberTrackingObjectFactory();
const std::string s1="", s2="";
std::vector<mitk::BaseData::Pointer> infile = mitk::BaseDataIO::LoadBaseDataFromFile( argv[1], s1, s2, false );
mitkQballImage = dynamic_cast<mitk::QBallImage*>(infile.at(0).GetPointer());
MITK_TEST_CONDITION_REQUIRED(mitkQballImage.IsNotNull(),"check qball image")
infile = mitk::BaseDataIO::LoadBaseDataFromFile( argv[2], s1, s2, false );
mitkMaskImage = dynamic_cast<mitk::Image*>(infile.at(0).GetPointer());
MITK_TEST_CONDITION_REQUIRED(mitkMaskImage.IsNotNull(),"check mask image")
infile = mitk::BaseDataIO::LoadBaseDataFromFile( argv[4], s1, s2, false );
fib1 = dynamic_cast<mitk::FiberBundleX*>(infile.at(0).GetPointer());
MITK_TEST_CONDITION_REQUIRED(fib1.IsNotNull(),"check fiber bundle")
typedef itk::Vector<float, QBALL_ODFSIZE> OdfVectorType;
typedef itk::Image<OdfVectorType,3> OdfVectorImgType;
typedef itk::Image<float,3> MaskImgType;
typedef itk::GibbsTrackingFilter<OdfVectorImgType> GibbsTrackingFilterType;
OdfVectorImgType::Pointer itk_qbi = OdfVectorImgType::New();
mitk::CastToItkImage<OdfVectorImgType>(mitkQballImage, itk_qbi);
MaskImgType::Pointer itk_mask = MaskImgType::New();
mitk::CastToItkImage<MaskImgType>(mitkMaskImage, itk_mask);
GibbsTrackingFilterType::Pointer gibbsTracker = GibbsTrackingFilterType::New();
gibbsTracker->SetQBallImage(itk_qbi.GetPointer());
gibbsTracker->SetMaskImage(itk_mask);
gibbsTracker->SetDuplicateImage(false);
gibbsTracker->SetRandomSeed(1);
gibbsTracker->SetLoadParameterFile(argv[3]);
gibbsTracker->Update();
mitk::FiberBundleX::Pointer fib2 = mitk::FiberBundleX::New(gibbsTracker->GetFiberBundle());
MITK_TEST_CONDITION_REQUIRED(fib1->Equals(fib2), "check if gibbs tracking has changed");
gibbsTracker->SetRandomSeed(0);
gibbsTracker->Update();
fib2 = mitk::FiberBundleX::New(gibbsTracker->GetFiberBundle());
MITK_TEST_CONDITION_REQUIRED(!fib1->Equals(fib2), "check if gibbs tracking has changed after wrong seed");
}
catch(...)
{
return EXIT_FAILURE;
}
// always end with this!
MITK_TEST_END();
}
