void mitk::OtsuTool3D::RunSegmentation(int regions, bool useValley, int numberOfBins)
{
//this->m_OtsuSegmentationDialog->setCursor(Qt::WaitCursor);
int numberOfThresholds = regions - 1;
unsigned int timestep = mitk::RenderingManager::GetInstance()->GetTimeNavigationController()->GetTime()->GetPos();
mitk::Image::Pointer image3D = Get3DImage(m_OriginalImage, timestep);
mitk::OtsuSegmentationFilter::Pointer otsuFilter = mitk::OtsuSegmentationFilter::New();
otsuFilter->SetNumberOfThresholds( numberOfThresholds );
otsuFilter->SetValleyEmphasis( useValley );
otsuFilter->SetNumberOfBins( numberOfBins );
otsuFilter->SetInput( image3D );
try
{
otsuFilter->Update();
}
catch( ... )
{
mitkThrow() << "itkOtsuFilter error (image dimension must be in {2, 3} and image must not be RGB)";
}
m_ToolManager->GetDataStorage()->Remove( this->m_MultiLabelResultNode );
m_MultiLabelResultNode = NULL;
m_MultiLabelResultNode = mitk::DataNode::New();
m_MultiLabelResultNode->SetName("Otsu_Preview");
m_MultiLabelResultNode->SetVisibility(true);
m_ToolManager->GetDataStorage()->Add( this->m_MultiLabelResultNode );
m_MultiLabelResultNode->SetOpacity(1.0);
this->m_MultiLabelResultNode->SetData( otsuFilter->GetOutput() );
m_MultiLabelResultNode->SetProperty("binary", mitk::BoolProperty::New(false));
mitk::RenderingModeProperty::Pointer renderingMode = mitk::RenderingModeProperty::New();
renderingMode->SetValue( mitk::RenderingModeProperty::LOOKUPTABLE_LEVELWINDOW_COLOR );
m_MultiLabelResultNode->SetProperty("Image Rendering.Mode", renderingMode);
mitk::LookupTable::Pointer lut = mitk::LookupTable::New();
mitk::LookupTableProperty::Pointer prop = mitk::LookupTableProperty::New(lut);
vtkSmartPointer<vtkLookupTable> lookupTable = vtkSmartPointer<vtkLookupTable>::New();
lookupTable->SetHueRange(1.0, 0.0);
lookupTable->SetSaturationRange(1.0, 1.0);
lookupTable->SetValueRange(1.0, 1.0);
lookupTable->SetTableRange(-1.0, 1.0);
lookupTable->Build();
lut->SetVtkLookupTable(lookupTable);
prop->SetLookupTable(lut);
m_MultiLabelResultNode->SetProperty("LookupTable",prop);
mitk::LevelWindowProperty::Pointer levWinProp = mitk::LevelWindowProperty::New();
mitk::LevelWindow levelwindow;
levelwindow.SetRangeMinMax(0, numberOfThresholds + 1);
levWinProp->SetLevelWindow( levelwindow );
m_MultiLabelResultNode->SetProperty( "levelwindow", levWinProp );
//m_BinaryPreviewNode->SetVisibility(false);
// m_MultiLabelResultNode->SetVisibility(true);
//this->m_OtsuSegmentationDialog->setCursor(Qt::ArrowCursor);
mitk::RenderingManager::GetInstance()->RequestUpdateAll();
}
void mitk::WatershedTool::DoIt()
{
// get image from tool manager
mitk::DataNode::Pointer referenceData = m_ToolManager->GetReferenceData(0);
mitk::Image::Pointer input = dynamic_cast<mitk::Image*>(referenceData->GetData());
if (input.IsNull())
return;
unsigned int timestep = mitk::RenderingManager::GetInstance()->GetTimeNavigationController()->GetTime()->GetPos();
input = Get3DImage(input, timestep);
mitk::Image::Pointer output;
try {
// create and run itk filter pipeline
AccessByItk_1(input.GetPointer(),ITKWatershed,output);
// create a new datanode for output
mitk::DataNode::Pointer dataNode = mitk::DataNode::New();
dataNode->SetData(output);
// set properties of datanode
dataNode->SetProperty("binary", mitk::BoolProperty::New(false));
dataNode->SetProperty("name", mitk::StringProperty::New("Watershed Result"));
mitk::RenderingModeProperty::Pointer renderingMode = mitk::RenderingModeProperty::New();
renderingMode->SetValue( mitk::RenderingModeProperty::LOOKUPTABLE_LEVELWINDOW_COLOR );
dataNode->SetProperty("Image Rendering.Mode", renderingMode);
// since we create a multi label image, define a vtk lookup table
mitk::LookupTable::Pointer lut = mitk::LookupTable::New();
mitk::LookupTableProperty::Pointer prop = mitk::LookupTableProperty::New(lut);
vtkSmartPointer<vtkLookupTable> lookupTable = vtkSmartPointer<vtkLookupTable>::New();
lookupTable->SetHueRange(1.0, 0.0);
lookupTable->SetSaturationRange(1.0, 1.0);
lookupTable->SetValueRange(1.0, 1.0);
lookupTable->SetTableRange(-1.0, 1.0);
lookupTable->Build();
lookupTable->SetTableValue(1,0,0,0);
lut->SetVtkLookupTable(lookupTable);
prop->SetLookupTable(lut);
dataNode->SetProperty("LookupTable",prop);
// make the levelwindow fit to right values
mitk::LevelWindowProperty::Pointer levWinProp = mitk::LevelWindowProperty::New();
mitk::LevelWindow levelwindow;
levelwindow.SetRangeMinMax(0, output->GetStatistics()->GetScalarValueMax());
levWinProp->SetLevelWindow( levelwindow );
dataNode->SetProperty( "levelwindow", levWinProp );
dataNode->SetProperty( "opacity", mitk::FloatProperty::New(0.5));
// set name of data node
std::string name = referenceData->GetName() + "_Watershed";
dataNode->SetName( name );
// look, if there is already a node with this name
mitk::DataStorage::SetOfObjects::ConstPointer children = m_ToolManager->GetDataStorage()->GetDerivations(referenceData);
mitk::DataStorage::SetOfObjects::ConstIterator currentNode = children->Begin();
mitk::DataNode::Pointer removeNode;
while(currentNode != children->End())
{
if(dataNode->GetName().compare(currentNode->Value()->GetName()) == 0)
{
removeNode = currentNode->Value();
}
currentNode++;
}
// remove node with same name
if(removeNode.IsNotNull())
m_ToolManager->GetDataStorage()->Remove(removeNode);
// add output to the data storage
m_ToolManager->GetDataStorage()->Add(dataNode,referenceData);
}
catch(itk::ExceptionObject& e)
{
MITK_ERROR<<"Watershed Filter Error: " << e.GetDescription();
}
RenderingManager::GetInstance()->RequestUpdateAll();
}
