void mitk::CorrectorAlgorithm::GenerateData()
{
Image::Pointer inputImage = const_cast<Image*>(ImageToImageFilter::GetInput(0));
if (inputImage.IsNull() || inputImage->GetDimension() != 2)
{
itkExceptionMacro("CorrectorAlgorithm needs a 2D image as input.");
}
if (m_Contour.IsNull())
{
itkExceptionMacro("CorrectorAlgorithm needs a Contour object as input.");
}
// copy the input (since m_WorkingImage will be changed later)
m_WorkingImage = inputImage;
TimeGeometry::Pointer originalGeometry = NULL;
if (inputImage->GetTimeGeometry() )
{
originalGeometry = inputImage->GetTimeGeometry()->Clone();
m_WorkingImage->SetTimeGeometry( originalGeometry );
}
else
{
itkExceptionMacro("Original image does not have a 'Time sliced geometry'! Cannot copy.");
}
Image::Pointer temporarySlice;
// Convert to ipMITKSegmentationTYPE (because TobiasHeimannCorrectionAlgorithm relys on that data type)
{
itk::Image< ipMITKSegmentationTYPE, 2 >::Pointer correctPixelTypeImage;
CastToItkImage( m_WorkingImage, correctPixelTypeImage );
assert (correctPixelTypeImage.IsNotNull() );
// possible bug in CastToItkImage ?
// direction maxtrix is wrong/broken/not working after CastToItkImage, leading to a failed assertion in
// mitk/Core/DataStructures/mitkSlicedGeometry3D.cpp, 479:
// virtual void mitk::SlicedGeometry3D::SetSpacing(const mitk::Vector3D&): Assertion `aSpacing[0]>0 && aSpacing[1]>0 && aSpacing[2]>0' failed
// solution here: we overwrite it with an unity matrix
itk::Image< ipMITKSegmentationTYPE, 2 >::DirectionType imageDirection;
imageDirection.SetIdentity();
//correctPixelTypeImage->SetDirection(imageDirection);
temporarySlice = this->GetOutput();
// temporarySlice = ImportItkImage( correctPixelTypeImage );
m_FillColor = 1;
m_EraseColor = 0;
ImprovedHeimannCorrectionAlgorithm(correctPixelTypeImage);
CastToMitkImage( correctPixelTypeImage, temporarySlice );
}
temporarySlice->SetTimeGeometry(originalGeometry);
}
void mitk::CollectionGrayOpening::PerformGrayOpening(mitk::DataCollection *dataCollection,
std::string name,
std::string suffix)
{
for (size_t patient = 0; patient < dataCollection->Size(); ++patient)
{
DataCollection *dataPatient = dynamic_cast<DataCollection *>(dataCollection->GetData(patient).GetPointer());
if (dataPatient == nullptr)
MITK_ERROR << "PerformGrayOpening - Structure of DataCollection is invalid at patient level. Data inconsistent!";
if (dataPatient->Size() == 0)
MITK_ERROR << "Empty Patient Collective. Probably Fatal.";
for (size_t timeStep = 0; timeStep < dataPatient->Size(); ++timeStep)
{
DataCollection *dataTimeStep = dynamic_cast<DataCollection *>(dataPatient->GetData(timeStep).GetPointer());
if (dataTimeStep == nullptr)
MITK_ERROR
<< "DilateBinaryByName- Structure of DataCollection is invalid at time step level. Data inconsistent!";
// BinaryImage::Pointer itkImage = BinaryImage::New();
ImageType::Pointer itkImage = ImageType::New();
Image::Pointer tmp = dataTimeStep->GetMitkImage(name).GetPointer();
if (tmp.IsNull())
MITK_ERROR << "null";
CastToItkImage(tmp, itkImage);
if (itkImage.IsNull())
MITK_ERROR << "Image " << name << " does not exist. Fatal.";
typedef itk::FlatStructuringElement<3> StructuringElementType;
StructuringElementType::RadiusType elementRadius;
elementRadius.Fill(1);
elementRadius[2] = 0;
StructuringElementType structuringElement = StructuringElementType::Box(elementRadius);
typedef itk::GrayscaleMorphologicalOpeningImageFilter<ImageType, ImageType, StructuringElementType>
DilateImageFilterType;
DilateImageFilterType::Pointer dilateFilter0 = DilateImageFilterType::New();
dilateFilter0->SetInput(itkImage);
dilateFilter0->SetKernel(structuringElement);
dilateFilter0->Update();
DilateImageFilterType::Pointer dilateFilter1 = DilateImageFilterType::New();
dilateFilter1->SetInput(dilateFilter0->GetOutput());
dilateFilter1->SetKernel(structuringElement);
dilateFilter1->Update();
Image::Pointer dil = GrabItkImageMemory(dilateFilter1->GetOutput());
dataTimeStep->AddData(dil.GetPointer(), name + suffix, "");
}
}
}
void mitk::SetRegionTool::OnMouseReleased(StateMachineAction *, InteractionEvent *interactionEvent)
{
auto *positionEvent = dynamic_cast<mitk::InteractionPositionEvent *>(interactionEvent);
if (!positionEvent)
return;
assert(positionEvent->GetSender()->GetRenderWindow());
// 1. Hide the feedback contour, find out which slice the user clicked, find out which slice of the toolmanager's
// working image corresponds to that
FeedbackContourTool::SetFeedbackContourVisible(false);
mitk::RenderingManager::GetInstance()->RequestUpdate(positionEvent->GetSender()->GetRenderWindow());
int timeStep = positionEvent->GetSender()->GetTimeStep();
DataNode *workingNode(m_ToolManager->GetWorkingData(0));
if (!workingNode)
return;
auto *image = dynamic_cast<Image *>(workingNode->GetData());
const PlaneGeometry *planeGeometry((positionEvent->GetSender()->GetCurrentWorldPlaneGeometry()));
if (!image || !planeGeometry)
return;
Image::Pointer slice = FeedbackContourTool::GetAffectedImageSliceAs2DImage(positionEvent, image);
if (slice.IsNull())
{
MITK_ERROR << "Unable to extract slice." << std::endl;
return;
}
ContourModel *feedbackContour(FeedbackContourTool::GetFeedbackContour());
ContourModel::Pointer projectedContour = FeedbackContourTool::ProjectContourTo2DSlice(
slice, feedbackContour, false, false); // false: don't add 0.5 (done by FillContourInSlice)
// false: don't constrain the contour to the image's inside
if (projectedContour.IsNull())
return;
auto *labelImage = dynamic_cast<LabelSetImage *>(image);
int activeColor = 1;
if (labelImage != nullptr)
{
activeColor = labelImage->GetActiveLabel()->GetValue();
}
mitk::ContourModelUtils::FillContourInSlice(
projectedContour, timeStep, slice, image, m_PaintingPixelValue * activeColor);
this->WriteBackSegmentationResult(positionEvent, slice);
}
/**
Close the contour, project it to the image slice and fill it in 2D.
*/
bool mitk::ContourTool::OnMouseReleased( StateMachineAction*, InteractionEvent* interactionEvent )
{
// 1. Hide the feedback contour, find out which slice the user clicked, find out which slice of the toolmanager's working image corresponds to that
FeedbackContourTool::SetFeedbackContourVisible(false);
mitk::InteractionPositionEvent* positionEvent = dynamic_cast<mitk::InteractionPositionEvent*>( interactionEvent );
//const PositionEvent* positionEvent = dynamic_cast<const PositionEvent*>(stateEvent->GetEvent());
if (!positionEvent) return false;
assert( positionEvent->GetSender()->GetRenderWindow() );
mitk::RenderingManager::GetInstance()->RequestUpdate( positionEvent->GetSender()->GetRenderWindow() );
DataNode* workingNode( m_ToolManager->GetWorkingData(0) );
if (!workingNode) return false;
Image* image = dynamic_cast<Image*>(workingNode->GetData());
const PlaneGeometry* planeGeometry( dynamic_cast<const PlaneGeometry*> (positionEvent->GetSender()->GetCurrentWorldPlaneGeometry() ) );
if ( !image || !planeGeometry ) return false;
const AbstractTransformGeometry* abstractTransformGeometry( dynamic_cast<const AbstractTransformGeometry*> (positionEvent->GetSender()->GetCurrentWorldPlaneGeometry() ) );
if ( !image || abstractTransformGeometry ) return false;
// 2. Slice is known, now we try to get it as a 2D image and project the contour into index coordinates of this slice
Image::Pointer slice = SegTool2D::GetAffectedImageSliceAs2DImage( positionEvent, image );
if ( slice.IsNull() )
{
MITK_ERROR << "Unable to extract slice." << std::endl;
return false;
}
ContourModel* feedbackContour = FeedbackContourTool::GetFeedbackContour();
ContourModel::Pointer projectedContour = FeedbackContourTool::ProjectContourTo2DSlice( slice, feedbackContour, true, false ); // true: actually no idea why this is neccessary, but it works :-(
if (projectedContour.IsNull()) return false;
int timestep = positionEvent->GetSender()->GetTimeStep();
FeedbackContourTool::FillContourInSlice( projectedContour, timestep, slice, m_PaintingPixelValue );
this->WriteBackSegmentationResult(positionEvent, slice);
// 4. Make sure the result is drawn again --> is visible then.
assert( positionEvent->GetSender()->GetRenderWindow() );
return true;
}
bool mitk::SetRegionTool::OnMouseReleased( StateMachineAction*, InteractionEvent* interactionEvent )
{
// 1. Hide the feedback contour, find out which slice the user clicked, find out which slice of the toolmanager's working image corresponds to that
FeedbackContourTool::SetFeedbackContourVisible(false);
mitk::InteractionPositionEvent* positionEvent = dynamic_cast<mitk::InteractionPositionEvent*>( interactionEvent );
if (!positionEvent) return false;
assert( positionEvent->GetSender()->GetRenderWindow() );
mitk::RenderingManager::GetInstance()->RequestUpdate(positionEvent->GetSender()->GetRenderWindow());
int timeStep = positionEvent->GetSender()->GetTimeStep();
if (!m_FillContour && !m_StatusFillWholeSlice) return true;
DataNode* workingNode( m_ToolManager->GetWorkingData(0) );
if (!workingNode) return false;
Image* image = dynamic_cast<Image*>(workingNode->GetData());
const AbstractTransformGeometry* abstractTransformGeometry( dynamic_cast<const AbstractTransformGeometry*> (positionEvent->GetSender()->GetCurrentWorldPlaneGeometry() ) );
const PlaneGeometry* planeGeometry( dynamic_cast<const PlaneGeometry*> (positionEvent->GetSender()->GetCurrentWorldPlaneGeometry() ) );
if ( !image || !planeGeometry || abstractTransformGeometry ) return false;
Image::Pointer slice = FeedbackContourTool::GetAffectedImageSliceAs2DImage( positionEvent, image );
if ( slice.IsNull() )
{
MITK_ERROR << "Unable to extract slice." << std::endl;
return false;
}
ContourModel* feedbackContour( FeedbackContourTool::GetFeedbackContour() );
ContourModel::Pointer projectedContour = FeedbackContourTool::ProjectContourTo2DSlice( slice, feedbackContour, false, false ); // false: don't add 0.5 (done by FillContourInSlice)
// false: don't constrain the contour to the image's inside
if (projectedContour.IsNull()) return false;
FeedbackContourTool::FillContourInSlice( projectedContour, timeStep, slice, m_PaintingPixelValue );
this->WriteBackSegmentationResult(positionEvent, slice);
m_WholeImageContourInWorldCoordinates = NULL;
m_SegmentationContourInWorldCoordinates = NULL;
return true;
}
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::SetRegionTool::OnMousePressed(StateMachineAction *, InteractionEvent *interactionEvent)
{
auto *positionEvent = dynamic_cast<mitk::InteractionPositionEvent *>(interactionEvent);
if (!positionEvent)
return;
m_LastEventSender = positionEvent->GetSender();
m_LastEventSlice = m_LastEventSender->GetSlice();
// 1. Get the working image
Image::Pointer workingSlice = FeedbackContourTool::GetAffectedWorkingSlice(positionEvent);
if (workingSlice.IsNull())
return; // can't do anything without the segmentation
// if click was outside the image, don't continue
const BaseGeometry *sliceGeometry = workingSlice->GetGeometry();
itk::Index<3> projectedPointIn2D;
sliceGeometry->WorldToIndex(positionEvent->GetPositionInWorld(), projectedPointIn2D);
if (!sliceGeometry->IsIndexInside(projectedPointIn2D))
{
MITK_ERROR << "point apparently not inside segmentation slice" << std::endl;
return; // can't use that as a seed point
}
typedef itk::Image<DefaultSegmentationDataType, 2> InputImageType;
typedef InputImageType::IndexType IndexType;
typedef itk::ConnectedThresholdImageFilter<InputImageType, InputImageType> RegionGrowingFilterType;
RegionGrowingFilterType::Pointer regionGrower = RegionGrowingFilterType::New();
// convert world coordinates to image indices
IndexType seedIndex;
sliceGeometry->WorldToIndex(positionEvent->GetPositionInWorld(), seedIndex);
// perform region growing in desired segmented region
InputImageType::Pointer itkImage = InputImageType::New();
CastToItkImage(workingSlice, itkImage);
regionGrower->SetInput(itkImage);
regionGrower->AddSeed(seedIndex);
InputImageType::PixelType bound = itkImage->GetPixel(seedIndex);
regionGrower->SetLower(bound);
regionGrower->SetUpper(bound);
regionGrower->SetReplaceValue(1);
itk::BinaryFillholeImageFilter<InputImageType>::Pointer fillHolesFilter =
itk::BinaryFillholeImageFilter<InputImageType>::New();
fillHolesFilter->SetInput(regionGrower->GetOutput());
fillHolesFilter->SetForegroundValue(1);
// Store result and preview
mitk::Image::Pointer resultImage = mitk::GrabItkImageMemory(fillHolesFilter->GetOutput());
resultImage->SetGeometry(workingSlice->GetGeometry());
// Get the current working color
DataNode *workingNode(m_ToolManager->GetWorkingData(0));
if (!workingNode)
return;
mitk::ImageToContourModelFilter::Pointer contourextractor = mitk::ImageToContourModelFilter::New();
contourextractor->SetInput(resultImage);
contourextractor->Update();
mitk::ContourModel::Pointer awesomeContour = contourextractor->GetOutput();
FeedbackContourTool::SetFeedbackContour(awesomeContour);
FeedbackContourTool::SetFeedbackContourVisible(true);
mitk::RenderingManager::GetInstance()->RequestUpdate(positionEvent->GetSender()->GetRenderWindow());
}
void QmitkCreatePolygonModelAction::Run(const QList<DataNode::Pointer> &selectedNodes)
{
DataNode::Pointer selectedNode = selectedNodes[0];
Image::Pointer image = dynamic_cast<mitk::Image *>(selectedNode->GetData());
if (image.IsNull())
{
return;
}
try
{
// Get preference properties for smoothing and decimation
IPreferencesService::Pointer prefService = Platform::GetServiceRegistry().GetServiceById<IPreferencesService>(IPreferencesService::ID);
IPreferences::Pointer segPref = prefService->GetSystemPreferences()->Node("/org.mitk.views.segmentation");
bool smoothingHint = segPref->GetBool("smoothing hint", true);
ScalarType smoothing = segPref->GetDouble("smoothing value", 1.0);
ScalarType decimation = segPref->GetDouble("decimation rate", 0.5);
if (smoothingHint)
{
smoothing = 0.0;
Vector3D spacing = image->GetGeometry()->GetSpacing();
for (Vector3D::Iterator iter = spacing.Begin(); iter != spacing.End(); ++iter)
smoothing = max(smoothing, *iter);
}
ShowSegmentationAsSurface::Pointer surfaceFilter = ShowSegmentationAsSurface::New();
// Activate callback functions
itk::SimpleMemberCommand<QmitkCreatePolygonModelAction>::Pointer successCommand = itk::SimpleMemberCommand<QmitkCreatePolygonModelAction>::New();
successCommand->SetCallbackFunction(this, &QmitkCreatePolygonModelAction::OnSurfaceCalculationDone);
surfaceFilter->AddObserver(ResultAvailable(), successCommand);
itk::SimpleMemberCommand<QmitkCreatePolygonModelAction>::Pointer errorCommand = itk::SimpleMemberCommand<QmitkCreatePolygonModelAction>::New();
errorCommand->SetCallbackFunction(this, &QmitkCreatePolygonModelAction::OnSurfaceCalculationDone);
surfaceFilter->AddObserver(ProcessingError(), errorCommand);
// set filter parameter
surfaceFilter->SetDataStorage(*m_DataStorage);
surfaceFilter->SetPointerParameter("Input", image);
surfaceFilter->SetPointerParameter("Group node", selectedNode);
surfaceFilter->SetParameter("Show result", true);
surfaceFilter->SetParameter("Sync visibility", false);
surfaceFilter->SetParameter("Median kernel size", 3u);
surfaceFilter->SetParameter("Decimate mesh", m_IsDecimated);
surfaceFilter->SetParameter("Decimation rate", (float) decimation);
if (m_IsSmoothed)
{
surfaceFilter->SetParameter("Apply median", true);
surfaceFilter->SetParameter("Smooth", true);
surfaceFilter->SetParameter("Gaussian SD", sqrtf(smoothing)); // use sqrt to account for setting of variance in preferences
StatusBar::GetInstance()->DisplayText("Smoothed surface creation started in background...");
}
else
{
surfaceFilter->SetParameter("Apply median", false);
surfaceFilter->SetParameter("Smooth", false);
StatusBar::GetInstance()->DisplayText("Surface creation started in background...");
}
surfaceFilter->StartAlgorithm();
}
catch(...)
{
MITK_ERROR << "Surface creation failed!";
}
}
void mitk::CorrectorAlgorithm::GenerateData()
{
Image::Pointer inputImage = const_cast<Image*>(ImageToImageFilter::GetInput(0));
if (inputImage.IsNull() || inputImage->GetDimension() != 2)
{
itkExceptionMacro("CorrectorAlgorithm needs a 2D image as input.");
}
if (m_Contour.IsNull())
{
itkExceptionMacro("CorrectorAlgorithm needs a Contour object as input.");
}
// copy the input (since m_WorkingImage will be changed later)
m_WorkingImage = Image::New();
m_WorkingImage->Initialize( inputImage );
m_WorkingImage->SetVolume( inputImage.GetPointer()->GetData() );
if (inputImage->GetTimeSlicedGeometry() )
{
AffineGeometryFrame3D::Pointer originalGeometryAGF = inputImage->GetTimeSlicedGeometry()->Clone();
TimeSlicedGeometry::Pointer originalGeometry = dynamic_cast<TimeSlicedGeometry*>( originalGeometryAGF.GetPointer() );
m_WorkingImage->SetGeometry( originalGeometry );
}
else
{
itkExceptionMacro("Original image does not have a 'Time sliced geometry'! Cannot copy.");
}
// Convert to ipMITKSegmentationTYPE (because TobiasHeimannCorrectionAlgorithm relys on that data type)
itk::Image< ipMITKSegmentationTYPE, 2 >::Pointer correctPixelTypeImage;
CastToItkImage( m_WorkingImage, correctPixelTypeImage );
assert (correctPixelTypeImage.IsNotNull() );
// possible bug in CastToItkImage ?
// direction maxtrix is wrong/broken/not working after CastToItkImage, leading to a failed assertion in
// mitk/Core/DataStructures/mitkSlicedGeometry3D.cpp, 479:
// virtual void mitk::SlicedGeometry3D::SetSpacing(const mitk::Vector3D&): Assertion `aSpacing[0]>0 && aSpacing[1]>0 && aSpacing[2]>0' failed
// solution here: we overwrite it with an unity matrix
itk::Image< ipMITKSegmentationTYPE, 2 >::DirectionType imageDirection;
imageDirection.SetIdentity();
correctPixelTypeImage->SetDirection(imageDirection);
Image::Pointer temporarySlice = this->GetOutput();
// temporarySlice = ImportItkImage( correctPixelTypeImage );
CastToMitkImage( correctPixelTypeImage, temporarySlice );
TobiasHeimannCorrectionAlgorithm( temporarySlice->GetSliceData()->GetPicDescriptor() );
// temporarySlice is our return value (user can get it by calling GetOutput() )
CalculateDifferenceImage( temporarySlice, inputImage );
if ( m_DifferenceImage.IsNotNull() && inputImage->GetTimeSlicedGeometry() )
{
AffineGeometryFrame3D::Pointer originalGeometryAGF = inputImage->GetTimeSlicedGeometry()->Clone();
TimeSlicedGeometry::Pointer originalGeometry = dynamic_cast<TimeSlicedGeometry*>( originalGeometryAGF.GetPointer() );
m_DifferenceImage->SetGeometry( originalGeometry );
}
else
{
itkExceptionMacro("Original image does not have a 'Time sliced geometry'! Cannot copy.");
}
}
void mitk::SurfaceBasedInterpolationController::Interpolate()
{
if (m_MapOfContourLists[m_ActiveLabel].size() < 2)
{
// If no interpolation is possible reset the interpolation result
m_InterpolationResult = nullptr;
return;
}
m_InterpolateSurfaceFilter->Reset();
// MLI TODO
// m_InterpolateSurfaceFilter->SetReferenceImage( m_WorkingImage );
// CreateDistanceImageFromSurfaceFilter::Pointer interpolateSurfaceFilter =
// CreateDistanceImageFromSurfaceFilter::New();
vtkSmartPointer<vtkAppendPolyData> polyDataAppender = vtkSmartPointer<vtkAppendPolyData>::New();
for (unsigned int i = 0; i < m_MapOfContourLists[m_ActiveLabel].size(); i++)
{
mitk::ContourModelToSurfaceFilter::Pointer converter = mitk::ContourModelToSurfaceFilter::New();
converter->SetInput(m_MapOfContourLists[m_ActiveLabel].at(i).first);
converter->Update();
mitk::Surface::Pointer surface = converter->GetOutput();
surface->DisconnectPipeline();
ReduceContourSetFilter::Pointer reduceFilter = ReduceContourSetFilter::New();
reduceFilter->SetUseProgressBar(false);
reduceFilter->SetInput(surface);
reduceFilter->SetMinSpacing(m_MinSpacing);
reduceFilter->SetMaxSpacing(m_MaxSpacing);
reduceFilter->Update();
ComputeContourSetNormalsFilter::Pointer normalsFilter = ComputeContourSetNormalsFilter::New();
normalsFilter->SetUseProgressBar(false);
normalsFilter->SetInput(reduceFilter->GetOutput());
normalsFilter->SetMaxSpacing(m_MaxSpacing);
// MLI TODO
// normalsFilter->SetSegmentationBinaryImage(m_WorkingImage, m_ActiveLabel);
// normalsFilter->Update();
m_InterpolateSurfaceFilter->SetInput(i, normalsFilter->GetOutput());
polyDataAppender->AddInputData(reduceFilter->GetOutput()->GetVtkPolyData());
}
polyDataAppender->Update();
m_Contours->SetVtkPolyData(polyDataAppender->GetOutput());
// update the filter and get the resulting distance-image
m_InterpolateSurfaceFilter->Update();
Image::Pointer distanceImage = m_InterpolateSurfaceFilter->GetOutput();
if (distanceImage.IsNull())
{
// If no interpolation is possible reset the interpolation result
m_InterpolationResult = nullptr;
return;
}
// create a surface from the distance-image
mitk::ImageToSurfaceFilter::Pointer imageToSurfaceFilter = mitk::ImageToSurfaceFilter::New();
imageToSurfaceFilter->SetInput(distanceImage);
imageToSurfaceFilter->SetThreshold(0);
imageToSurfaceFilter->SetSmooth(true);
imageToSurfaceFilter->SetSmoothIteration(20);
imageToSurfaceFilter->Update();
m_InterpolationResult = imageToSurfaceFilter->GetOutput();
m_InterpolationResult->DisconnectPipeline();
}
void QmitkCreatePolygonModelAction::Run(const QList<DataNode::Pointer> &selectedNodes)
{
DataNode::Pointer selectedNode = selectedNodes[0];
Image::Pointer image = dynamic_cast<mitk::Image *>(selectedNode->GetData());
if (image.IsNull())
return;
try
{
if (!m_IsSmoothed)
{
ShowSegmentationAsSurface::Pointer surfaceFilter = ShowSegmentationAsSurface::New();
itk::SimpleMemberCommand<QmitkCreatePolygonModelAction>::Pointer successCommand = itk::SimpleMemberCommand<QmitkCreatePolygonModelAction>::New();
successCommand->SetCallbackFunction(this, &QmitkCreatePolygonModelAction::OnSurfaceCalculationDone);
surfaceFilter->AddObserver(ResultAvailable(), successCommand);
itk::SimpleMemberCommand<QmitkCreatePolygonModelAction>::Pointer errorCommand = itk::SimpleMemberCommand<QmitkCreatePolygonModelAction>::New();
errorCommand->SetCallbackFunction(this, &QmitkCreatePolygonModelAction::OnSurfaceCalculationDone);
surfaceFilter->AddObserver(ProcessingError(), errorCommand);
surfaceFilter->SetDataStorage(*m_DataStorage);
surfaceFilter->SetPointerParameter("Input", image);
surfaceFilter->SetPointerParameter("Group node", selectedNode);
surfaceFilter->SetParameter("Show result", true);
surfaceFilter->SetParameter("Sync visibility", false);
surfaceFilter->SetParameter("Smooth", false);
surfaceFilter->SetParameter("Apply median", false);
surfaceFilter->SetParameter("Median kernel size", 3u);
surfaceFilter->SetParameter("Gaussian SD", 1.5f);
surfaceFilter->SetParameter("Decimate mesh", m_IsDecimated);
surfaceFilter->SetParameter("Decimation rate", 0.8f);
StatusBar::GetInstance()->DisplayText("Surface creation started in background...");
surfaceFilter->StartAlgorithm();
}
else
{
ShowSegmentationAsSmoothedSurface::Pointer surfaceFilter = ShowSegmentationAsSmoothedSurface::New();
itk::SimpleMemberCommand<QmitkCreatePolygonModelAction>::Pointer successCommand = itk::SimpleMemberCommand<QmitkCreatePolygonModelAction>::New();
successCommand->SetCallbackFunction(this, &QmitkCreatePolygonModelAction::OnSurfaceCalculationDone);
surfaceFilter->AddObserver(mitk::ResultAvailable(), successCommand);
itk::SimpleMemberCommand<QmitkCreatePolygonModelAction>::Pointer errorCommand = itk::SimpleMemberCommand<QmitkCreatePolygonModelAction>::New();
errorCommand->SetCallbackFunction(this, &QmitkCreatePolygonModelAction::OnSurfaceCalculationDone);
surfaceFilter->AddObserver(mitk::ProcessingError(), errorCommand);
surfaceFilter->SetDataStorage(*m_DataStorage);
surfaceFilter->SetPointerParameter("Input", image);
surfaceFilter->SetPointerParameter("Group node", selectedNode);
berry::IWorkbenchPart::Pointer activePart =
berry::PlatformUI::GetWorkbench()->GetActiveWorkbenchWindow()->GetActivePage()->GetActivePart();
mitk::IRenderWindowPart* renderPart = dynamic_cast<mitk::IRenderWindowPart*>(activePart.GetPointer());
mitk::SliceNavigationController* timeNavController = 0;
if (renderPart != 0)
{
timeNavController = renderPart->GetRenderingManager()->GetTimeNavigationController();
}
int timeNr = timeNavController != 0 ? timeNavController->GetTime()->GetPos() : 0;
surfaceFilter->SetParameter("TimeNr", timeNr);
IPreferencesService::Pointer prefService = Platform::GetServiceRegistry().GetServiceById<IPreferencesService>(IPreferencesService::ID);
IPreferences::Pointer segPref = prefService->GetSystemPreferences()->Node("/org.mitk.views.segmentation");
bool smoothingHint = segPref->GetBool("smoothing hint", true);
float smoothing = (float)segPref->GetDouble("smoothing value", 1.0);
float decimation = (float)segPref->GetDouble("decimation rate", 0.5);
float closing = (float)segPref->GetDouble("closing ratio", 0.0);
if (smoothingHint)
{
smoothing = 0.0;
Vector3D spacing = image->GetGeometry()->GetSpacing();
for (Vector3D::Iterator iter = spacing.Begin(); iter != spacing.End(); ++iter)
smoothing = max(smoothing, *iter);
}
surfaceFilter->SetParameter("Smoothing", smoothing);
surfaceFilter->SetParameter("Decimation", decimation);
surfaceFilter->SetParameter("Closing", closing);
ProgressBar::GetInstance()->AddStepsToDo(8);
StatusBar::GetInstance()->DisplayText("Smoothed surface creation started in background...");
try {
surfaceFilter->StartAlgorithm();
} catch (...)
{
MITK_ERROR<<"Error creating smoothed polygon model: Not enough memory!";
}
}
}
catch(...)
{
MITK_ERROR << "Surface creation failed!";
}
}
bool mitk::SetRegionTool::OnMousePressed ( StateMachineAction*, InteractionEvent* interactionEvent )
{
mitk::InteractionPositionEvent* positionEvent = dynamic_cast<mitk::InteractionPositionEvent*>( interactionEvent );
//const PositionEvent* positionEvent = dynamic_cast<const PositionEvent*>(stateEvent->GetEvent());
if (!positionEvent) return false;
m_LastEventSender = positionEvent->GetSender();
m_LastEventSlice = m_LastEventSender->GetSlice();
int timeStep = positionEvent->GetSender()->GetTimeStep();
// 1. Get the working image
Image::Pointer workingSlice = FeedbackContourTool::GetAffectedWorkingSlice( positionEvent );
if ( workingSlice.IsNull() ) return false; // can't do anything without the segmentation
// if click was outside the image, don't continue
const BaseGeometry* sliceGeometry = workingSlice->GetGeometry();
itk::Index<2> projectedPointIn2D;
sliceGeometry->WorldToIndex( positionEvent->GetPositionInWorld(), projectedPointIn2D );
if ( !sliceGeometry->IsIndexInside( projectedPointIn2D ) )
{
MITK_ERROR << "point apparently not inside segmentation slice" << std::endl;
return false; // can't use that as a seed point
}
// Convert to ipMITKSegmentationTYPE (because ipMITKSegmentationGetContour8N relys on that data type)
itk::Image< ipMITKSegmentationTYPE, 2 >::Pointer correctPixelTypeImage;
CastToItkImage( workingSlice, correctPixelTypeImage );
assert (correctPixelTypeImage.IsNotNull() );
// possible bug in CastToItkImage ?
// direction maxtrix is wrong/broken/not working after CastToItkImage, leading to a failed assertion in
// mitk/Core/DataStructures/mitkSlicedGeometry3D.cpp, 479:
// virtual void mitk::SlicedGeometry3D::SetSpacing(const mitk::Vector3D&): Assertion `aSpacing[0]>0 && aSpacing[1]>0 && aSpacing[2]>0' failed
// solution here: we overwrite it with an unity matrix
itk::Image< ipMITKSegmentationTYPE, 2 >::DirectionType imageDirection;
imageDirection.SetIdentity();
correctPixelTypeImage->SetDirection(imageDirection);
Image::Pointer temporarySlice = Image::New();
// temporarySlice = ImportItkImage( correctPixelTypeImage );
CastToMitkImage( correctPixelTypeImage, temporarySlice );
// check index positions
mitkIpPicDescriptor* originalPicSlice = mitkIpPicNew();
CastToIpPicDescriptor( temporarySlice, originalPicSlice );
int m_SeedPointMemoryOffset = projectedPointIn2D[1] * originalPicSlice->n[0] + projectedPointIn2D[0];
if ( m_SeedPointMemoryOffset >= static_cast<int>( originalPicSlice->n[0] * originalPicSlice->n[1] ) ||
m_SeedPointMemoryOffset < 0 )
{
MITK_ERROR << "Memory offset calculation if mitk::SetRegionTool has some serious flaw! Aborting.." << std::endl;
return false;
}
// 2. Determine the contour that surronds the selected "piece of the image"
// find a contour seed point
unsigned int oneContourOffset = static_cast<unsigned int>( m_SeedPointMemoryOffset ); // safe because of earlier check if m_SeedPointMemoryOffset < 0
/**
* The logic of finding a starting point for the contour is the following:
*
* - If the initial seed point is 0, we are either inside a hole or outside of every segmentation.
* We move to the right until we hit a 1, which must be part of a contour.
*
* - If the initial seed point is 1, then ...
* we now do the same (running to the right) until we hit a 1
*
* In both cases the found contour point is used to extract a contour and
* then a test is applied to find out if the initial seed point is contained
* in the contour. If this is the case, filling should be applied, otherwise
* nothing is done.
*/
unsigned int size = originalPicSlice->n[0] * originalPicSlice->n[1];
/*
unsigned int rowSize = originalPicSlice->n[0];
*/
ipMITKSegmentationTYPE* data = static_cast<ipMITKSegmentationTYPE*>(originalPicSlice->data);
if ( data[oneContourOffset] == 0 ) // initial seed 0
{
for ( ; oneContourOffset < size; ++oneContourOffset )
{
if ( data[oneContourOffset] > 0 ) break;
}
}
else if ( data[oneContourOffset] == 1 ) // initial seed 1
{
unsigned int lastValidPixel = size-1; // initialization, will be changed lateron
bool inSeg = true; // inside segmentation?
for ( ; oneContourOffset < size; ++oneContourOffset )
{
if ( ( data[oneContourOffset] == 0 ) && inSeg ) // pixel 0 and inside-flag set: this happens at the first pixel outside a filled region
{
inSeg = false;
lastValidPixel = oneContourOffset - 1; // store the last pixel position inside a filled region
break;
}
else // pixel 1, inside-flag doesn't matter: this happens while we are inside a filled region
{
inSeg = true; // first iteration lands here
}
}
oneContourOffset = lastValidPixel;
}
else
{
MITK_ERROR << "Fill/Erase was never intended to work with other than binary images." << std::endl;
m_FillContour = false;
return false;
}
if (oneContourOffset == size) // nothing found until end of slice
{
m_FillContour = false;
return false;
}
int numberOfContourPoints( 0 );
int newBufferSize( 0 );
//MITK_INFO << "getting contour from offset " << oneContourOffset << " ("<<oneContourOffset%originalPicSlice->n[0]<<","<<oneContourOffset/originalPicSlice->n[0]<<")"<<std::endl;
float* contourPoints = ipMITKSegmentationGetContour8N( originalPicSlice, oneContourOffset, numberOfContourPoints, newBufferSize ); // memory allocated with malloc
//MITK_INFO << "contourPoints " << contourPoints << " (N="<<numberOfContourPoints<<")"<<std::endl;
assert(contourPoints == NULL || numberOfContourPoints > 0);
bool cursorInsideContour = ipMITKSegmentationIsInsideContour( contourPoints, numberOfContourPoints, projectedPointIn2D[0], projectedPointIn2D[1]);
// decide if contour should be filled or not
m_FillContour = cursorInsideContour;
if (m_FillContour)
{
// copy point from float* to mitk::Contour
ContourModel::Pointer contourInImageIndexCoordinates = ContourModel::New();
contourInImageIndexCoordinates->Expand(timeStep + 1);
contourInImageIndexCoordinates->SetClosed(true, timeStep);
Point3D newPoint;
for (int index = 0; index < numberOfContourPoints; ++index)
{
newPoint[0] = contourPoints[ 2 * index + 0 ] - 0.5;
newPoint[1] = contourPoints[ 2 * index + 1] - 0.5;
newPoint[2] = 0;
contourInImageIndexCoordinates->AddVertex(newPoint, timeStep);
}
m_SegmentationContourInWorldCoordinates = FeedbackContourTool::BackProjectContourFrom2DSlice( workingSlice->GetGeometry(), contourInImageIndexCoordinates, true ); // true, correct the result from ipMITKSegmentationGetContour8N
// 3. Show the contour
FeedbackContourTool::SetFeedbackContour( *m_SegmentationContourInWorldCoordinates );
FeedbackContourTool::SetFeedbackContourVisible(true);
mitk::RenderingManager::GetInstance()->RequestUpdate(positionEvent->GetSender()->GetRenderWindow());
}
// always generate a second contour, containing the whole image (used when CTRL is pressed)
{
// copy point from float* to mitk::Contour
ContourModel::Pointer contourInImageIndexCoordinates = ContourModel::New();
contourInImageIndexCoordinates->Expand(timeStep + 1);
contourInImageIndexCoordinates->SetClosed(true, timeStep);
Point3D newPoint;
newPoint[0] = 0; newPoint[1] = 0; newPoint[2] = 0.0;
contourInImageIndexCoordinates->AddVertex( newPoint, timeStep );
newPoint[0] = originalPicSlice->n[0]; newPoint[1] = 0; newPoint[2] = 0.0;
contourInImageIndexCoordinates->AddVertex( newPoint, timeStep );
newPoint[0] = originalPicSlice->n[0]; newPoint[1] = originalPicSlice->n[1]; newPoint[2] = 0.0;
contourInImageIndexCoordinates->AddVertex( newPoint, timeStep );
newPoint[0] = 0; newPoint[1] = originalPicSlice->n[1]; newPoint[2] = 0.0;
contourInImageIndexCoordinates->AddVertex( newPoint, timeStep );
m_WholeImageContourInWorldCoordinates = FeedbackContourTool::BackProjectContourFrom2DSlice( workingSlice->GetGeometry(), contourInImageIndexCoordinates, true ); // true, correct the result from ipMITKSegmentationGetContour8N
// 3. Show the contour
FeedbackContourTool::SetFeedbackContour( *m_SegmentationContourInWorldCoordinates );
FeedbackContourTool::SetFeedbackContourVisible(true);
mitk::RenderingManager::GetInstance()->RequestUpdate(positionEvent->GetSender()->GetRenderWindow());
}
free(contourPoints);
return true;
}