void mitk::RegionGrow3DTool::StartRegionGrowing(itk::Image<TPixel, VImageDimension>* itkImage, mitk::Geometry3D* imageGeometry, mitk::PointSet::PointType seedPoint)
{
typedef itk::Image<TPixel, VImageDimension> InputImageType;
typedef typename InputImageType::IndexType IndexType;
typedef itk::ConnectedAdaptiveThresholdImageFilter<InputImageType, InputImageType> RegionGrowingFilterType;
typename RegionGrowingFilterType::Pointer regionGrower = RegionGrowingFilterType::New();
if ( !imageGeometry->IsInside(seedPoint) )
{
return;
}
IndexType seedIndex;
imageGeometry->WorldToIndex( seedPoint, seedIndex);// convert world coordinates to image indices
//int seedValue = itkImage->GetPixel(seedIndex);
regionGrower->SetInput( itkImage );
regionGrower->AddSeed( seedIndex );
regionGrower->SetLower( m_LowerThreshold );
regionGrower->SetUpper( m_UpperThreshold );
regionGrower->SetGrowingDirectionIsUpwards( m_CurrentRGDirectionIsUpwards );
try
{
regionGrower->Update();
}
catch( ... )
{
MITK_ERROR << "Something went wrong!" << endl;
return;
}
m_SeedpointValue = regionGrower->GetSeedpointValue();
//initialize slider
if(m_CurrentRGDirectionIsUpwards)
{
UpperThresholdValueChanged.Send(m_UpperThreshold);
LowerThresholdValueChanged.Send(m_SeedpointValue);
}
else
{
UpperThresholdValueChanged.Send(m_SeedpointValue);
LowerThresholdValueChanged.Send(m_LowerThreshold);
}
m_DetectedLeakagePoint = regionGrower->GetLeakagePoint();
mitk::Image::Pointer resultImage = mitk::ImportItkImage(regionGrower->GetOutput())->Clone();
m_FeedbackNode->SetData( resultImage );
m_FeedbackNode->SetVisibility(true);
InitializeLevelWindow();
}
void QmitkAdaptiveRegionGrowingToolGUI::StartRegionGrowing(itk::Image<TPixel, VImageDimension>* itkImage, mitk::BaseGeometry* imageGeometry, mitk::PointSet::PointType seedPoint)
{
typedef itk::Image<TPixel, VImageDimension> InputImageType;
typedef typename InputImageType::IndexType IndexType;
typedef itk::ConnectedAdaptiveThresholdImageFilter<InputImageType, InputImageType> RegionGrowingFilterType;
typename RegionGrowingFilterType::Pointer regionGrower = RegionGrowingFilterType::New();
typedef itk::MinimumMaximumImageCalculator<InputImageType> MinMaxValueFilterType;
if ( !imageGeometry->IsInside(seedPoint) )
{
QApplication::restoreOverrideCursor();//reset cursor to be able to click ok with the regular mouse cursor
QMessageBox::information( NULL, "Segmentation functionality", "The seed point is outside of the image! Please choose a position inside the image!");
return;
}
IndexType seedIndex;
imageGeometry->WorldToIndex( seedPoint, seedIndex);// convert world coordinates to image indices
if (m_SeedpointValue>m_UPPERTHRESHOLD || m_SeedpointValue<m_LOWERTHRESHOLD)
{
QApplication::restoreOverrideCursor();//reset cursor to be able to click ok with the regular mouse cursor
QMessageBox::information( NULL, "Segmentation functionality", "The seed point is outside the defined thresholds! Please set a new seed point or adjust the thresholds.");
MITK_INFO << "Mean: " <<m_SeedPointValueMean;
return;
}
//Setting the direction of the regiongrowing. For dark structures e.g. the lung the regiongrowing
//is performed starting at the upper value going to the lower one
regionGrower->SetGrowingDirectionIsUpwards( m_CurrentRGDirectionIsUpwards );
regionGrower->SetInput( itkImage );
regionGrower->AddSeed( seedIndex );
//In some cases we have to subtract 1 for the lower threshold and add 1 to the upper.
//Otherwise no region growing is done. Maybe a bug in the ConnectiveAdaptiveThresholdFilter
regionGrower->SetLower( m_LOWERTHRESHOLD-1 );
regionGrower->SetUpper( m_UPPERTHRESHOLD+1);
try
{
regionGrower->Update();
}
catch(itk::ExceptionObject &exc)
{
QMessageBox errorInfo;
errorInfo.setWindowTitle("Adaptive RG Segmentation Functionality");
errorInfo.setIcon(QMessageBox::Critical);
errorInfo.setText("An error occurred during region growing!");
errorInfo.setDetailedText(exc.what());
errorInfo.exec();
return; // can't work
}
catch( ... )
{
QMessageBox::critical( NULL, "Adaptive RG Segmentation Functionality", "An error occurred during region growing!");
return;
}
mitk::Image::Pointer resultImage = mitk::ImportItkImage(regionGrower->GetOutput())->Clone();
//initialize slider
m_Controls.m_PreviewSlider->setMinimum(m_LOWERTHRESHOLD);
mitk::ScalarType max = m_LOWERTHRESHOLD+resultImage->GetStatistics()->GetScalarValueMax();
if (max < m_UPPERTHRESHOLD)
m_Controls.m_PreviewSlider->setMaximum(max);
else
m_Controls.m_PreviewSlider->setMaximum(m_UPPERTHRESHOLD);
this->m_DetectedLeakagePoint = regionGrower->GetLeakagePoint();
if(m_CurrentRGDirectionIsUpwards)
{
m_Controls.m_PreviewSlider->setValue(m_SeedPointValueMean-1);
}
else
{
m_Controls.m_PreviewSlider->setValue(m_SeedPointValueMean+1);
}
this->m_SliderInitialized = true;
//create new node and then delete the old one if there is one
mitk::DataNode::Pointer newNode = mitk::DataNode::New();
newNode->SetData( resultImage );
// set some properties
newNode->SetProperty("name", mitk::StringProperty::New(m_NAMEFORLABLEDSEGMENTATIONIMAGE));
newNode->SetProperty("helper object", mitk::BoolProperty::New(true));
newNode->SetProperty("color", mitk::ColorProperty::New(0.0,1.0,0.0));
newNode->SetProperty("layer", mitk::IntProperty::New(1));
newNode->SetProperty("opacity", mitk::FloatProperty::New(0.7));
//delete the old image, if there was one:
mitk::DataNode::Pointer binaryNode = m_DataStorage->GetNamedNode(m_NAMEFORLABLEDSEGMENTATIONIMAGE);
m_DataStorage->Remove(binaryNode);
// now add result to data tree
m_DataStorage->Add( newNode, m_InputImageNode );
this->InitializeLevelWindow();
if(m_UseVolumeRendering)
this->EnableVolumeRendering(true);
m_UpdateSuggestedThreshold = true;// reset first stored threshold value
//Setting progress to finished
mitk::ProgressBar::GetInstance()->Progress(357);
mitk::RenderingManager::GetInstance()->RequestUpdateAll();
}
