diff --git a/Modules/Segmentation/Interactions/mitkLiveWireTool2D.cpp b/Modules/Segmentation/Interactions/mitkLiveWireTool2D.cpp index 68039bc454..2366f0f6d3 100644 --- a/Modules/Segmentation/Interactions/mitkLiveWireTool2D.cpp +++ b/Modules/Segmentation/Interactions/mitkLiveWireTool2D.cpp @@ -1,615 +1,613 @@ /*=================================================================== The Medical Imaging Interaction Toolkit (MITK) Copyright (c) German Cancer Research Center, Division of Medical and Biological Informatics. All rights reserved. This software is distributed WITHOUT ANY WARRANTY; without even the implied warranty of MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See LICENSE.txt or http://www.mitk.org for details. ===================================================================*/ #include "mitkLiveWireTool2D.h" #include "mitkToolManager.h" #include "mitkBaseRenderer.h" #include "mitkRenderingManager.h" #include "mitkLiveWireTool2D.xpm" #include #include #include #include "mitkContourUtils.h" #include "mitkContour.h" #include namespace mitk { MITK_TOOL_MACRO(Segmentation_EXPORT, LiveWireTool2D, "LiveWire tool"); } mitk::LiveWireTool2D::LiveWireTool2D() :SegTool2D("LiveWireTool") { m_Contour = mitk::ContourModel::New(); m_ContourModelNode = mitk::DataNode::New(); m_ContourModelNode->SetData( m_Contour ); m_ContourModelNode->SetProperty("name", StringProperty::New("working contour node")); m_ContourModelNode->SetProperty("visible", BoolProperty::New(true)); m_ContourModelNode->AddProperty( "color", ColorProperty::New(0.9, 1.0, 0.1), NULL, true ); m_ContourModelNode->AddProperty( "selectedcolor", ColorProperty::New(1.0, 0.0, 0.1), NULL, true ); m_LiveWireContour = mitk::ContourModel::New(); m_LiveWireContourNode = mitk::DataNode::New(); //m_LiveWireContourNode->SetData( m_LiveWireContour ); m_LiveWireContourNode->SetProperty("name", StringProperty::New("active livewire node")); m_LiveWireContourNode->SetProperty("visible", BoolProperty::New(true)); m_LiveWireContourNode->AddProperty( "color", ColorProperty::New(0.1, 1.0, 0.1), NULL, true ); m_LiveWireContourNode->AddProperty( "selectedcolor", ColorProperty::New(0.5, 0.5, 0.1), NULL, true ); m_LiveWireFilter = mitk::ImageLiveWireContourModelFilter::New(); // great magic numbers CONNECT_ACTION( AcINITNEWOBJECT, OnInitLiveWire ); CONNECT_ACTION( AcADDPOINT, OnAddPoint ); CONNECT_ACTION( AcMOVE, OnMouseMoved ); CONNECT_ACTION( AcCHECKPOINT, OnCheckPoint ); CONNECT_ACTION( AcFINISH, OnFinish ); CONNECT_ACTION( AcDELETEPOINT, OnLastSegmentDelete ); CONNECT_ACTION( AcADDLINE, OnMouseMoveNoDynamicCosts ); } mitk::LiveWireTool2D::~LiveWireTool2D() { + m_Contours.clear(); } const char** mitk::LiveWireTool2D::GetXPM() const { return mitkLiveWireTool2D_xpm; } const char* mitk::LiveWireTool2D::GetName() const { return "LiveWire"; } void mitk::LiveWireTool2D::Activated() { Superclass::Activated(); } void mitk::LiveWireTool2D::Deactivated() { this->FinishTool(); DataNode* workingNode( m_ToolManager->GetWorkingData(0) ); if ( !workingNode ) return; Image* workingImage = dynamic_cast(workingNode->GetData()); if ( !workingImage ) return; ContourUtils::Pointer contourUtils = mitk::ContourUtils::New(); /*+++++++++++++++++++++++ for all contours in list (currently created by tool) ++++++++++++++++++++++++++++++++++++*/ std::vector< std::pair >::iterator it = m_Contours.begin(); while(it != m_Contours.end() ) { //++++++++++if node contains data if( it->first->GetData() ) { //+++++++++++++++if this is a contourModel mitk::ContourModel* contourModel = dynamic_cast(it->first->GetData()); if( contourModel ) { //++++++++++++++++++++++ for each timestep of this contourModel for( int currentTimestep = 0; currentTimestep < contourModel->GetTimeSlicedGeometry()->GetTimeSteps(); currentTimestep++) { //get the segmentation image slice at current timestep mitk::Image::Pointer workingSlice = this->GetAffectedImageSliceAs2DImage(it->second, workingImage, currentTimestep); /*++++++++++++++++++++++ transfer to plain old contour to use contour util functionality +++++++++++++++++++++++*/ mitk::Contour::Pointer plainOldContour = mitk::Contour::New(); mitk::ContourModel::VertexIterator iter = contourModel->IteratorBegin(currentTimestep); while(iter != contourModel->IteratorEnd(currentTimestep) ) { plainOldContour->AddVertex( (*iter)->Coordinates ); iter++; } /*-------------------------------------------------------------------------------*/ mitk::Contour::Pointer projectedContour = contourUtils->ProjectContourTo2DSlice(workingSlice, plainOldContour, true, false); contourUtils->FillContourInSlice(projectedContour, workingSlice, 1.0); //write back to image volume this->WriteBackSegmentationResult(it->second, workingSlice, currentTimestep); } //remove contour node from datastorage m_ToolManager->GetDataStorage()->Remove( it->first ); } } ++it; } m_Contours.clear(); Superclass::Deactivated(); } bool mitk::LiveWireTool2D::OnInitLiveWire (Action* action, const StateEvent* stateEvent) { const PositionEvent* positionEvent = dynamic_cast(stateEvent->GetEvent()); if (!positionEvent) return false; m_LastEventSender = positionEvent->GetSender(); m_LastEventSlice = m_LastEventSender->GetSlice(); if ( Superclass::CanHandleEvent(stateEvent) < 1.0 ) return false; int timestep = positionEvent->GetSender()->GetTimeStep(); m_Contour->Expand(timestep+1); m_ToolManager->GetDataStorage()->Add( m_ContourModelNode ); m_ToolManager->GetDataStorage()->Add( m_LiveWireContourNode ); //set current slice as input for ImageToLiveWireContourFilter m_WorkingSlice = this->GetAffectedReferenceSlice(positionEvent); m_LiveWireFilter->SetInput(m_WorkingSlice); //map click to pixel coordinates mitk::Point3D click = const_cast(positionEvent->GetWorldPosition()); itk::Index<3> idx; m_WorkingSlice->GetGeometry()->WorldToIndex(click, idx); /*+++++++++++++++++++++++ get the pixel the gradient in region of 5x5 ++++++++++++++++++++++++++*/ itk::Index<3> indexWithHighestGradient; AccessFixedDimensionByItk_2(m_WorkingSlice, FindHighestGradientMagnitudeByITK, 2, idx, indexWithHighestGradient); /*----------------------------------------------------------------------------------------------------------------*/ //itk::Index to mitk::Point3D click[0] = indexWithHighestGradient[0]; click[1] = indexWithHighestGradient[1]; click[2] = indexWithHighestGradient[2]; m_WorkingSlice->GetGeometry()->IndexToWorld(click, click); //set initial start point m_Contour->AddVertex( click, true, timestep ); m_LiveWireFilter->SetStartPoint(click); m_CreateAndUseDynamicCosts = true; - //save contour and corresponding plane geometry to list - std::pair contourPair(m_ContourModelNode.GetPointer(), dynamic_cast(positionEvent->GetSender()->GetCurrentWorldGeometry2D()->Clone().GetPointer()) ); - m_Contours.push_back(contourPair); - - //render assert( positionEvent->GetSender()->GetRenderWindow() ); mitk::RenderingManager::GetInstance()->RequestUpdate( positionEvent->GetSender()->GetRenderWindow() ); return true; } bool mitk::LiveWireTool2D::OnAddPoint (Action* action, const StateEvent* stateEvent) { //complete LiveWire interaction for last segment //add current LiveWire contour to the finished contour and reset //to start new segment and computation /* check if event can be handled */ const PositionEvent* positionEvent = dynamic_cast(stateEvent->GetEvent()); if (!positionEvent) return false; if ( Superclass::CanHandleEvent(stateEvent) < 1.0 ) return false; /* END check if event can be handled */ int timestep = positionEvent->GetSender()->GetTimeStep(); //remove duplicate first vertex, it's already contained in m_Contour m_LiveWireContour->RemoveVertexAt(0, timestep); /* TODO fix this hack*/ //set last to active added point if( m_LiveWireContour->GetNumberOfVertices(timestep) > 0) { const_cast( m_LiveWireContour->GetVertexAt(m_LiveWireContour->GetNumberOfVertices(timestep)-1, timestep) )->IsControlPoint = true; } //merge contours m_Contour->Concatenate(m_LiveWireContour, timestep); //clear the livewire contour and reset the corresponding datanode m_LiveWireContour->Clear(timestep); //set new start point m_LiveWireFilter->SetStartPoint(const_cast(positionEvent->GetWorldPosition())); if( m_CreateAndUseDynamicCosts ) { //use dynamic cost map for next update m_LiveWireFilter->CreateDynamicCostMap(m_Contour); m_LiveWireFilter->SetUseDynamicCostMap(true); //m_CreateAndUseDynamicCosts = false; } //render assert( positionEvent->GetSender()->GetRenderWindow() ); mitk::RenderingManager::GetInstance()->RequestUpdate( positionEvent->GetSender()->GetRenderWindow() ); return true; } bool mitk::LiveWireTool2D::OnMouseMoved( Action* action, const StateEvent* stateEvent) { //compute LiveWire segment from last control point to current mouse position /* check if event can be handled */ if ( Superclass::CanHandleEvent(stateEvent) < 1.0 ) return false; const PositionEvent* positionEvent = dynamic_cast(stateEvent->GetEvent()); if (!positionEvent) return false; /* END check if event can be handled */ /* actual LiveWire computation */ int timestep = positionEvent->GetSender()->GetTimeStep(); m_LiveWireFilter->SetEndPoint(const_cast(positionEvent->GetWorldPosition())); m_LiveWireFilter->SetTimestep(timestep); m_LiveWireFilter->Update(); //ContourModel::VertexType* currentVertex = const_cast(m_LiveWireContour->GetVertexAt(0)); this->m_LiveWireContour = this->m_LiveWireFilter->GetOutput(); this->m_LiveWireContourNode->SetData(this->m_LiveWireFilter->GetOutput()); /* END actual LiveWire computation */ //render assert( positionEvent->GetSender()->GetRenderWindow() ); mitk::RenderingManager::GetInstance()->RequestUpdate( positionEvent->GetSender()->GetRenderWindow() ); return true; } bool mitk::LiveWireTool2D::OnMouseMoveNoDynamicCosts(Action* action, const StateEvent* stateEvent) { //do not use dynamic cost map m_LiveWireFilter->SetUseDynamicCostMap(false); OnMouseMoved(action, stateEvent); m_LiveWireFilter->SetUseDynamicCostMap(true); return true; } bool mitk::LiveWireTool2D::OnCheckPoint( Action* action, const StateEvent* stateEvent) { //check double click on first control point to finish the LiveWire tool // //Check distance to first point. //Transition YES if click close to first control point // mitk::StateEvent* newStateEvent = NULL; const PositionEvent* positionEvent = dynamic_cast(stateEvent->GetEvent()); if (!positionEvent) { //stay in current state newStateEvent = new mitk::StateEvent(EIDNO, stateEvent->GetEvent()); } else { int timestep = positionEvent->GetSender()->GetTimeStep(); mitk::Point3D click = positionEvent->GetWorldPosition(); mitk::Point3D first = this->m_Contour->GetVertexAt(0, timestep)->Coordinates; if (first.EuclideanDistanceTo(click) < 1.5) { //finish newStateEvent = new mitk::StateEvent(EIDYES, stateEvent->GetEvent()); }else { //stay active newStateEvent = new mitk::StateEvent(EIDNO, stateEvent->GetEvent()); } } this->HandleEvent( newStateEvent ); return true; } bool mitk::LiveWireTool2D::OnFinish( Action* action, const StateEvent* stateEvent) { // finish livewire tool interaction /* check if event can be handled */ if ( Superclass::CanHandleEvent(stateEvent) < 1.0 ) return false; const PositionEvent* positionEvent = dynamic_cast(stateEvent->GetEvent()); if (!positionEvent) return false; /* END check if event can be handled */ //actual timestep int timestep = positionEvent->GetSender()->GetTimeStep(); //remove last control point being added by double click m_Contour->RemoveVertexAt(m_Contour->GetNumberOfVertices(timestep) - 1, timestep); + //save contour and corresponding plane geometry to list + std::pair contourPair(m_ContourModelNode.GetPointer(), dynamic_cast(positionEvent->GetSender()->GetCurrentWorldGeometry2D()->Clone().GetPointer()) ); + m_Contours.push_back(contourPair); m_LiveWireFilter->SetUseDynamicCostMap(false); this->FinishTool(); return true; } void mitk::LiveWireTool2D::FinishTool() { - //const mitk::TimeBounds &timeBounds = m_Contour->GetGeometry()->GetTimeBounds(); unsigned int numberOfTimesteps = m_Contour->GetTimeSlicedGeometry()->GetTimeSteps(); //close contour in each timestep for( int i = 0; i <= numberOfTimesteps; i++) { m_Contour->Close(i); } //clear LiveWire node m_ToolManager->GetDataStorage()->Remove( m_LiveWireContourNode ); m_LiveWireContourNode = NULL; m_LiveWireContour = NULL; //TODO visual feedback for completing livewire tool m_ContourModelNode->AddProperty( "color", ColorProperty::New(1.0, 1.0, 0.1), NULL, true ); m_ContourModelNode->SetProperty("name", StringProperty::New("contour node")); //set the livewire interactor to edit control points mitk::ContourModelLiveWireInteractor::Pointer interactor = mitk::ContourModelLiveWireInteractor::New(m_ContourModelNode); interactor->SetWorkingImage(this->m_WorkingSlice); m_ContourModelNode->SetInteractor(interactor); //add interactor to globalInteraction instance mitk::GlobalInteraction::GetInstance()->AddInteractor(interactor); /* END complete livewire tool interaction */ /* reset contours and datanodes */ m_Contour = mitk::ContourModel::New(); m_ContourModelNode = mitk::DataNode::New(); m_ContourModelNode->SetData( m_Contour ); m_ContourModelNode->SetProperty("name", StringProperty::New("working contour node")); m_ContourModelNode->SetProperty("visible", BoolProperty::New(true)); m_ContourModelNode->AddProperty( "color", ColorProperty::New(0.9, 1.0, 0.1), NULL, true ); m_ContourModelNode->AddProperty( "selectedcolor", ColorProperty::New(1.0, 0.0, 0.1), NULL, true ); m_LiveWireContour = mitk::ContourModel::New(); m_LiveWireContourNode = mitk::DataNode::New(); //m_LiveWireContourNode->SetData( m_LiveWireContour ); m_LiveWireContourNode->SetProperty("name", StringProperty::New("active livewire node")); m_LiveWireContourNode->SetProperty("visible", BoolProperty::New(true)); m_LiveWireContourNode->AddProperty( "color", ColorProperty::New(0.1, 1.0, 0.1), NULL, true ); m_LiveWireContourNode->AddProperty( "selectedcolor", ColorProperty::New(0.5, 0.5, 0.1), NULL, true ); /* END reset contours and datanodes */ } bool mitk::LiveWireTool2D::OnLastSegmentDelete( Action* action, const StateEvent* stateEvent) { int timestep = stateEvent->GetEvent()->GetSender()->GetTimeStep(); //if last point of current contour will be removed go to start state and remove nodes if( m_Contour->GetNumberOfVertices(timestep) <= 1 ) { m_ToolManager->GetDataStorage()->Remove( m_LiveWireContourNode ); m_ToolManager->GetDataStorage()->Remove( m_ContourModelNode ); m_LiveWireContour = mitk::ContourModel::New(); m_Contour = mitk::ContourModel::New(); m_ContourModelNode->SetData( m_Contour ); m_LiveWireContourNode->SetData( m_LiveWireContour ); Superclass::Deactivated(); //go to start state } else //remove last segment from contour and reset livewire contour { m_LiveWireContour = mitk::ContourModel::New(); m_LiveWireContourNode->SetData(m_LiveWireContour); mitk::ContourModel::Pointer newContour = mitk::ContourModel::New(); newContour->Expand(m_Contour->GetTimeSteps()+1); mitk::ContourModel::VertexIterator begin = m_Contour->IteratorBegin(); //iterate from last point to next active point mitk::ContourModel::VertexIterator newLast = m_Contour->IteratorBegin() + (m_Contour->GetNumberOfVertices() - 1); //go at least one down if(newLast != begin) { newLast--; } //search next active control point while(newLast != begin && !((*newLast)->IsControlPoint) ) { newLast--; } //set position of start point for livewire filter to coordinates of the new last point m_LiveWireFilter->SetStartPoint((*newLast)->Coordinates); mitk::ContourModel::VertexIterator it = m_Contour->IteratorBegin(); //fill new Contour while(it <= newLast) { newContour->AddVertex((*it)->Coordinates, (*it)->IsControlPoint, timestep); it++; } newContour->SetIsClosed(m_Contour->IsClosed()); //set new contour visible m_ContourModelNode->SetData(newContour); m_Contour = newContour; assert( stateEvent->GetEvent()->GetSender()->GetRenderWindow() ); mitk::RenderingManager::GetInstance()->RequestUpdate( stateEvent->GetEvent()->GetSender()->GetRenderWindow() ); } return true; } template void mitk::LiveWireTool2D::FindHighestGradientMagnitudeByITK(itk::Image* inputImage, itk::Index<3> &index, itk::Index<3> &returnIndex) { typedef itk::Image InputImageType; typedef InputImageType::IndexType IndexType; unsigned long xMAX = inputImage->GetLargestPossibleRegion().GetSize()[0]; unsigned long yMAX = inputImage->GetLargestPossibleRegion().GetSize()[1]; returnIndex[0] = index[0]; returnIndex[1] = index[1]; returnIndex[2] = 0.0; double gradientMagnitude = 0.0; double maxGradientMagnitude = 0.0; //maximum value in each direction for size typename InputImageType::SizeType size; size[0] = 7; size[1] = 7; //minimum value in each direction for startRegion typename IndexType startRegion; startRegion[0] = index[0] - 3; startRegion[1] = index[1] - 3; if(startRegion[0] < 0) startRegion[0] = 0; if(startRegion[1] < 0) startRegion[1] = 0; if(xMAX - index[0] < 7) startRegion[0] = xMAX - 7; if(yMAX - index[1] < 7) startRegion[1] = yMAX - 7; index[0] = startRegion[0] + 3; index[1] = startRegion[1] + 3; typename InputImageType::RegionType region; region.SetSize( size ); region.SetIndex( startRegion ); typedef itk::GradientMagnitudeImageFilter< typename InputImageType, typename InputImageType> GradientMagnitudeFilterType; typename GradientMagnitudeFilterType::Pointer gradientFilter = GradientMagnitudeFilterType::New(); gradientFilter->SetInput(inputImage); gradientFilter->GetOutput()->SetRequestedRegion(region); gradientFilter->Update(); InputImageType::Pointer gradientMagnImage; gradientMagnImage = gradientFilter->GetOutput(); IndexType currentIndex; currentIndex[0] = 0; currentIndex[1] = 0; // search max (approximate) gradient magnitude for( int x = -2; x <= 2; ++x) { currentIndex[0] = index[0] + x; for( int y = -2; y <= 2; ++y) { currentIndex[1] = index[1] + y; gradientMagnitude = gradientMagnImage->GetPixel(currentIndex); //check for new max if(maxGradientMagnitude < gradientMagnitude) { maxGradientMagnitude = gradientMagnitude; returnIndex[0] = currentIndex[0]; returnIndex[1] = currentIndex[1]; returnIndex[2] = 0.0; }//end if }//end for y currentIndex[1] = index[1]; }//end for x } \ No newline at end of file