diff --git a/Modules/DiffusionImaging/Connectomics/CMakeLists.txt b/Modules/DiffusionImaging/Connectomics/CMakeLists.txt index e1571dbb2d..4094285b4a 100644 --- a/Modules/DiffusionImaging/Connectomics/CMakeLists.txt +++ b/Modules/DiffusionImaging/Connectomics/CMakeLists.txt @@ -1,7 +1,7 @@ MITK_CREATE_MODULE( Connectomics SUBPROJECTS MITK-DTI INCLUDE_DIRS Algorithms IODataStructures Rendering ${CMAKE_CURRENT_BINARY_DIR} - DEPENDS DiffusionCore FiberTracking + DEPENDS DiffusionCore FiberTracking QmitkExt ) -add_subdirectory(Testing) \ No newline at end of file +add_subdirectory(Testing) diff --git a/Modules/DiffusionImaging/Connectomics/Rendering/mitkConnectomicsNetworkMapper3D.cpp b/Modules/DiffusionImaging/Connectomics/Rendering/mitkConnectomicsNetworkMapper3D.cpp index c660e9d9e1..0ecc6babbd 100644 --- a/Modules/DiffusionImaging/Connectomics/Rendering/mitkConnectomicsNetworkMapper3D.cpp +++ b/Modules/DiffusionImaging/Connectomics/Rendering/mitkConnectomicsNetworkMapper3D.cpp @@ -1,756 +1,757 @@ /*=================================================================== 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 "mitkConnectomicsNetworkMapper3D.h" #include #include "vtkGraphLayout.h" #include #include "vtkGraphToPolyData.h" #include #include "vtkGlyph3D.h" #include "vtkGlyphSource2D.h" #include "mitkConnectomicsRenderingProperties.h" #include "mitkConnectomicsRenderingSchemeProperty.h" #include "mitkConnectomicsRenderingEdgeFilteringProperty.h" #include "mitkConnectomicsRenderingNodeFilteringProperty.h" #include "mitkConnectomicsRenderingNodeColorParameterProperty.h" #include "mitkConnectomicsRenderingNodeRadiusParameterProperty.h" #include "mitkConnectomicsRenderingEdgeColorParameterProperty.h" #include "mitkConnectomicsRenderingEdgeRadiusParameterProperty.h" #include "mitkConnectomicsRenderingNodeThresholdParameterProperty.h" #include "mitkConnectomicsRenderingEdgeThresholdParameterProperty.h" #include mitk::ConnectomicsNetworkMapper3D::ConnectomicsNetworkMapper3D() { m_NetworkAssembly = vtkPropAssembly::New(); } mitk::ConnectomicsNetworkMapper3D:: ~ConnectomicsNetworkMapper3D() { m_NetworkAssembly->Delete(); } void mitk::ConnectomicsNetworkMapper3D::GenerateDataForRenderer(mitk::BaseRenderer* renderer) { if( this->GetInput() == NULL ) { return; } bool propertiesHaveChanged = this->PropertiesChanged(); if( this->GetInput()->GetIsModified( ) || propertiesHaveChanged ) { m_NetworkAssembly->Delete(); m_NetworkAssembly = vtkPropAssembly::New(); // Here is the part where a graph is given and converted to points and connections between points... std::vector< mitk::ConnectomicsNetwork::NetworkNode > vectorOfNodes = this->GetInput()->GetVectorOfAllNodes(); std::vector< std::pair< std::pair< mitk::ConnectomicsNetwork::NetworkNode, mitk::ConnectomicsNetwork::NetworkNode > , mitk::ConnectomicsNetwork::NetworkEdge > > vectorOfEdges = this->GetInput()->GetVectorOfAllEdges(); // Decide on the style of rendering due to property if( m_ChosenRenderingScheme == connectomicsRenderingMITKScheme ) { mitk::Point3D tempWorldPoint, tempCNFGeometryPoint; //////////////////////Prepare coloring and radius//////////// std::vector< double > vectorOfNodeRadiusParameterValues; vectorOfNodeRadiusParameterValues.resize( vectorOfNodes.size() ); double maxNodeRadiusParameterValue( FillNodeParameterVector( &vectorOfNodeRadiusParameterValues, m_NodeRadiusParameter ) ); std::vector< double > vectorOfNodeColorParameterValues; vectorOfNodeColorParameterValues.resize( vectorOfNodes.size() ); double maxNodeColorParameterValue( FillNodeParameterVector( &vectorOfNodeColorParameterValues, m_NodeColorParameter ) ); std::vector< double > vectorOfEdgeRadiusParameterValues; vectorOfEdgeRadiusParameterValues.resize( vectorOfEdges.size() ); double maxEdgeRadiusParameterValue( FillEdgeParameterVector( &vectorOfEdgeRadiusParameterValues, m_EdgeRadiusParameter ) ); std::vector< double > vectorOfEdgeColorParameterValues; vectorOfEdgeColorParameterValues.resize( vectorOfEdges.size() ); double maxEdgeColorParameterValue( FillEdgeParameterVector( &vectorOfEdgeColorParameterValues, m_EdgeColorParameter ) ); //////////////////////Prepare Filtering////////////////////// // true will be rendered std::vector< bool > vectorOfNodeFilterBools( vectorOfNodes.size(), true ); if( m_ChosenNodeFilter == connectomicsRenderingNodeThresholdingFilter ) { FillNodeFilterBoolVector( &vectorOfNodeFilterBools, m_NodeThresholdParameter ); } std::vector< bool > vectorOfEdgeFilterBools( vectorOfEdges.size(), true ); if( m_ChosenEdgeFilter == connectomicsRenderingEdgeThresholdFilter ) { FillEdgeFilterBoolVector( &vectorOfEdgeFilterBools, m_EdgeThresholdParameter ); } //////////////////////Create Spheres///////////////////////// for(unsigned int i = 0; i < vectorOfNodes.size(); i++) { vtkSmartPointer sphereSource = vtkSmartPointer::New(); for(unsigned int dimension = 0; dimension < 3; dimension++) { tempCNFGeometryPoint.SetElement( dimension , vectorOfNodes[i].coordinates[dimension] ); } GetDataNode()->GetData()->GetGeometry()->IndexToWorld( tempCNFGeometryPoint, tempWorldPoint ); sphereSource->SetCenter( tempWorldPoint[0] , tempWorldPoint[1], tempWorldPoint[2] ); // determine radius double radiusFactor = vectorOfNodeRadiusParameterValues[i] / maxNodeRadiusParameterValue; double radius = m_NodeRadiusStart + ( m_NodeRadiusEnd - m_NodeRadiusStart) * radiusFactor; sphereSource->SetRadius( radius ); vtkSmartPointer mapper = vtkSmartPointer::New(); mapper->SetInput(sphereSource->GetOutput()); vtkSmartPointer actor = vtkSmartPointer::New(); actor->SetMapper(mapper); // determine color double colorFactor = vectorOfNodeColorParameterValues[i] / maxNodeColorParameterValue; double redStart = m_NodeColorStart.GetElement( 0 ); double greenStart = m_NodeColorStart.GetElement( 1 ); double blueStart = m_NodeColorStart.GetElement( 2 ); double redEnd = m_NodeColorEnd.GetElement( 0 ); double greenEnd = m_NodeColorEnd.GetElement( 1 ); double blueEnd = m_NodeColorEnd.GetElement( 2 ); double red = redStart + ( redEnd - redStart ) * colorFactor; double green = greenStart + ( greenEnd - greenStart ) * colorFactor; double blue = blueStart + ( blueEnd - blueStart ) * colorFactor; actor->GetProperty()->SetColor( red, green, blue); if( vectorOfNodeFilterBools[i] ) { m_NetworkAssembly->AddPart(actor); } } //////////////////////Create Tubes///////////////////////// double maxWeight = (double) this->GetInput()->GetMaximumWeight(); for(unsigned int i = 0; i < vectorOfEdges.size(); i++) { vtkSmartPointer lineSource = vtkSmartPointer::New(); for(unsigned int dimension = 0; dimension < 3; dimension++) { tempCNFGeometryPoint[ dimension ] = vectorOfEdges[i].first.first.coordinates[dimension]; } GetDataNode()->GetData()->GetGeometry()->IndexToWorld( tempCNFGeometryPoint, tempWorldPoint ); lineSource->SetPoint1(tempWorldPoint[0], tempWorldPoint[1],tempWorldPoint[2] ); for(unsigned int dimension = 0; dimension < 3; dimension++) { tempCNFGeometryPoint[ dimension ] = vectorOfEdges[i].first.second.coordinates[dimension]; } GetDataNode()->GetData()->GetGeometry()->IndexToWorld( tempCNFGeometryPoint, tempWorldPoint ); lineSource->SetPoint2(tempWorldPoint[0], tempWorldPoint[1], tempWorldPoint[2] ); vtkSmartPointer tubes = vtkSmartPointer::New(); tubes->SetInput( lineSource->GetOutput() ); tubes->SetNumberOfSides( 12 ); // determine radius double radiusFactor = vectorOfEdgeRadiusParameterValues[i] / maxEdgeRadiusParameterValue; double radius = m_EdgeRadiusStart + ( m_EdgeRadiusEnd - m_EdgeRadiusStart) * radiusFactor; tubes->SetRadius( radius ); // originally we used a logarithmic scaling, // double radiusFactor = 1.0 + ((double) vectorOfEdges[i].second.weight) / 10.0 ; // tubes->SetRadius( std::log10( radiusFactor ) ); vtkSmartPointer mapper2 = vtkSmartPointer::New(); mapper2->SetInput( tubes->GetOutput() ); vtkSmartPointer actor = vtkSmartPointer::New(); actor->SetMapper(mapper2); // determine color double colorFactor = vectorOfEdgeColorParameterValues[i] / maxEdgeColorParameterValue; double redStart = m_EdgeColorStart.GetElement( 0 ); double greenStart = m_EdgeColorStart.GetElement( 1 ); double blueStart = m_EdgeColorStart.GetElement( 2 ); double redEnd = m_EdgeColorEnd.GetElement( 0 ); double greenEnd = m_EdgeColorEnd.GetElement( 1 ); double blueEnd = m_EdgeColorEnd.GetElement( 2 ); double red = redStart + ( redEnd - redStart ) * colorFactor; double green = greenStart + ( greenEnd - greenStart ) * colorFactor; double blue = blueStart + ( blueEnd - blueStart ) * colorFactor; actor->GetProperty()->SetColor( red, green, blue); if( vectorOfEdgeFilterBools[i] ) { m_NetworkAssembly->AddPart(actor); } } } else if( m_ChosenRenderingScheme == connectomicsRenderingVTKScheme ) { vtkSmartPointer graph = vtkSmartPointer::New(); std::vector< vtkIdType > networkToVTKvector; networkToVTKvector.resize(vectorOfNodes.size()); for(unsigned int i = 0; i < vectorOfNodes.size(); i++) { networkToVTKvector[vectorOfNodes[i].id] = graph->AddVertex(); } for(unsigned int i = 0; i < vectorOfEdges.size(); i++) { graph->AddEdge(networkToVTKvector[vectorOfEdges[i].first.first.id], networkToVTKvector[vectorOfEdges[i].first.second.id]); } vtkSmartPointer points = vtkSmartPointer::New(); for(unsigned int i = 0; i < vectorOfNodes.size(); i++) { double x = vectorOfNodes[i].coordinates[0]; double y = vectorOfNodes[i].coordinates[1]; double z = vectorOfNodes[i].coordinates[2]; points->InsertNextPoint( x, y, z); } graph->SetPoints(points); vtkGraphLayout* layout = vtkGraphLayout::New(); layout->SetInput(graph); - layout->SetLayoutStrategy(vtkPassThroughLayoutStrategy::New()); + vtkPassThroughLayoutStrategy* ptls = vtkPassThroughLayoutStrategy::New(); + layout->SetLayoutStrategy( ptls ); vtkGraphToPolyData* graphToPoly = vtkGraphToPolyData::New(); graphToPoly->SetInputConnection(layout->GetOutputPort()); // Create the standard VTK polydata mapper and actor // for the connections (edges) in the tree. vtkPolyDataMapper* edgeMapper = vtkPolyDataMapper::New(); edgeMapper->SetInputConnection(graphToPoly->GetOutputPort()); vtkActor* edgeActor = vtkActor::New(); edgeActor->SetMapper(edgeMapper); edgeActor->GetProperty()->SetColor(0.0, 0.5, 1.0); // Glyph the points of the tree polydata to create // VTK_VERTEX cells at each vertex in the tree. vtkGlyph3D* vertGlyph = vtkGlyph3D::New(); vertGlyph->SetInputConnection(0, graphToPoly->GetOutputPort()); vtkGlyphSource2D* glyphSource = vtkGlyphSource2D::New(); glyphSource->SetGlyphTypeToVertex(); vertGlyph->SetInputConnection(1, glyphSource->GetOutputPort()); // Create a mapper for the vertices, and tell the mapper // to use the specified color array. vtkPolyDataMapper* vertMapper = vtkPolyDataMapper::New(); vertMapper->SetInputConnection(vertGlyph->GetOutputPort()); /*if (colorArray) { vertMapper->SetScalarModeToUsePointFieldData(); vertMapper->SelectColorArray(colorArray); vertMapper->SetScalarRange(colorRange); }*/ // Create an actor for the vertices. Move the actor forward // in the z direction so it is drawn on top of the edge actor. vtkActor* vertActor = vtkActor::New(); vertActor->SetMapper(vertMapper); vertActor->GetProperty()->SetPointSize(5); vertActor->SetPosition(0, 0, 0.001); m_NetworkAssembly->AddPart(edgeActor); m_NetworkAssembly->AddPart(vertActor); } (static_cast ( GetDataNode()->GetData() ) )->SetIsModified( false ); } } const mitk::ConnectomicsNetwork* mitk::ConnectomicsNetworkMapper3D::GetInput() { return static_cast ( GetDataNode()->GetData() ); } void mitk::ConnectomicsNetworkMapper3D::SetDefaultProperties(DataNode* node, BaseRenderer* renderer , bool overwrite) { // Initialize enumeration properties mitk::ConnectomicsRenderingSchemeProperty::Pointer connectomicsRenderingScheme = mitk::ConnectomicsRenderingSchemeProperty::New(); mitk::ConnectomicsRenderingEdgeFilteringProperty::Pointer connectomicsRenderingEdgeFiltering = mitk::ConnectomicsRenderingEdgeFilteringProperty::New(); mitk::ConnectomicsRenderingNodeFilteringProperty::Pointer connectomicsRenderingNodeFiltering = mitk::ConnectomicsRenderingNodeFilteringProperty::New(); mitk::ConnectomicsRenderingNodeColorParameterProperty::Pointer connectomicsRenderingNodeGradientColorParameter = mitk::ConnectomicsRenderingNodeColorParameterProperty::New(); mitk::ConnectomicsRenderingNodeRadiusParameterProperty::Pointer connectomicsRenderingNodeRadiusParameter = mitk::ConnectomicsRenderingNodeRadiusParameterProperty::New(); mitk::ConnectomicsRenderingEdgeColorParameterProperty::Pointer connectomicsRenderingEdgeGradientColorParameter = mitk::ConnectomicsRenderingEdgeColorParameterProperty::New(); mitk::ConnectomicsRenderingEdgeRadiusParameterProperty::Pointer connectomicsRenderingEdgeRadiusParameter = mitk::ConnectomicsRenderingEdgeRadiusParameterProperty::New(); mitk::ConnectomicsRenderingNodeThresholdParameterProperty::Pointer connectomicsRenderingNodeThresholdParameter = mitk::ConnectomicsRenderingNodeThresholdParameterProperty::New(); mitk::ConnectomicsRenderingEdgeThresholdParameterProperty::Pointer connectomicsRenderingEdgeThresholdParameter = mitk::ConnectomicsRenderingEdgeThresholdParameterProperty::New(); // set the properties node->AddProperty( connectomicsRenderingSchemePropertyName.c_str(), connectomicsRenderingScheme, renderer, overwrite ); node->AddProperty( connectomicsRenderingEdgeFilteringPropertyName.c_str(), connectomicsRenderingEdgeFiltering, renderer, overwrite ); node->AddProperty( connectomicsRenderingEdgeThresholdFilterParameterName.c_str(), connectomicsRenderingEdgeThresholdParameter, renderer, overwrite ); node->AddProperty( connectomicsRenderingEdgeThresholdFilterThresholdName.c_str(), connectomicsRenderingEdgeThresholdFilterThresholdDefault, renderer, overwrite ); node->AddProperty( connectomicsRenderingNodeFilteringPropertyName.c_str(), connectomicsRenderingNodeFiltering, renderer, overwrite ); node->AddProperty( connectomicsRenderingNodeThresholdFilterParameterName.c_str(), connectomicsRenderingNodeThresholdParameter, renderer, overwrite ); node->AddProperty( connectomicsRenderingNodeThresholdFilterThresholdName.c_str(), connectomicsRenderingNodeThresholdFilterThresholdDefault, renderer, overwrite ); node->AddProperty( connectomicsRenderingNodeGradientStartColorName.c_str(), connectomicsRenderingNodeGradientStartColorDefault, renderer, overwrite ); node->AddProperty( connectomicsRenderingNodeGradientEndColorName.c_str(), connectomicsRenderingNodeGradientEndColorDefault, renderer, overwrite ); node->AddProperty( connectomicsRenderingNodeGradientColorParameterName.c_str(), connectomicsRenderingNodeGradientColorParameter, renderer, overwrite ); node->AddProperty( connectomicsRenderingNodeRadiusStartName.c_str(), connectomicsRenderingNodeRadiusStartDefault, renderer, overwrite ); node->AddProperty( connectomicsRenderingNodeRadiusEndName.c_str(), connectomicsRenderingNodeRadiusEndDefault, renderer, overwrite ); node->AddProperty( connectomicsRenderingNodeRadiusParameterName.c_str(), connectomicsRenderingNodeRadiusParameter, renderer, overwrite ); node->AddProperty( connectomicsRenderingNodeChosenNodeName.c_str(), connectomicsRenderingNodeChosenNodeDefault, renderer, overwrite ); node->AddProperty( connectomicsRenderingEdgeGradientStartColorName.c_str(), connectomicsRenderingEdgeGradientStartColorDefault, renderer, overwrite ); node->AddProperty( connectomicsRenderingEdgeGradientEndColorName.c_str(), connectomicsRenderingEdgeGradientEndColorDefault, renderer, overwrite ); node->AddProperty( connectomicsRenderingEdgeGradientColorParameterName.c_str(), connectomicsRenderingEdgeGradientColorParameter, renderer, overwrite ); node->AddProperty( connectomicsRenderingEdgeRadiusStartName.c_str(), connectomicsRenderingEdgeRadiusStartDefault, renderer, overwrite ); node->AddProperty( connectomicsRenderingEdgeRadiusEndName.c_str(), connectomicsRenderingEdgeRadiusEndDefault, renderer, overwrite ); node->AddProperty( connectomicsRenderingEdgeRadiusParameterName.c_str(), connectomicsRenderingEdgeRadiusParameter, renderer, overwrite ); Superclass::SetDefaultProperties(node, renderer, overwrite); } void mitk::ConnectomicsNetworkMapper3D::ApplyProperties(mitk::BaseRenderer* renderer) { //TODO: implement } void mitk::ConnectomicsNetworkMapper3D::SetVtkMapperImmediateModeRendering(vtkMapper *mapper) { //TODO: implement } void mitk::ConnectomicsNetworkMapper3D::UpdateVtkObjects() { //TODO: implement } vtkProp* mitk::ConnectomicsNetworkMapper3D::GetVtkProp(mitk::BaseRenderer *renderer) { return m_NetworkAssembly; } bool mitk::ConnectomicsNetworkMapper3D::PropertiesChanged() { mitk::ConnectomicsRenderingSchemeProperty * renderingScheme = static_cast< mitk::ConnectomicsRenderingSchemeProperty * > ( this->GetDataNode()->GetProperty( connectomicsRenderingSchemePropertyName.c_str() ) ); mitk::ConnectomicsRenderingEdgeFilteringProperty * edgeFilter = static_cast< mitk::ConnectomicsRenderingEdgeFilteringProperty * > ( this->GetDataNode()->GetProperty( connectomicsRenderingEdgeFilteringPropertyName.c_str() ) ); mitk::FloatProperty * edgeThreshold = static_cast< mitk::FloatProperty * > ( this->GetDataNode()->GetProperty( connectomicsRenderingEdgeThresholdFilterThresholdName.c_str() ) ); mitk::ConnectomicsRenderingNodeFilteringProperty * nodeFilter = static_cast< mitk::ConnectomicsRenderingNodeFilteringProperty * > ( this->GetDataNode()->GetProperty( connectomicsRenderingNodeFilteringPropertyName.c_str() ) ); mitk::ConnectomicsRenderingNodeThresholdParameterProperty * nodeThresholdParameter = static_cast< mitk::ConnectomicsRenderingNodeThresholdParameterProperty * > ( this->GetDataNode()->GetProperty( connectomicsRenderingNodeThresholdFilterParameterName.c_str() ) ); mitk::ConnectomicsRenderingEdgeThresholdParameterProperty * edgeThresholdParameter = static_cast< mitk::ConnectomicsRenderingEdgeThresholdParameterProperty * > ( this->GetDataNode()->GetProperty( connectomicsRenderingEdgeThresholdFilterParameterName.c_str() ) ); mitk::FloatProperty * nodeThreshold = static_cast< mitk::FloatProperty * > ( this->GetDataNode()->GetProperty( connectomicsRenderingNodeThresholdFilterThresholdName.c_str() ) ); mitk::ColorProperty * nodeColorStart = static_cast< mitk::ColorProperty * > ( this->GetDataNode()->GetProperty( connectomicsRenderingNodeGradientStartColorName.c_str() ) ); mitk::ColorProperty * nodeColorEnd = static_cast< mitk::ColorProperty * > ( this->GetDataNode()->GetProperty( connectomicsRenderingNodeGradientEndColorName.c_str() ) ); mitk::FloatProperty * nodeRadiusStart = static_cast< mitk::FloatProperty * > ( this->GetDataNode()->GetProperty( connectomicsRenderingNodeRadiusStartName.c_str() ) ); mitk::FloatProperty * nodeRadiusEnd = static_cast< mitk::FloatProperty * > ( this->GetDataNode()->GetProperty( connectomicsRenderingNodeRadiusEndName.c_str() ) ); mitk::StringProperty * chosenNode = static_cast< mitk::StringProperty * > ( this->GetDataNode()->GetProperty( connectomicsRenderingNodeChosenNodeName.c_str() ) ); mitk::ColorProperty * edgeColorStart = static_cast< mitk::ColorProperty * > ( this->GetDataNode()->GetProperty( connectomicsRenderingEdgeGradientStartColorName.c_str() ) ); mitk::ColorProperty * edgeColorEnd = static_cast< mitk::ColorProperty * > ( this->GetDataNode()->GetProperty( connectomicsRenderingEdgeGradientEndColorName.c_str() ) ); mitk::FloatProperty * edgeRadiusStart = static_cast< mitk::FloatProperty * > ( this->GetDataNode()->GetProperty( connectomicsRenderingEdgeRadiusStartName.c_str() ) ); mitk::FloatProperty * edgeRadiusEnd = static_cast< mitk::FloatProperty * > ( this->GetDataNode()->GetProperty( connectomicsRenderingEdgeRadiusEndName.c_str() ) ); mitk::ConnectomicsRenderingNodeColorParameterProperty * nodeColorParameter = static_cast< mitk::ConnectomicsRenderingNodeColorParameterProperty * > ( this->GetDataNode()->GetProperty( connectomicsRenderingNodeGradientColorParameterName.c_str() ) ); mitk::ConnectomicsRenderingNodeRadiusParameterProperty * nodeRadiusParameter = static_cast< mitk::ConnectomicsRenderingNodeRadiusParameterProperty * > ( this->GetDataNode()->GetProperty( connectomicsRenderingNodeRadiusParameterName.c_str() ) ); mitk::ConnectomicsRenderingEdgeColorParameterProperty * edgeColorParameter = static_cast< mitk::ConnectomicsRenderingEdgeColorParameterProperty * > ( this->GetDataNode()->GetProperty( connectomicsRenderingEdgeGradientColorParameterName.c_str() ) ); mitk::ConnectomicsRenderingEdgeRadiusParameterProperty * edgeRadiusParameter = static_cast< mitk::ConnectomicsRenderingEdgeRadiusParameterProperty * > ( this->GetDataNode()->GetProperty( connectomicsRenderingEdgeRadiusParameterName.c_str() ) ); if( m_ChosenRenderingScheme != renderingScheme->GetValueAsString() || m_ChosenEdgeFilter != edgeFilter->GetValueAsString() || m_EdgeThreshold != edgeThreshold->GetValue() || m_EdgeThresholdParameter != edgeThresholdParameter->GetValueAsString() || m_ChosenNodeFilter != nodeFilter->GetValueAsString() || m_NodeThreshold != nodeThreshold->GetValue() || m_NodeThresholdParameter != nodeThresholdParameter->GetValueAsString() || m_NodeColorStart != nodeColorStart->GetValue() || m_NodeColorEnd != nodeColorEnd->GetValue() || m_NodeRadiusStart != nodeRadiusStart->GetValue() || m_NodeRadiusEnd != nodeRadiusEnd->GetValue() || m_ChosenNodeLabel != chosenNode->GetValueAsString() || m_EdgeColorStart != edgeColorStart->GetValue() || m_EdgeColorEnd != edgeColorEnd->GetValue() || m_EdgeRadiusStart != edgeRadiusStart->GetValue() || m_EdgeRadiusEnd != edgeRadiusEnd->GetValue() || m_NodeColorParameter != nodeColorParameter->GetValueAsString() || m_NodeRadiusParameter != nodeRadiusParameter->GetValueAsString() || m_EdgeColorParameter != edgeColorParameter->GetValueAsString() || m_EdgeRadiusParameter != edgeRadiusParameter->GetValueAsString() ) { m_ChosenRenderingScheme = renderingScheme->GetValueAsString(); m_ChosenEdgeFilter = edgeFilter->GetValueAsString(); m_EdgeThreshold = edgeThreshold->GetValue(); m_EdgeThresholdParameter = edgeThresholdParameter->GetValueAsString(); m_ChosenNodeFilter = nodeFilter->GetValueAsString(); m_NodeThreshold = nodeThreshold->GetValue(); m_NodeThresholdParameter = nodeThresholdParameter->GetValueAsString(); m_NodeColorStart = nodeColorStart->GetValue(); m_NodeColorEnd = nodeColorEnd->GetValue(); m_NodeRadiusStart = nodeRadiusStart->GetValue(); m_NodeRadiusEnd = nodeRadiusEnd->GetValue(); m_ChosenNodeLabel = chosenNode->GetValueAsString(); m_EdgeColorStart = edgeColorStart->GetValue(); m_EdgeColorEnd = edgeColorEnd->GetValue(); m_EdgeRadiusStart = edgeRadiusStart->GetValue(); m_EdgeRadiusEnd = edgeRadiusEnd->GetValue(); m_NodeColorParameter = nodeColorParameter->GetValueAsString(); m_NodeRadiusParameter = nodeRadiusParameter->GetValueAsString(); m_EdgeColorParameter = edgeColorParameter->GetValueAsString(); m_EdgeRadiusParameter = edgeRadiusParameter->GetValueAsString(); return true; } return false; } double mitk::ConnectomicsNetworkMapper3D::FillNodeParameterVector( std::vector< double > * parameterVector, std::string parameterName ) { int end( parameterVector->size() ); // constant parameter - uniform style if( parameterName == connectomicsRenderingNodeParameterConstant ) { for(int index(0); index < end; index++) { parameterVector->at( index ) = 1.0; } return 1.0; } double maximum( 0.0 ); // using the degree as parameter if( parameterName == connectomicsRenderingNodeParameterDegree ) { std::vector< int > vectorOfDegree = this->GetInput()->GetDegreeOfNodes(); for(int index(0); index < end; index++) { parameterVector->at( index ) = vectorOfDegree[ index ]; } maximum = *std::max_element( parameterVector->begin(), parameterVector->end() ); } // using betweenness centrality as parameter if( parameterName == connectomicsRenderingNodeParameterBetweenness ) { std::vector< double > vectorOfBetweenness = this->GetInput()->GetNodeBetweennessVector(); for(int index(0); index < end; index++) { parameterVector->at( index ) = vectorOfBetweenness[index]; } maximum = *std::max_element( parameterVector->begin(), parameterVector->end() ); } // using clustering coefficient as parameter if( parameterName == connectomicsRenderingNodeParameterClustering ) { const std::vector< double > vectorOfClustering = this->GetInput()->GetLocalClusteringCoefficients(); for(int index(0); index < end; index++) { parameterVector->at( index ) = vectorOfClustering[index]; } maximum = *std::max_element( parameterVector->begin(), parameterVector->end() ); } // using distance to a specific node as parameter if( parameterName == connectomicsRenderingNodeParameterColoringShortestPath ) { bool labelFound( this->GetInput()->CheckForLabel( m_ChosenNodeLabel ) ); // check whether the chosen node is valid if( !labelFound ) { MITK_WARN << "Node chosen for rendering is not valid."; for(int index(0); index < end; index++) { parameterVector->at( index ) = 1.0; } return 1.0; } else { const std::vector< double > distanceVector = this->GetInput()->GetShortestDistanceVectorFromLabel( m_ChosenNodeLabel ); for(int index(0); index < end; index++) { parameterVector->at( index ) = distanceVector[index]; } maximum = *std::max_element( parameterVector->begin(), parameterVector->end() ); } } // if the maximum is nearly zero if( std::abs( maximum ) < mitk::eps ) { maximum = 1.0; } return maximum; } double mitk::ConnectomicsNetworkMapper3D::FillEdgeParameterVector( std::vector< double > * parameterVector, std::string parameterName ) { int end( parameterVector->size() ); // constant parameter - uniform style if( parameterName == connectomicsRenderingEdgeParameterConstant ) { for(int index(0); index < end; index++) { parameterVector->at( index ) = 1.0; } return 1.0; } double maximum( 0.0 ); // using the weight as parameter if( parameterName == connectomicsRenderingEdgeParameterWeight ) { std::vector< std::pair< std::pair< mitk::ConnectomicsNetwork::NetworkNode, mitk::ConnectomicsNetwork::NetworkNode > , mitk::ConnectomicsNetwork::NetworkEdge > > vectorOfEdges = this->GetInput()->GetVectorOfAllEdges(); for(int index(0); index < end; index++) { parameterVector->at( index ) = vectorOfEdges[ index ].second.weight; } maximum = *std::max_element( parameterVector->begin(), parameterVector->end() ); } // using the edge centrality as parameter if( parameterName == connectomicsRenderingEdgeParameterCentrality ) { const std::vector< double > vectorOfCentrality = this->GetInput()->GetEdgeBetweennessVector(); for(int index(0); index < end; index++) { parameterVector->at( index ) = vectorOfCentrality[index]; } maximum = *std::max_element( parameterVector->begin(), parameterVector->end() ); } // if the maximum is nearly zero if( std::abs( maximum ) < mitk::eps ) { maximum = 1.0; } return maximum; } void mitk::ConnectomicsNetworkMapper3D::FillNodeFilterBoolVector( std::vector< bool > * boolVector, std::string parameterName ) { std::vector< double > parameterVector; parameterVector.resize( boolVector->size() ); int end( parameterVector.size() ); // using the degree as parameter if( parameterName == connectomicsRenderingNodeParameterDegree ) { std::vector< int > vectorOfDegree = this->GetInput()->GetDegreeOfNodes(); for(int index(0); index < end; index++) { parameterVector.at( index ) = vectorOfDegree[ index ]; } } // using betweenness centrality as parameter if( parameterName == connectomicsRenderingNodeParameterBetweenness ) { std::vector< double > vectorOfBetweenness = this->GetInput()->GetNodeBetweennessVector(); for(int index(0); index < end; index++) { parameterVector.at( index ) = vectorOfBetweenness[index]; } } // using clustering coefficient as parameter if( parameterName == connectomicsRenderingNodeParameterClustering ) { const std::vector< double > vectorOfClustering = this->GetInput()->GetLocalClusteringCoefficients(); for(int index(0); index < end; index++) { parameterVector.at( index ) = vectorOfClustering[index]; } } for( int index( 0 ), end( boolVector->size() ); index < end; index++ ) { if( parameterVector.at( index ) >= m_NodeThreshold ) { boolVector->at( index ) = true; } else { boolVector->at( index ) = false; } } return; } void mitk::ConnectomicsNetworkMapper3D::FillEdgeFilterBoolVector( std::vector< bool > * boolVector, std::string parameterName ) { std::vector< double > parameterVector; parameterVector.resize( boolVector->size() ); int end( parameterVector.size() ); // using the weight as parameter if( parameterName == connectomicsRenderingEdgeParameterWeight ) { std::vector< std::pair< std::pair< mitk::ConnectomicsNetwork::NetworkNode, mitk::ConnectomicsNetwork::NetworkNode > , mitk::ConnectomicsNetwork::NetworkEdge > > vectorOfEdges = this->GetInput()->GetVectorOfAllEdges(); for(int index(0); index < end; index++) { parameterVector.at( index ) = vectorOfEdges[ index ].second.weight; } } // using the edge centrality as parameter if( parameterName == connectomicsRenderingEdgeParameterCentrality ) { const std::vector< double > vectorOfCentrality = this->GetInput()->GetEdgeBetweennessVector(); for(int index(0); index < end; index++) { parameterVector.at( index ) = vectorOfCentrality[index]; } } for( int index( 0 ), end( boolVector->size() ); index < end; index++ ) { if( parameterVector.at( index ) >= m_EdgeThreshold ) { boolVector->at( index ) = true; } else { boolVector->at( index ) = false; } } return; } diff --git a/Modules/DiffusionImaging/DiffusionCore/Algorithms/itkAdcImageFilter.txx b/Modules/DiffusionImaging/DiffusionCore/Algorithms/itkAdcImageFilter.txx index 9b205df5ad..85453a830e 100644 --- a/Modules/DiffusionImaging/DiffusionCore/Algorithms/itkAdcImageFilter.txx +++ b/Modules/DiffusionImaging/DiffusionCore/Algorithms/itkAdcImageFilter.txx @@ -1,130 +1,130 @@ /*=================================================================== 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. ===================================================================*/ #ifndef __itkAdcImageFilter_txx #define __itkAdcImageFilter_txx #include #include #include #define _USE_MATH_DEFINES #include #include "itkImageRegionConstIterator.h" #include "itkImageRegionConstIteratorWithIndex.h" #include "itkImageRegionIterator.h" namespace itk { template< class TInPixelType, class TOutPixelType > AdcImageFilter< TInPixelType, TOutPixelType> ::AdcImageFilter() { this->SetNumberOfRequiredInputs( 1 ); } template< class TInPixelType, class TOutPixelType > void AdcImageFilter< TInPixelType, TOutPixelType> ::BeforeThreadedGenerateData() { typename OutputImageType::Pointer outputImage = static_cast< OutputImageType * >(this->ProcessObject::GetOutput(0)); outputImage->FillBuffer(0.0); } template< class TInPixelType, class TOutPixelType > void AdcImageFilter< TInPixelType, TOutPixelType> ::ThreadedGenerateData(const OutputImageRegionType& outputRegionForThread, ThreadIdType ) { typename OutputImageType::Pointer outputImage = static_cast< OutputImageType * >(this->ProcessObject::GetOutput(0)); ImageRegionIterator< OutputImageType > oit(outputImage, outputRegionForThread); oit.GoToBegin(); typedef ImageRegionConstIterator< InputImageType > InputIteratorType; typename InputImageType::Pointer inputImagePointer = NULL; inputImagePointer = static_cast< InputImageType * >( this->ProcessObject::GetInput(0) ); InputIteratorType git( inputImagePointer, outputRegionForThread ); git.GoToBegin(); while( !git.IsAtEnd() ) { typename InputImageType::PixelType pix = git.Get(); TOutPixelType outval = 0; double S0 = 0; int c = 0; for (int i=0; iGetVectorLength(); i++) { GradientDirectionType g = m_GradientDirections->GetElement(i); if (g.magnitude()<0.001) { S0 += pix[i]; c++; } } if (c>0) S0 /= c; if (S0>0) { c = 0; for (int i=0; iGetVectorLength(); i++) { GradientDirectionType g = m_GradientDirections->GetElement(i); if (g.magnitude()>0.001) { double twonorm = g.two_norm(); double b = m_B_value*twonorm*twonorm; if (b>0) { double S = pix[i]; - outval += -std::log(S/S0)/b; + outval -= std::log(S/S0)/b; c++; } } } if (c>0) outval /= c; } if (outval==outval && outval<10000) oit.Set( outval ); ++oit; ++git; } std::cout << "One Thread finished calculation" << std::endl; } template< class TInPixelType, class TOutPixelType > void AdcImageFilter< TInPixelType, TOutPixelType> ::PrintSelf(std::ostream& os, Indent indent) const { Superclass::PrintSelf(os,indent); } } #endif // __itkAdcImageFilter_txx diff --git a/Modules/DiffusionImaging/DiffusionCore/CMakeLists.txt b/Modules/DiffusionImaging/DiffusionCore/CMakeLists.txt index c2a1616048..432911237c 100644 --- a/Modules/DiffusionImaging/DiffusionCore/CMakeLists.txt +++ b/Modules/DiffusionImaging/DiffusionCore/CMakeLists.txt @@ -1,17 +1,17 @@ find_package(ITK) if(ITK_GDCM_DIR) include(${ITK_GDCM_DIR}/GDCMConfig.cmake) if(GDCM_MAJOR_VERSION EQUAL 2) add_definitions(-DGDCM2) set(ITK_USES_GDCM2 1) endif(GDCM_MAJOR_VERSION EQUAL 2) endif(ITK_GDCM_DIR) MITK_CREATE_MODULE( DiffusionCore SUBPROJECTS MITK-DTI INCLUDE_DIRS Algorithms Algorithms/Reconstruction DicomImport IODataStructures/DiffusionWeightedImages IODataStructures/QBallImages IODataStructures/TensorImages IODataStructures Rendering ${CMAKE_CURRENT_BINARY_DIR} - DEPENDS MitkExt SceneSerializationBase QmitkExt + DEPENDS MitkExt SceneSerializationBase # QmitkExt PACKAGE_DEPENDS Boost ) -add_subdirectory(Testing) \ No newline at end of file +add_subdirectory(Testing) diff --git a/Modules/DiffusionImaging/FiberTracking/Algorithms/itkFibersFromPlanarFiguresFilter.cpp b/Modules/DiffusionImaging/FiberTracking/Algorithms/itkFibersFromPlanarFiguresFilter.cpp index d8eebc61dd..3ffb27fb47 100644 --- a/Modules/DiffusionImaging/FiberTracking/Algorithms/itkFibersFromPlanarFiguresFilter.cpp +++ b/Modules/DiffusionImaging/FiberTracking/Algorithms/itkFibersFromPlanarFiguresFilter.cpp @@ -1,254 +1,254 @@ /*=================================================================== 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 "itkFibersFromPlanarFiguresFilter.h" #define _USE_MATH_DEFINES #include // MITK #include #include #include #include #include #include #include #include #include // ITK #include #include #include #include // MISC #include #include #include #include namespace itk{ FibersFromPlanarFiguresFilter::FibersFromPlanarFiguresFilter() : m_Density(1000) - , m_FiberSampling(5) + , m_FiberSampling(1) , m_Tension(0) , m_Continuity(0) , m_Bias(0) , m_FiberDistribution(DISTRIBUTE_UNIFORM) , m_Variance(0.1) { } FibersFromPlanarFiguresFilter::~FibersFromPlanarFiguresFilter() { } void FibersFromPlanarFiguresFilter::GeneratePoints() { Statistics::MersenneTwisterRandomVariateGenerator::Pointer randGen = Statistics::MersenneTwisterRandomVariateGenerator::New(); randGen->SetSeed((unsigned int)0); m_2DPoints.clear(); int count = 0; while (count < m_Density) { mitk::Vector2D p; switch (m_FiberDistribution) { case DISTRIBUTE_GAUSSIAN: p[0] = randGen->GetNormalVariate(0, m_Variance); p[1] = randGen->GetNormalVariate(0, m_Variance); break; default: p[0] = randGen->GetUniformVariate(-1, 1); p[1] = randGen->GetUniformVariate(-1, 1); } if (sqrt(p[0]*p[0]+p[1]*p[1]) <= 1) { m_2DPoints.push_back(p); count++; } } } // perform global tracking void FibersFromPlanarFiguresFilter::GenerateData() { // check if enough fiducials are available for (int i=0; i m_VtkCellArray = vtkSmartPointer::New(); vtkSmartPointer m_VtkPoints = vtkSmartPointer::New(); vector< mitk::PlanarEllipse::Pointer > bundle = m_Fiducials.at(i); vector< unsigned int > fliplist; if (i container = vtkSmartPointer::New(); mitk::PlanarEllipse::Pointer figure = bundle.at(0); mitk::Point2D p0 = figure->GetControlPoint(0); mitk::Point2D p1 = figure->GetControlPoint(1); mitk::Point2D p2 = figure->GetControlPoint(2); mitk::Point2D p3 = figure->GetControlPoint(3); float r1 = p0.EuclideanDistanceTo(p1); float r2 = p0.EuclideanDistanceTo(p2); mitk::Vector2D eDir = p1-p0; eDir.Normalize(); mitk::Vector2D tDir = p3-p0; tDir.Normalize(); // apply twist vnl_matrix_fixed tRot; tRot[0][0] = tDir[0]; tRot[1][1] = tRot[0][0]; tRot[1][0] = sin(acos(tRot[0][0])); tRot[0][1] = -tRot[1][0]; if (tDir[1]<0) tRot.inplace_transpose(); m_2DPoints[j].SetVnlVector(tRot*m_2DPoints[j].GetVnlVector()); // apply new ellipse shape vnl_vector_fixed< float, 2 > newP; newP[0] = m_2DPoints.at(j)[0]; newP[1] = m_2DPoints.at(j)[1]; float alpha = acos(eDir[0]); if (eDir[1]>0) alpha = 2*M_PI-alpha; vnl_matrix_fixed eRot; eRot[0][0] = cos(alpha); eRot[1][1] = eRot[0][0]; eRot[1][0] = sin(alpha); eRot[0][1] = -eRot[1][0]; newP = eRot*newP; newP[0] *= r1; newP[1] *= r2; newP = eRot.transpose()*newP; p0[0] += newP[0]; p0[1] += newP[1]; const mitk::Geometry2D* pfgeometry = figure->GetGeometry2D(); const mitk::PlaneGeometry* planeGeo = dynamic_cast(pfgeometry); mitk::Point3D w, wc; planeGeo->Map(p0, w); wc = figure->GetWorldControlPoint(0); vtkIdType id = m_VtkPoints->InsertNextPoint(w.GetDataPointer()); container->GetPointIds()->InsertNextId(id); vnl_vector_fixed< float, 3 > n = planeGeo->GetNormalVnl(); for (int k=1; kGetControlPoint(0); p1 = figure->GetControlPoint(1); p2 = figure->GetControlPoint(2); p3 = figure->GetControlPoint(3); r1 = p0.EuclideanDistanceTo(p1); r2 = p0.EuclideanDistanceTo(p2); eDir = p1-p0; eDir.Normalize(); mitk::Vector2D tDir2 = p3-p0; tDir2.Normalize(); mitk::Vector2D temp; temp.SetVnlVector(tRot.transpose() * tDir2.GetVnlVector()); // apply twist tRot[0][0] = tDir[0]*tDir2[0] + tDir[1]*tDir2[1]; tRot[1][1] = tRot[0][0]; tRot[1][0] = sin(acos(tRot[0][0])); tRot[0][1] = -tRot[1][0]; if (temp[1]<0) tRot.inplace_transpose(); m_2DPoints[j].SetVnlVector(tRot*m_2DPoints[j].GetVnlVector()); tDir = tDir2; // apply new ellipse shape newP[0] = m_2DPoints.at(j)[0]; newP[1] = m_2DPoints.at(j)[1]; // calculate normal mitk::Geometry2D* pfgeometry = const_cast(figure->GetGeometry2D()); mitk::PlaneGeometry* planeGeo = dynamic_cast(pfgeometry); mitk::Vector3D perp = wc-planeGeo->ProjectPointOntoPlane(wc); perp.Normalize(); vnl_vector_fixed< float, 3 > n2 = planeGeo->GetNormalVnl(); wc = figure->GetWorldControlPoint(0); // is flip needed? if (dot_product(perp.GetVnlVector(),n2)>0 && dot_product(n,n2)<=0.00001) newP[0] *= -1; if (fliplist.at(k)>0) newP[0] *= -1; n = n2; alpha = acos(eDir[0]); if (eDir[1]>0) alpha = 2*M_PI-alpha; eRot[0][0] = cos(alpha); eRot[1][1] = eRot[0][0]; eRot[1][0] = sin(alpha); eRot[0][1] = -eRot[1][0]; newP = eRot*newP; newP[0] *= r1; newP[1] *= r2; newP = eRot.transpose()*newP; p0[0] += newP[0]; p0[1] += newP[1]; mitk::Point3D w; planeGeo->Map(p0, w); vtkIdType id = m_VtkPoints->InsertNextPoint(w.GetDataPointer()); container->GetPointIds()->InsertNextId(id); } m_VtkCellArray->InsertNextCell(container); } vtkSmartPointer fiberPolyData = vtkSmartPointer::New(); fiberPolyData->SetPoints(m_VtkPoints); fiberPolyData->SetLines(m_VtkCellArray); mitk::FiberBundleX::Pointer mitkFiberBundle = mitk::FiberBundleX::New(fiberPolyData); mitkFiberBundle->DoFiberSmoothing(m_FiberSampling, m_Tension, m_Continuity, m_Bias); m_FiberBundles.push_back(mitkFiberBundle); } } } diff --git a/Modules/DiffusionImaging/FiberTracking/Algorithms/itkFibersFromPlanarFiguresFilter.h b/Modules/DiffusionImaging/FiberTracking/Algorithms/itkFibersFromPlanarFiguresFilter.h index a582ddad06..b0d24d3530 100644 --- a/Modules/DiffusionImaging/FiberTracking/Algorithms/itkFibersFromPlanarFiguresFilter.h +++ b/Modules/DiffusionImaging/FiberTracking/Algorithms/itkFibersFromPlanarFiguresFilter.h @@ -1,105 +1,105 @@ /*=================================================================== 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. ===================================================================*/ #ifndef itkFibersFromPlanarFiguresFilter_h #define itkFibersFromPlanarFiguresFilter_h // MITK #include #include // ITK #include // VTK #include #include #include #include #include using namespace std; namespace itk{ /** * \brief Generates artificial fibers distributed in and interpolated between the input planar figures. */ class FibersFromPlanarFiguresFilter : public ProcessObject { public: enum FiberDistribution{ DISTRIBUTE_UNIFORM, // distribute fibers uniformly in the ROIs DISTRIBUTE_GAUSSIAN // distribute fibers using a 2D gaussian }; typedef FibersFromPlanarFiguresFilter Self; typedef ProcessObject Superclass; typedef SmartPointer< Self > Pointer; typedef SmartPointer< const Self > ConstPointer; typedef vector< vector< mitk::PlanarEllipse::Pointer > > FiducialListType; typedef vector< vector< unsigned int > > FlipListType; typedef mitk::FiberBundleX::Pointer FiberType; typedef vector< mitk::FiberBundleX::Pointer > FiberContainerType; itkNewMacro(Self) itkTypeMacro( FibersFromPlanarFiguresFilter, ProcessObject ) void GenerateData(); virtual void Update(){ this->GenerateData(); } // input void SetFlipList(FlipListType fliplist){ m_FlipList = fliplist; } ///< contains flags indicating a flip of the 2D fiber x-coordinates (needed to resolve some unwanted fiber twisting) void SetFiducials(FiducialListType fiducials){ m_Fiducials = fiducials; } ///< container of the planar ellipses used as fiducials for the fiber generation process itkSetMacro(Density, int) ///< number of fibers per bundle - itkSetMacro(FiberSampling, int) ///< sampling points of the fibers per cm + itkSetMacro(FiberSampling, double) ///< sampling points of the fibers per cm itkSetMacro(Tension, double) ///< tension parameter of the Kochanek-Bartels splines itkSetMacro(Continuity, double) ///< continuity parameter of the Kochanek-Bartels splines itkSetMacro(Bias, double) ///< bias parameter of the Kochanek-Bartels splines itkSetMacro(FiberDistribution, FiberDistribution) ///< flag to switch between uniform and gaussian distribution of the fiber waypoints inside of the fiducials itkSetMacro(Variance, double) ///< variance of the gaussian waypoint distribution // output FiberContainerType GetFiberBundles(){ return m_FiberBundles; } protected: FibersFromPlanarFiguresFilter(); virtual ~FibersFromPlanarFiguresFilter(); void GeneratePoints(); FiberDistribution m_FiberDistribution; ///< flag to switch between uniform and gaussian distribution of the fiber waypoints inside of the fiducials FlipListType m_FlipList; ///< contains flags indicating a flip of the 2D fiber x-coordinates (needed to resolve some unwanted fiber twisting) FiducialListType m_Fiducials; ///< container of the planar ellipses used as fiducials for the fiber generation process FiberContainerType m_FiberBundles; ///< container for the output fiber bundles int m_Density; ///< number of fibers per bundle - int m_FiberSampling; ///< sampling points of the fibers per cm + double m_FiberSampling; ///< sampling points of the fibers per cm double m_Tension; ///< tension parameter of the Kochanek-Bartels splines double m_Continuity; ///< continuity parameter of the Kochanek-Bartels splines double m_Bias; ///< bias parameter of the Kochanek-Bartels splines double m_Variance; ///< variance of the gaussian waypoint distribution vector< mitk::Vector2D > m_2DPoints; ///< container for the 2D fiber waypoints }; } #ifndef ITK_MANUAL_INSTANTIATION #include "itkFibersFromPlanarFiguresFilter.cpp" #endif #endif diff --git a/Modules/DiffusionImaging/FiberTracking/Algorithms/itkGibbsTrackingFilter.cpp b/Modules/DiffusionImaging/FiberTracking/Algorithms/itkGibbsTrackingFilter.cpp index ed4dedef0b..a93e25619b 100644 --- a/Modules/DiffusionImaging/FiberTracking/Algorithms/itkGibbsTrackingFilter.cpp +++ b/Modules/DiffusionImaging/FiberTracking/Algorithms/itkGibbsTrackingFilter.cpp @@ -1,509 +1,510 @@ /*=================================================================== 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 "itkGibbsTrackingFilter.h" // MITK #include #include #include #include #include //#include #include #include // ITK #include #include #include // MISC #include -#include +// #include #include #include #include +#include +#include namespace itk{ template< class ItkQBallImageType > GibbsTrackingFilter< ItkQBallImageType >::GibbsTrackingFilter(): m_StartTemperature(0.1), m_EndTemperature(0.001), m_Iterations(500000), m_ParticleWeight(0), m_ParticleWidth(0), m_ParticleLength(0), m_ConnectionPotential(10), m_InexBalance(0), m_ParticlePotential(0.2), m_MinFiberLength(10), m_AbortTracking(false), m_NumConnections(0), m_NumParticles(0), m_NumAcceptedFibers(0), m_CurrentStep(0), m_BuildFibers(false), m_Steps(10), m_ProposalAcceptance(0), m_CurvatureThreshold(0.7), m_DuplicateImage(true), m_RandomSeed(-1), m_LoadParameterFile(""), m_LutPath(""), m_IsInValidState(true) { } template< class ItkQBallImageType > GibbsTrackingFilter< ItkQBallImageType >::~GibbsTrackingFilter() { } // fill output fiber bundle datastructure template< class ItkQBallImageType > typename GibbsTrackingFilter< ItkQBallImageType >::FiberPolyDataType GibbsTrackingFilter< ItkQBallImageType >::GetFiberBundle() { if (!m_AbortTracking) { m_BuildFibers = true; while (m_BuildFibers){} } return m_FiberPolyData; } template< class ItkQBallImageType > void GibbsTrackingFilter< ItkQBallImageType > ::EstimateParticleWeight() { MITK_INFO << "GibbsTrackingFilter: estimating particle weight"; float minSpacing; if(m_QBallImage->GetSpacing()[0]GetSpacing()[1] && m_QBallImage->GetSpacing()[0]GetSpacing()[2]) minSpacing = m_QBallImage->GetSpacing()[0]; else if (m_QBallImage->GetSpacing()[1] < m_QBallImage->GetSpacing()[2]) minSpacing = m_QBallImage->GetSpacing()[1]; else minSpacing = m_QBallImage->GetSpacing()[2]; float m_ParticleLength = 1.5*minSpacing; float m_ParticleWidth = 0.5*minSpacing; // seed random generators Statistics::MersenneTwisterRandomVariateGenerator::Pointer randGen = Statistics::MersenneTwisterRandomVariateGenerator::New(); if (m_RandomSeed>-1) randGen->SetSeed(m_RandomSeed); else randGen->SetSeed(); // instantiate all necessary components SphereInterpolator* interpolator = new SphereInterpolator(m_LutPath); // handle lookup table not found cases if( !interpolator->IsInValidState() ) { m_IsInValidState = false; m_AbortTracking = true; m_BuildFibers = false; mitkThrow() << "Unable to load lookup tables."; } ParticleGrid* particleGrid = new ParticleGrid(m_MaskImage, m_ParticleLength, m_ParticleGridCellCapacity); GibbsEnergyComputer* encomp = new GibbsEnergyComputer(m_QBallImage, m_MaskImage, particleGrid, interpolator, randGen); // EnergyComputer* encomp = new EnergyComputer(m_QBallImage, m_MaskImage, particleGrid, interpolator, randGen); MetropolisHastingsSampler* sampler = new MetropolisHastingsSampler(particleGrid, encomp, randGen, m_CurvatureThreshold); float alpha = log(m_EndTemperature/m_StartTemperature); m_ParticleWeight = 0.01; int ppv = 0; // main loop int neededParts = 3000; while (ppvSetParameters(m_ParticleWeight,m_ParticleWidth,m_ConnectionPotential*m_ParticleLength*m_ParticleLength,m_CurvatureThreshold,m_InexBalance,m_ParticlePotential); for( int step = 0; step < 10; step++ ) { // update temperatur for simulated annealing process float temperature = m_StartTemperature * exp(alpha*(((1.0)*step)/((1.0)*10))); sampler->SetTemperature(temperature); for (unsigned long i=0; i<10000; i++) sampler->MakeProposal(); } ppv = particleGrid->m_NumParticles; particleGrid->ResetGrid(); } delete sampler; delete encomp; delete particleGrid; delete interpolator; MITK_INFO << "GibbsTrackingFilter: finished estimating particle weight"; } // perform global tracking template< class ItkQBallImageType > void GibbsTrackingFilter< ItkQBallImageType >::GenerateData() { TimeProbe preClock; preClock.Start(); // check if input is qball or tensor image and generate qball if necessary if (m_QBallImage.IsNull() && m_TensorImage.IsNotNull()) { TensorImageToQBallImageFilter::Pointer filter = TensorImageToQBallImageFilter::New(); filter->SetInput( m_TensorImage ); filter->Update(); m_QBallImage = filter->GetOutput(); } else if (m_DuplicateImage) // generate local working copy of QBall image (if not disabled) { typedef itk::ImageDuplicator< ItkQBallImageType > DuplicateFilterType; typename DuplicateFilterType::Pointer duplicator = DuplicateFilterType::New(); duplicator->SetInputImage( m_QBallImage ); duplicator->Update(); m_QBallImage = duplicator->GetOutput(); } // perform mean subtraction on odfs typedef ImageRegionIterator< ItkQBallImageType > InputIteratorType; InputIteratorType it(m_QBallImage, m_QBallImage->GetLargestPossibleRegion() ); it.GoToBegin(); while (!it.IsAtEnd()) { itk::OrientationDistributionFunction odf(it.Get().GetDataPointer()); float mean = odf.GetMeanValue(); odf -= mean; it.Set(odf.GetDataPointer()); ++it; } // check if mask image is given if it needs resampling PrepareMaskImage(); // load parameter file LoadParameters(); // prepare parameters float minSpacing; if(m_QBallImage->GetSpacing()[0]GetSpacing()[1] && m_QBallImage->GetSpacing()[0]GetSpacing()[2]) minSpacing = m_QBallImage->GetSpacing()[0]; else if (m_QBallImage->GetSpacing()[1] < m_QBallImage->GetSpacing()[2]) minSpacing = m_QBallImage->GetSpacing()[1]; else minSpacing = m_QBallImage->GetSpacing()[2]; if(m_ParticleLength == 0) m_ParticleLength = 1.5*minSpacing; if(m_ParticleWidth == 0) m_ParticleWidth = 0.5*minSpacing; if(m_ParticleWeight == 0) EstimateParticleWeight(); float alpha = log(m_EndTemperature/m_StartTemperature); m_Steps = m_Iterations/10000; if (m_Steps<10) m_Steps = 10; if (m_Steps>m_Iterations) { MITK_INFO << "GibbsTrackingFilter: not enough iterations!"; m_AbortTracking = true; } if (m_CurvatureThreshold < mitk::eps) m_CurvatureThreshold = 0; unsigned long singleIts = (unsigned long)((1.0*m_Iterations) / (1.0*m_Steps)); // seed random generators Statistics::MersenneTwisterRandomVariateGenerator::Pointer randGen = Statistics::MersenneTwisterRandomVariateGenerator::New(); if (m_RandomSeed>-1) randGen->SetSeed(m_RandomSeed); else randGen->SetSeed(); // load sphere interpolator to evaluate the ODFs SphereInterpolator* interpolator = new SphereInterpolator(m_LutPath); // handle lookup table not found cases if( !interpolator->IsInValidState() ) { m_IsInValidState = false; m_AbortTracking = true; m_BuildFibers = false; mitkThrow() << "Unable to load lookup tables."; } // initialize the actual tracking components (ParticleGrid, Metropolis Hastings Sampler and Energy Computer) ParticleGrid* particleGrid; GibbsEnergyComputer* encomp; MetropolisHastingsSampler* sampler; try{ particleGrid = new ParticleGrid(m_MaskImage, m_ParticleLength, m_ParticleGridCellCapacity); encomp = new GibbsEnergyComputer(m_QBallImage, m_MaskImage, particleGrid, interpolator, randGen); encomp->SetParameters(m_ParticleWeight,m_ParticleWidth,m_ConnectionPotential*m_ParticleLength*m_ParticleLength,m_CurvatureThreshold,m_InexBalance,m_ParticlePotential); sampler = new MetropolisHastingsSampler(particleGrid, encomp, randGen, m_CurvatureThreshold); } catch(...) { MITK_ERROR << "Particle grid allocation failed. Not enough memory? Try to increase the particle length."; m_IsInValidState = false; m_AbortTracking = true; m_BuildFibers = false; return; } MITK_INFO << "----------------------------------------"; MITK_INFO << "Iterations: " << m_Iterations; MITK_INFO << "Steps: " << m_Steps; MITK_INFO << "Particle length: " << m_ParticleLength; MITK_INFO << "Particle width: " << m_ParticleWidth; MITK_INFO << "Particle weight: " << m_ParticleWeight; MITK_INFO << "Start temperature: " << m_StartTemperature; MITK_INFO << "End temperature: " << m_EndTemperature; MITK_INFO << "In/Ex balance: " << m_InexBalance; MITK_INFO << "Min. fiber length: " << m_MinFiberLength; MITK_INFO << "Curvature threshold: " << m_CurvatureThreshold; MITK_INFO << "Random seed: " << m_RandomSeed; MITK_INFO << "----------------------------------------"; // main loop preClock.Stop(); TimeProbe clock; clock.Start(); m_NumAcceptedFibers = 0; unsigned long counter = 1; boost::progress_display disp(m_Steps*singleIts); if (!m_AbortTracking) for( m_CurrentStep = 1; m_CurrentStep <= m_Steps; m_CurrentStep++ ) { // update temperatur for simulated annealing process float temperature = m_StartTemperature * exp(alpha*(((1.0)*m_CurrentStep)/((1.0)*m_Steps))); sampler->SetTemperature(temperature); for (unsigned long i=0; iMakeProposal(); if (m_BuildFibers || (i==singleIts-1 && m_CurrentStep==m_Steps)) { m_ProposalAcceptance = (float)sampler->GetNumAcceptedProposals()/counter; m_NumParticles = particleGrid->m_NumParticles; m_NumConnections = particleGrid->m_NumConnections; FiberBuilder fiberBuilder(particleGrid, m_MaskImage); m_FiberPolyData = fiberBuilder.iterate(m_MinFiberLength); m_NumAcceptedFibers = m_FiberPolyData->GetNumberOfLines(); m_BuildFibers = false; } counter++; } m_ProposalAcceptance = (float)sampler->GetNumAcceptedProposals()/counter; m_NumParticles = particleGrid->m_NumParticles; m_NumConnections = particleGrid->m_NumConnections; if (m_AbortTracking) break; } if (m_AbortTracking) { FiberBuilder fiberBuilder(particleGrid, m_MaskImage); m_FiberPolyData = fiberBuilder.iterate(m_MinFiberLength); m_NumAcceptedFibers = m_FiberPolyData->GetNumberOfLines(); } clock.Stop(); delete sampler; delete encomp; delete interpolator; delete particleGrid; m_AbortTracking = true; m_BuildFibers = false; int h = clock.GetTotal()/3600; int m = ((int)clock.GetTotal()%3600)/60; int s = (int)clock.GetTotal()%60; MITK_INFO << "GibbsTrackingFilter: finished gibbs tracking in " << h << "h, " << m << "m and " << s << "s"; m = (int)preClock.GetTotal()/60; s = (int)preClock.GetTotal()%60; MITK_INFO << "GibbsTrackingFilter: preparation of the data took " << m << "m and " << s << "s"; MITK_INFO << "GibbsTrackingFilter: " << m_NumAcceptedFibers << " fibers accepted"; SaveParameters(); } template< class ItkQBallImageType > void GibbsTrackingFilter< ItkQBallImageType >::PrepareMaskImage() { if(m_MaskImage.IsNull()) { MITK_INFO << "GibbsTrackingFilter: generating default mask image"; m_MaskImage = ItkFloatImageType::New(); m_MaskImage->SetSpacing( m_QBallImage->GetSpacing() ); m_MaskImage->SetOrigin( m_QBallImage->GetOrigin() ); m_MaskImage->SetDirection( m_QBallImage->GetDirection() ); m_MaskImage->SetRegions( m_QBallImage->GetLargestPossibleRegion() ); m_MaskImage->Allocate(); m_MaskImage->FillBuffer(1.0); } else if ( m_MaskImage->GetLargestPossibleRegion().GetSize()[0]!=m_QBallImage->GetLargestPossibleRegion().GetSize()[0] || m_MaskImage->GetLargestPossibleRegion().GetSize()[1]!=m_QBallImage->GetLargestPossibleRegion().GetSize()[1] || m_MaskImage->GetLargestPossibleRegion().GetSize()[2]!=m_QBallImage->GetLargestPossibleRegion().GetSize()[2] || m_MaskImage->GetSpacing()[0]!=m_QBallImage->GetSpacing()[0] || m_MaskImage->GetSpacing()[1]!=m_QBallImage->GetSpacing()[1] || m_MaskImage->GetSpacing()[2]!=m_QBallImage->GetSpacing()[2] ) { MITK_INFO << "GibbsTrackingFilter: resampling mask image"; typedef itk::ResampleImageFilter< ItkFloatImageType, ItkFloatImageType, float > ResamplerType; ResamplerType::Pointer resampler = ResamplerType::New(); resampler->SetOutputSpacing( m_QBallImage->GetSpacing() ); resampler->SetOutputOrigin( m_QBallImage->GetOrigin() ); resampler->SetOutputDirection( m_QBallImage->GetDirection() ); resampler->SetSize( m_QBallImage->GetLargestPossibleRegion().GetSize() ); resampler->SetInput( m_MaskImage ); resampler->SetDefaultPixelValue(0.0); resampler->Update(); m_MaskImage = resampler->GetOutput(); MITK_INFO << "GibbsTrackingFilter: resampling finished"; } } // load tracking paramters from xml file (.gtp) template< class ItkQBallImageType > bool GibbsTrackingFilter< ItkQBallImageType >::LoadParameters() { m_AbortTracking = true; try { if( m_LoadParameterFile.length()==0 ) { m_AbortTracking = false; return true; } MITK_INFO << "GibbsTrackingFilter: loading parameter file " << m_LoadParameterFile; TiXmlDocument doc( m_LoadParameterFile ); doc.LoadFile(); TiXmlHandle hDoc(&doc); TiXmlElement* pElem; TiXmlHandle hRoot(0); pElem = hDoc.FirstChildElement().Element(); hRoot = TiXmlHandle(pElem); pElem = hRoot.FirstChildElement("parameter_set").Element(); - QString iterations(pElem->Attribute("iterations")); - m_Iterations = iterations.toULong(); + string iterations(pElem->Attribute("iterations")); + m_Iterations = boost::lexical_cast(iterations); - QString particleLength(pElem->Attribute("particle_length")); - m_ParticleLength = particleLength.toFloat(); + string particleLength(pElem->Attribute("particle_length")); + m_ParticleLength = boost::lexical_cast(particleLength); - QString particleWidth(pElem->Attribute("particle_width")); - m_ParticleWidth = particleWidth.toFloat(); + string particleWidth(pElem->Attribute("particle_width")); + m_ParticleWidth = boost::lexical_cast(particleWidth); - QString partWeight(pElem->Attribute("particle_weight")); - m_ParticleWeight = partWeight.toFloat(); + string partWeight(pElem->Attribute("particle_weight")); + m_ParticleWeight = boost::lexical_cast(partWeight); - QString startTemp(pElem->Attribute("temp_start")); - m_StartTemperature = startTemp.toFloat(); + string startTemp(pElem->Attribute("temp_start")); + m_StartTemperature = boost::lexical_cast(startTemp); - QString endTemp(pElem->Attribute("temp_end")); - m_EndTemperature = endTemp.toFloat(); + string endTemp(pElem->Attribute("temp_end")); + m_EndTemperature = boost::lexical_cast(endTemp); - QString inExBalance(pElem->Attribute("inexbalance")); - m_InexBalance = inExBalance.toFloat(); + string inExBalance(pElem->Attribute("inexbalance")); + m_InexBalance = boost::lexical_cast(inExBalance); - QString fiberLength(pElem->Attribute("fiber_length")); - m_MinFiberLength = fiberLength.toFloat(); + string fiberLength(pElem->Attribute("fiber_length")); + m_MinFiberLength = boost::lexical_cast(fiberLength); - QString curvThres(pElem->Attribute("curvature_threshold")); - m_CurvatureThreshold = cos(curvThres.toFloat()*M_PI/180); + string curvThres(pElem->Attribute("curvature_threshold")); + m_CurvatureThreshold = cos(boost::lexical_cast(curvThres)*M_PI/180); m_AbortTracking = false; MITK_INFO << "GibbsTrackingFilter: parameter file loaded successfully"; return true; } catch(...) { MITK_INFO << "GibbsTrackingFilter: could not load parameter file"; return false; } } // save current tracking paramters to xml file (.gtp) template< class ItkQBallImageType > bool GibbsTrackingFilter< ItkQBallImageType >::SaveParameters() { try { if( m_SaveParameterFile.length()==0 ) { MITK_INFO << "GibbsTrackingFilter: no filename specified to save parameters"; return true; } MITK_INFO << "GibbsTrackingFilter: saving parameter file " << m_SaveParameterFile; TiXmlDocument documentXML; TiXmlDeclaration* declXML = new TiXmlDeclaration( "1.0", "", "" ); documentXML.LinkEndChild( declXML ); TiXmlElement* mainXML = new TiXmlElement("global_tracking_parameter_file"); mainXML->SetAttribute("file_version", "0.1"); documentXML.LinkEndChild(mainXML); TiXmlElement* paramXML = new TiXmlElement("parameter_set"); - paramXML->SetAttribute("iterations", QString::number(m_Iterations).toStdString()); - paramXML->SetAttribute("particle_length", QString::number(m_ParticleLength).toStdString()); - paramXML->SetAttribute("particle_width", QString::number(m_ParticleWidth).toStdString()); - paramXML->SetAttribute("particle_weight", QString::number(m_ParticleWeight).toStdString()); - paramXML->SetAttribute("temp_start", QString::number(m_StartTemperature).toStdString()); - paramXML->SetAttribute("temp_end", QString::number(m_EndTemperature).toStdString()); - paramXML->SetAttribute("inexbalance", QString::number(m_InexBalance).toStdString()); - paramXML->SetAttribute("fiber_length", QString::number(m_MinFiberLength).toStdString()); - paramXML->SetAttribute("curvature_threshold", QString::number(m_CurvatureThreshold).toStdString()); + paramXML->SetAttribute("iterations", boost::lexical_cast(m_Iterations)); + paramXML->SetAttribute("particle_length", boost::lexical_cast(m_ParticleLength)); + paramXML->SetAttribute("particle_width", boost::lexical_cast(m_ParticleWidth)); + paramXML->SetAttribute("particle_weight", boost::lexical_cast(m_ParticleWeight)); + paramXML->SetAttribute("temp_start", boost::lexical_cast(m_StartTemperature)); + paramXML->SetAttribute("temp_end", boost::lexical_cast(m_EndTemperature)); + paramXML->SetAttribute("inexbalance", boost::lexical_cast(m_InexBalance)); + paramXML->SetAttribute("fiber_length", boost::lexical_cast(m_MinFiberLength)); + paramXML->SetAttribute("curvature_threshold", boost::lexical_cast(m_CurvatureThreshold)); mainXML->LinkEndChild(paramXML); - QString filename(m_SaveParameterFile.c_str()); - if(!filename.endsWith(".gtp")) - filename += ".gtp"; - documentXML.SaveFile( filename.toStdString() ); + if(!boost::algorithm::ends_with(m_SaveParameterFile, ".gtp")) + m_SaveParameterFile.append(".gtp"); + documentXML.SaveFile( m_SaveParameterFile ); MITK_INFO << "GibbsTrackingFilter: parameter file saved successfully"; return true; } catch(...) { MITK_INFO << "GibbsTrackingFilter: could not save parameter file"; return false; } } } diff --git a/Modules/DiffusionImaging/FiberTracking/Algorithms/itkKspaceImageFilter.cpp b/Modules/DiffusionImaging/FiberTracking/Algorithms/itkKspaceImageFilter.cpp index 80faef1148..7d34b094ff 100644 --- a/Modules/DiffusionImaging/FiberTracking/Algorithms/itkKspaceImageFilter.cpp +++ b/Modules/DiffusionImaging/FiberTracking/Algorithms/itkKspaceImageFilter.cpp @@ -1,236 +1,237 @@ /*=================================================================== 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. ===================================================================*/ #ifndef __itkKspaceImageFilter_txx #define __itkKspaceImageFilter_txx #include #include #include #include "itkKspaceImageFilter.h" #include #include #include #include #define _USE_MATH_DEFINES #include namespace itk { template< class TPixelType > KspaceImageFilter< TPixelType > ::KspaceImageFilter() : m_tLine(1) , m_kOffset(0) , m_FrequencyMap(NULL) , m_SimulateRelaxation(true) , m_SimulateEddyCurrents(false) , m_Tau(70) , m_EddyGradientMagnitude(30) , m_IsBaseline(true) , m_SignalScale(1) { m_DiffusionGradientDirection.Fill(0.0); } template< class TPixelType > void KspaceImageFilter< TPixelType > ::BeforeThreadedGenerateData() { typename OutputImageType::Pointer outputImage = OutputImageType::New(); outputImage->SetSpacing( m_CompartmentImages.at(0)->GetSpacing() ); outputImage->SetOrigin( m_CompartmentImages.at(0)->GetOrigin() ); outputImage->SetDirection( m_CompartmentImages.at(0)->GetDirection() ); itk::ImageRegion<2> region; region.SetSize(0, m_OutSize[0]); region.SetSize(1, m_OutSize[1]); outputImage->SetLargestPossibleRegion( region ); outputImage->SetBufferedRegion( region ); outputImage->SetRequestedRegion( region ); outputImage->Allocate(); m_TEMPIMAGE = InputImageType::New(); m_TEMPIMAGE->SetSpacing( m_CompartmentImages.at(0)->GetSpacing() ); m_TEMPIMAGE->SetOrigin( m_CompartmentImages.at(0)->GetOrigin() ); m_TEMPIMAGE->SetDirection( m_CompartmentImages.at(0)->GetDirection() ); m_TEMPIMAGE->SetLargestPossibleRegion( region ); m_TEMPIMAGE->SetBufferedRegion( region ); m_TEMPIMAGE->SetRequestedRegion( region ); m_TEMPIMAGE->Allocate(); m_SimulateDistortions = true; if (m_FrequencyMap.IsNull()) { m_SimulateDistortions = false; m_FrequencyMap = InputImageType::New(); m_FrequencyMap->SetSpacing( m_CompartmentImages.at(0)->GetSpacing() ); m_FrequencyMap->SetOrigin( m_CompartmentImages.at(0)->GetOrigin() ); m_FrequencyMap->SetDirection( m_CompartmentImages.at(0)->GetDirection() ); m_FrequencyMap->SetLargestPossibleRegion( m_CompartmentImages.at(0)->GetLargestPossibleRegion() ); m_FrequencyMap->SetBufferedRegion( m_CompartmentImages.at(0)->GetLargestPossibleRegion() ); m_FrequencyMap->SetRequestedRegion( m_CompartmentImages.at(0)->GetLargestPossibleRegion() ); m_FrequencyMap->Allocate(); m_FrequencyMap->FillBuffer(0); } double gamma = 42576000; // Gyromagnetic ratio in Hz/T if (m_DiffusionGradientDirection.GetNorm()>0.001) { m_DiffusionGradientDirection.Normalize(); m_EddyGradientMagnitude /= 1000; // eddy gradient magnitude in T/m m_DiffusionGradientDirection = m_DiffusionGradientDirection * m_EddyGradientMagnitude * gamma; m_IsBaseline = false; } else m_EddyGradientMagnitude = gamma*m_EddyGradientMagnitude/1000; this->SetNthOutput(0, outputImage); } template< class TPixelType > void KspaceImageFilter< TPixelType > ::ThreadedGenerateData(const OutputImageRegionType& outputRegionForThread, ThreadIdType threadId) { typename OutputImageType::Pointer outputImage = static_cast< OutputImageType * >(this->ProcessObject::GetOutput(0)); ImageRegionIterator< OutputImageType > oit(outputImage, outputRegionForThread); typedef ImageRegionConstIterator< InputImageType > InputIteratorType; double szx = outputImage->GetLargestPossibleRegion().GetSize(0); double szy = outputImage->GetLargestPossibleRegion().GetSize(1); double numPix = szx*szy; double dt = m_tLine/szx; double fromMaxEcho = - m_tLine*szy/2; double in_szx = m_CompartmentImages.at(0)->GetLargestPossibleRegion().GetSize(0); double in_szy = m_CompartmentImages.at(0)->GetLargestPossibleRegion().GetSize(1); int xOffset = in_szx-szx; int yOffset = in_szy-szy; while( !oit.IsAtEnd() ) { itk::Index< 2 > kIdx; kIdx[0] = oit.GetIndex()[0]; kIdx[1] = oit.GetIndex()[1]; double t = fromMaxEcho + ((double)kIdx[1]*szx+(double)kIdx[0])*dt; // dephasing time + + // rearrange slice + if( kIdx[0] < szx/2 ) + kIdx[0] = kIdx[0] + szx/2; + else + kIdx[0] = kIdx[0] - szx/2; + + if( kIdx[1] < szx/2 ) + kIdx[1] = kIdx[1] + szy/2; + else + kIdx[1] = kIdx[1] - szy/2; + // calculate eddy current decay factors double eddyDecay = 0; if (m_SimulateEddyCurrents) eddyDecay = exp(-(m_TE/2 + t)/m_Tau) * t/1000; // calcualte signal relaxation factors std::vector< double > relaxFactor; if (m_SimulateRelaxation) { for (int i=0; i s(0,0); InputIteratorType it(m_CompartmentImages.at(0), m_CompartmentImages.at(0)->GetLargestPossibleRegion() ); while( !it.IsAtEnd() ) { double x = it.GetIndex()[0]; double y = it.GetIndex()[1]; vcl_complex f(0, 0); // sum compartment signals and simulate relaxation for (int i=0; i( m_CompartmentImages.at(i)->GetPixel(it.GetIndex()) * relaxFactor.at(i) * m_SignalScale, 0); else f += std::complex( m_CompartmentImages.at(i)->GetPixel(it.GetIndex()) * m_SignalScale ); // simulate eddy currents and other distortions double omega_t = 0; if ( m_SimulateEddyCurrents ) { if (!m_IsBaseline) { itk::Vector< double, 3 > pos; pos[0] = x-szx/2; pos[1] = y-szy/2; pos[2] = m_Z; pos = m_DirectionMatrix*pos/1000; // vector from image center to current position (in meter) omega_t += (m_DiffusionGradientDirection[0]*pos[0]+m_DiffusionGradientDirection[1]*pos[1]+m_DiffusionGradientDirection[2]*pos[2])*eddyDecay; } else omega_t += m_EddyGradientMagnitude*eddyDecay; } if (m_SimulateDistortions) omega_t += m_FrequencyMap->GetPixel(it.GetIndex())*t/1000; // add gibbs ringing offset (cropps k-space) double tempOffsetX = 0; if (temp_kx>=szx/2) tempOffsetX = xOffset; double temp_ky = kIdx[1]; if (temp_ky>=szy/2) temp_ky += yOffset; // actual DFT term s += f * exp( std::complex(0, 2 * M_PI * ((temp_kx+tempOffsetX)*x/in_szx + temp_ky*y/in_szy) + omega_t ) ); ++it; } s /= numPix; - /* rearrange slice not needed - if( kIdx[0] < szx/2 ) - kIdx[0] = kIdx[0] + szx/2; - else - kIdx[0] = kIdx[0] - szx/2; - - if( kIdx[1] < szx/2 ) - kIdx[1] = kIdx[1] + szy/2; - else - kIdx[1] = kIdx[1] - szy/2;*/ - m_TEMPIMAGE->SetPixel(kIdx, sqrt(s.real()*s.real()+s.imag()*s.imag())); outputImage->SetPixel(kIdx, s); ++oit; } // typedef itk::ImageFileWriter< InputImageType > WriterType; // typename WriterType::Pointer writer = WriterType::New(); // writer->SetFileName("/local/kspace.nrrd"); // writer->SetInput(m_TEMPIMAGE); // writer->Update(); } template< class TPixelType > void KspaceImageFilter< TPixelType > ::AfterThreadedGenerateData() { } } #endif diff --git a/Modules/DiffusionImaging/FiberTracking/IODataStructures/FiberBundleX/mitkFiberBundleX.cpp b/Modules/DiffusionImaging/FiberTracking/IODataStructures/FiberBundleX/mitkFiberBundleX.cpp index 70bf2f97ec..2630199c5a 100755 --- a/Modules/DiffusionImaging/FiberTracking/IODataStructures/FiberBundleX/mitkFiberBundleX.cpp +++ b/Modules/DiffusionImaging/FiberTracking/IODataStructures/FiberBundleX/mitkFiberBundleX.cpp @@ -1,1703 +1,1787 @@ /*=================================================================== 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. ===================================================================*/ #define _USE_MATH_DEFINES #include "mitkFiberBundleX.h" #include #include #include #include #include #include #include #include #include #include #include #include #include #include #include #include #include #include #include #include const char* mitk::FiberBundleX::COLORCODING_ORIENTATION_BASED = "Color_Orient"; //const char* mitk::FiberBundleX::COLORCODING_FA_AS_OPACITY = "Color_Orient_FA_Opacity"; const char* mitk::FiberBundleX::COLORCODING_FA_BASED = "FA_Values"; const char* mitk::FiberBundleX::COLORCODING_CUSTOM = "custom"; const char* mitk::FiberBundleX::FIBER_ID_ARRAY = "Fiber_IDs"; using namespace std; mitk::FiberBundleX::FiberBundleX( vtkPolyData* fiberPolyData ) : m_CurrentColorCoding(NULL) , m_NumFibers(0) , m_FiberSampling(0) { m_FiberPolyData = vtkSmartPointer::New(); if (fiberPolyData != NULL) { m_FiberPolyData = fiberPolyData; //m_FiberPolyData->DeepCopy(fiberPolyData); this->DoColorCodingOrientationBased(); } this->UpdateFiberGeometry(); this->SetColorCoding(COLORCODING_ORIENTATION_BASED); this->GenerateFiberIds(); } mitk::FiberBundleX::~FiberBundleX() { } mitk::FiberBundleX::Pointer mitk::FiberBundleX::GetDeepCopy() { mitk::FiberBundleX::Pointer newFib = mitk::FiberBundleX::New(m_FiberPolyData); newFib->SetColorCoding(m_CurrentColorCoding); return newFib; } vtkSmartPointer mitk::FiberBundleX::GeneratePolyDataByIds(std::vector fiberIds) { MITK_DEBUG << "\n=====FINAL RESULT: fib_id ======\n"; MITK_DEBUG << "Number of new Fibers: " << fiberIds.size(); // iterate through the vectorcontainer hosting all desired fiber Ids vtkSmartPointer newFiberPolyData = vtkSmartPointer::New(); vtkSmartPointer newLineSet = vtkSmartPointer::New(); vtkSmartPointer newPointSet = vtkSmartPointer::New(); // if FA array available, initialize fa double array // if color orient array is available init color array vtkSmartPointer faValueArray; vtkSmartPointer colorsT; //colors and alpha value for each single point, RGBA = 4 components unsigned char rgba[4] = {0,0,0,0}; int componentSize = sizeof(rgba); if (m_FiberIdDataSet->GetPointData()->HasArray(COLORCODING_FA_BASED)){ MITK_DEBUG << "FA VALUES AVAILABLE, init array for new fiberbundle"; faValueArray = vtkSmartPointer::New(); } if (m_FiberIdDataSet->GetPointData()->HasArray(COLORCODING_ORIENTATION_BASED)){ MITK_DEBUG << "colorValues available, init array for new fiberbundle"; colorsT = vtkUnsignedCharArray::New(); colorsT->SetNumberOfComponents(componentSize); colorsT->SetName(COLORCODING_ORIENTATION_BASED); } std::vector::iterator finIt = fiberIds.begin(); while ( finIt != fiberIds.end() ) { if (*finIt < 0 || *finIt>GetNumFibers()){ MITK_INFO << "FiberID can not be negative or >NumFibers!!! check id Extraction!" << *finIt; break; } vtkSmartPointer fiber = m_FiberIdDataSet->GetCell(*finIt);//->DeepCopy(fiber); vtkSmartPointer fibPoints = fiber->GetPoints(); vtkSmartPointer newFiber = vtkSmartPointer::New(); newFiber->GetPointIds()->SetNumberOfIds( fibPoints->GetNumberOfPoints() ); for(int i=0; iGetNumberOfPoints(); i++) { // MITK_DEBUG << "id: " << fiber->GetPointId(i); // MITK_DEBUG << fibPoints->GetPoint(i)[0] << " | " << fibPoints->GetPoint(i)[1] << " | " << fibPoints->GetPoint(i)[2]; newFiber->GetPointIds()->SetId(i, newPointSet->GetNumberOfPoints()); newPointSet->InsertNextPoint(fibPoints->GetPoint(i)[0], fibPoints->GetPoint(i)[1], fibPoints->GetPoint(i)[2]); if (m_FiberIdDataSet->GetPointData()->HasArray(COLORCODING_FA_BASED)){ // MITK_DEBUG << m_FiberIdDataSet->GetPointData()->GetArray(FA_VALUE_ARRAY)->GetTuple(fiber->GetPointId(i)); } if (m_FiberIdDataSet->GetPointData()->HasArray(COLORCODING_ORIENTATION_BASED)){ // MITK_DEBUG << "ColorValue: " << m_FiberIdDataSet->GetPointData()->GetArray(COLORCODING_ORIENTATION_BASED)->GetTuple(fiber->GetPointId(i))[0]; } } newLineSet->InsertNextCell(newFiber); ++finIt; } newFiberPolyData->SetPoints(newPointSet); newFiberPolyData->SetLines(newLineSet); MITK_DEBUG << "new fiberbundle polydata points: " << newFiberPolyData->GetNumberOfPoints(); MITK_DEBUG << "new fiberbundle polydata lines: " << newFiberPolyData->GetNumberOfLines(); MITK_DEBUG << "=====================\n"; // mitk::FiberBundleX::Pointer newFib = mitk::FiberBundleX::New(newFiberPolyData); return newFiberPolyData; } // merge two fiber bundles mitk::FiberBundleX::Pointer mitk::FiberBundleX::AddBundle(mitk::FiberBundleX* fib) { if (fib==NULL) { MITK_WARN << "trying to call AddBundle with NULL argument"; return NULL; } MITK_INFO << "Adding fibers"; vtkSmartPointer vNewPolyData = vtkSmartPointer::New(); vtkSmartPointer vNewLines = vtkSmartPointer::New(); vtkSmartPointer vNewPoints = vtkSmartPointer::New(); // add current fiber bundle for (int i=0; iGetNumberOfCells(); i++) { vtkCell* cell = m_FiberPolyData->GetCell(i); int numPoints = cell->GetNumberOfPoints(); vtkPoints* points = cell->GetPoints(); vtkSmartPointer container = vtkSmartPointer::New(); for (int j=0; jGetPoint(j, p); vtkIdType id = vNewPoints->InsertNextPoint(p); container->GetPointIds()->InsertNextId(id); } vNewLines->InsertNextCell(container); } // add new fiber bundle for (int i=0; iGetFiberPolyData()->GetNumberOfCells(); i++) { vtkCell* cell = fib->GetFiberPolyData()->GetCell(i); int numPoints = cell->GetNumberOfPoints(); vtkPoints* points = cell->GetPoints(); vtkSmartPointer container = vtkSmartPointer::New(); for (int j=0; jGetPoint(j, p); vtkIdType id = vNewPoints->InsertNextPoint(p); container->GetPointIds()->InsertNextId(id); } vNewLines->InsertNextCell(container); } // initialize polydata vNewPolyData->SetPoints(vNewPoints); vNewPolyData->SetLines(vNewLines); // initialize fiber bundle mitk::FiberBundleX::Pointer newFib = mitk::FiberBundleX::New(vNewPolyData); return newFib; } // subtract two fiber bundles mitk::FiberBundleX::Pointer mitk::FiberBundleX::SubtractBundle(mitk::FiberBundleX* fib) { MITK_INFO << "Subtracting fibers"; vtkSmartPointer vNewPolyData = vtkSmartPointer::New(); vtkSmartPointer vNewLines = vtkSmartPointer::New(); vtkSmartPointer vNewPoints = vtkSmartPointer::New(); // iterate over current fibers int numFibers = GetNumFibers(); boost::progress_display disp(numFibers); for( int i=0; iGetCell(i); int numPoints = cell->GetNumberOfPoints(); vtkPoints* points = cell->GetPoints(); if (points==NULL || numPoints<=0) continue; int numFibers2 = fib->GetNumFibers(); bool contained = false; for( int i2=0; i2GetFiberPolyData()->GetCell(i2); int numPoints2 = cell2->GetNumberOfPoints(); vtkPoints* points2 = cell2->GetPoints(); if (points2==NULL || numPoints2<=0) continue; // check endpoints itk::Point point_start = GetItkPoint(points->GetPoint(0)); itk::Point point_end = GetItkPoint(points->GetPoint(numPoints-1)); itk::Point point2_start = GetItkPoint(points2->GetPoint(0)); itk::Point point2_end = GetItkPoint(points2->GetPoint(numPoints2-1)); if (point_start.SquaredEuclideanDistanceTo(point2_start)<=mitk::eps && point_end.SquaredEuclideanDistanceTo(point2_end)<=mitk::eps || point_start.SquaredEuclideanDistanceTo(point2_end)<=mitk::eps && point_end.SquaredEuclideanDistanceTo(point2_start)<=mitk::eps) { // further checking ??? if (numPoints2==numPoints) contained = true; } } // add to result because fiber is not subtracted if (!contained) { vtkSmartPointer container = vtkSmartPointer::New(); for( int j=0; jInsertNextPoint(points->GetPoint(j)); container->GetPointIds()->InsertNextId(id); } vNewLines->InsertNextCell(container); } } if(vNewLines->GetNumberOfCells()==0) return NULL; // initialize polydata vNewPolyData->SetPoints(vNewPoints); vNewPolyData->SetLines(vNewLines); // initialize fiber bundle mitk::FiberBundleX::Pointer newFib = mitk::FiberBundleX::New(vNewPolyData); return newFib; } itk::Point mitk::FiberBundleX::GetItkPoint(double point[3]) { itk::Point itkPoint; itkPoint[0] = point[0]; itkPoint[1] = point[1]; itkPoint[2] = point[2]; return itkPoint; } /* * set polydata (additional flag to recompute fiber geometry, default = true) */ void mitk::FiberBundleX::SetFiberPolyData(vtkSmartPointer fiberPD, bool updateGeometry) { if (fiberPD == NULL) this->m_FiberPolyData = vtkSmartPointer::New(); else { m_FiberPolyData->DeepCopy(fiberPD); DoColorCodingOrientationBased(); } m_NumFibers = m_FiberPolyData->GetNumberOfLines(); if (updateGeometry) UpdateFiberGeometry(); SetColorCoding(COLORCODING_ORIENTATION_BASED); GenerateFiberIds(); } /* * return vtkPolyData */ vtkSmartPointer mitk::FiberBundleX::GetFiberPolyData() { return m_FiberPolyData; } void mitk::FiberBundleX::DoColorCodingOrientationBased() { //===== FOR WRITING A TEST ======================== // colorT size == tupelComponents * tupelElements // compare color results // to cover this code 100% also polydata needed, where colorarray already exists // + one fiber with exactly 1 point // + one fiber with 0 points //================================================= /* make sure that processing colorcoding is only called when necessary */ if ( m_FiberPolyData->GetPointData()->HasArray(COLORCODING_ORIENTATION_BASED) && m_FiberPolyData->GetNumberOfPoints() == m_FiberPolyData->GetPointData()->GetArray(COLORCODING_ORIENTATION_BASED)->GetNumberOfTuples() ) { // fiberstructure is already colorcoded MITK_DEBUG << " NO NEED TO REGENERATE COLORCODING! " ; this->ResetFiberOpacity(); this->SetColorCoding(COLORCODING_ORIENTATION_BASED); return; } /* Finally, execute color calculation */ vtkPoints* extrPoints = NULL; extrPoints = m_FiberPolyData->GetPoints(); int numOfPoints = 0; if (extrPoints!=NULL) numOfPoints = extrPoints->GetNumberOfPoints(); //colors and alpha value for each single point, RGBA = 4 components unsigned char rgba[4] = {0,0,0,0}; // int componentSize = sizeof(rgba); int componentSize = 4; vtkSmartPointer colorsT = vtkSmartPointer::New(); colorsT->Allocate(numOfPoints * componentSize); colorsT->SetNumberOfComponents(componentSize); colorsT->SetName(COLORCODING_ORIENTATION_BASED); /* checkpoint: does polydata contain any fibers */ int numOfFibers = m_FiberPolyData->GetNumberOfLines(); if (numOfFibers < 1) { MITK_DEBUG << "\n ========= Number of Fibers is 0 and below ========= \n"; return; } /* extract single fibers of fiberBundle */ vtkCellArray* fiberList = m_FiberPolyData->GetLines(); fiberList->InitTraversal(); for (int fi=0; fiGetNextCell(pointsPerFiber, idList); // MITK_DEBUG << "Fib#: " << fi << " of " << numOfFibers << " pnts in fiber: " << pointsPerFiber ; /* single fiber checkpoints: is number of points valid */ if (pointsPerFiber > 1) { /* operate on points of single fiber */ for (int i=0; i 0) { /* The color value of the current point is influenced by the previous point and next point. */ vnl_vector_fixed< double, 3 > currentPntvtk(extrPoints->GetPoint(idList[i])[0], extrPoints->GetPoint(idList[i])[1],extrPoints->GetPoint(idList[i])[2]); vnl_vector_fixed< double, 3 > nextPntvtk(extrPoints->GetPoint(idList[i+1])[0], extrPoints->GetPoint(idList[i+1])[1], extrPoints->GetPoint(idList[i+1])[2]); vnl_vector_fixed< double, 3 > prevPntvtk(extrPoints->GetPoint(idList[i-1])[0], extrPoints->GetPoint(idList[i-1])[1], extrPoints->GetPoint(idList[i-1])[2]); vnl_vector_fixed< double, 3 > diff1; diff1 = currentPntvtk - nextPntvtk; vnl_vector_fixed< double, 3 > diff2; diff2 = currentPntvtk - prevPntvtk; vnl_vector_fixed< double, 3 > diff; diff = (diff1 - diff2) / 2.0; diff.normalize(); rgba[0] = (unsigned char) (255.0 * std::fabs(diff[0])); rgba[1] = (unsigned char) (255.0 * std::fabs(diff[1])); rgba[2] = (unsigned char) (255.0 * std::fabs(diff[2])); rgba[3] = (unsigned char) (255.0); } else if (i==0) { /* First point has no previous point, therefore only diff1 is taken */ vnl_vector_fixed< double, 3 > currentPntvtk(extrPoints->GetPoint(idList[i])[0], extrPoints->GetPoint(idList[i])[1],extrPoints->GetPoint(idList[i])[2]); vnl_vector_fixed< double, 3 > nextPntvtk(extrPoints->GetPoint(idList[i+1])[0], extrPoints->GetPoint(idList[i+1])[1], extrPoints->GetPoint(idList[i+1])[2]); vnl_vector_fixed< double, 3 > diff1; diff1 = currentPntvtk - nextPntvtk; diff1.normalize(); rgba[0] = (unsigned char) (255.0 * std::fabs(diff1[0])); rgba[1] = (unsigned char) (255.0 * std::fabs(diff1[1])); rgba[2] = (unsigned char) (255.0 * std::fabs(diff1[2])); rgba[3] = (unsigned char) (255.0); } else if (i==pointsPerFiber-1) { /* Last point has no next point, therefore only diff2 is taken */ vnl_vector_fixed< double, 3 > currentPntvtk(extrPoints->GetPoint(idList[i])[0], extrPoints->GetPoint(idList[i])[1],extrPoints->GetPoint(idList[i])[2]); vnl_vector_fixed< double, 3 > prevPntvtk(extrPoints->GetPoint(idList[i-1])[0], extrPoints->GetPoint(idList[i-1])[1], extrPoints->GetPoint(idList[i-1])[2]); vnl_vector_fixed< double, 3 > diff2; diff2 = currentPntvtk - prevPntvtk; diff2.normalize(); rgba[0] = (unsigned char) (255.0 * std::fabs(diff2[0])); rgba[1] = (unsigned char) (255.0 * std::fabs(diff2[1])); rgba[2] = (unsigned char) (255.0 * std::fabs(diff2[2])); rgba[3] = (unsigned char) (255.0); } colorsT->InsertTupleValue(idList[i], rgba); } //end for loop } else if (pointsPerFiber == 1) { /* a single point does not define a fiber (use vertex mechanisms instead */ continue; // colorsT->InsertTupleValue(0, rgba); } else { MITK_DEBUG << "Fiber with 0 points detected... please check your tractography algorithm!" ; continue; } }//end for loop m_FiberPolyData->GetPointData()->AddArray(colorsT); /*========================= - this is more relevant for renderer than for fiberbundleX datastructure - think about sourcing this to a explicit method which coordinates colorcoding */ this->SetColorCoding(COLORCODING_ORIENTATION_BASED); // =========================== //mini test, shall be ported to MITK TESTINGS! if (colorsT->GetSize() != numOfPoints*componentSize) MITK_DEBUG << "ALLOCATION ERROR IN INITIATING COLOR ARRAY"; } void mitk::FiberBundleX::DoColorCodingFaBased() { if(m_FiberPolyData->GetPointData()->HasArray(COLORCODING_FA_BASED) != 1 ) return; this->SetColorCoding(COLORCODING_FA_BASED); MITK_DEBUG << "FBX: done CC FA based"; this->GenerateFiberIds(); } void mitk::FiberBundleX::DoUseFaFiberOpacity() { if(m_FiberPolyData->GetPointData()->HasArray(COLORCODING_FA_BASED) != 1 ) return; if(m_FiberPolyData->GetPointData()->HasArray(COLORCODING_ORIENTATION_BASED) != 1 ) return; vtkDoubleArray* FAValArray = (vtkDoubleArray*) m_FiberPolyData->GetPointData()->GetArray(COLORCODING_FA_BASED); vtkUnsignedCharArray* ColorArray = dynamic_cast (m_FiberPolyData->GetPointData()->GetArray(COLORCODING_ORIENTATION_BASED)); for(long i=0; iGetNumberOfTuples(); i++) { double faValue = FAValArray->GetValue(i); faValue = faValue * 255.0; ColorArray->SetComponent(i,3, (unsigned char) faValue ); } this->SetColorCoding(COLORCODING_ORIENTATION_BASED); MITK_DEBUG << "FBX: done CC OPACITY"; this->GenerateFiberIds(); } void mitk::FiberBundleX::ResetFiberOpacity() { vtkUnsignedCharArray* ColorArray = dynamic_cast (m_FiberPolyData->GetPointData()->GetArray(COLORCODING_ORIENTATION_BASED)); if (ColorArray==NULL) return; for(long i=0; iGetNumberOfTuples(); i++) ColorArray->SetComponent(i,3, 255.0 ); } void mitk::FiberBundleX::SetFAMap(mitk::Image::Pointer FAimage) { MITK_DEBUG << "SetFAMap"; vtkSmartPointer faValues = vtkSmartPointer::New(); faValues->SetName(COLORCODING_FA_BASED); faValues->Allocate(m_FiberPolyData->GetNumberOfPoints()); faValues->SetNumberOfValues(m_FiberPolyData->GetNumberOfPoints()); vtkPoints* pointSet = m_FiberPolyData->GetPoints(); for(long i=0; iGetNumberOfPoints(); ++i) { Point3D px; px[0] = pointSet->GetPoint(i)[0]; px[1] = pointSet->GetPoint(i)[1]; px[2] = pointSet->GetPoint(i)[2]; double faPixelValue = 1-FAimage->GetPixelValueByWorldCoordinate(px); faValues->InsertValue(i, faPixelValue); } m_FiberPolyData->GetPointData()->AddArray(faValues); this->GenerateFiberIds(); if(m_FiberPolyData->GetPointData()->HasArray(COLORCODING_FA_BASED)) MITK_DEBUG << "FA VALUE ARRAY SET"; } void mitk::FiberBundleX::GenerateFiberIds() { if (m_FiberPolyData == NULL) return; vtkSmartPointer idFiberFilter = vtkSmartPointer::New(); idFiberFilter->SetInput(m_FiberPolyData); idFiberFilter->CellIdsOn(); // idFiberFilter->PointIdsOn(); // point id's are not needed idFiberFilter->SetIdsArrayName(FIBER_ID_ARRAY); idFiberFilter->FieldDataOn(); idFiberFilter->Update(); m_FiberIdDataSet = idFiberFilter->GetOutput(); MITK_DEBUG << "Generating Fiber Ids...[done] | " << m_FiberIdDataSet->GetNumberOfCells(); } mitk::FiberBundleX::Pointer mitk::FiberBundleX::ExtractFiberSubset(ItkUcharImgType* mask, bool anyPoint) { vtkSmartPointer polyData = m_FiberPolyData; if (anyPoint) { float minSpacing = 1; if(mask->GetSpacing()[0]GetSpacing()[1] && mask->GetSpacing()[0]GetSpacing()[2]) minSpacing = mask->GetSpacing()[0]; else if (mask->GetSpacing()[1] < mask->GetSpacing()[2]) minSpacing = mask->GetSpacing()[1]; else minSpacing = mask->GetSpacing()[2]; mitk::FiberBundleX::Pointer fibCopy = this->GetDeepCopy(); fibCopy->ResampleFibers(minSpacing/10); polyData = fibCopy->GetFiberPolyData(); } vtkSmartPointer vtkNewPoints = vtkSmartPointer::New(); vtkSmartPointer vtkNewCells = vtkSmartPointer::New(); MITK_INFO << "Extracting fibers"; boost::progress_display disp(m_NumFibers); for (int i=0; iGetCell(i); int numPoints = cell->GetNumberOfPoints(); vtkPoints* points = cell->GetPoints(); vtkCell* cellOriginal = m_FiberPolyData->GetCell(i); int numPointsOriginal = cellOriginal->GetNumberOfPoints(); vtkPoints* pointsOriginal = cellOriginal->GetPoints(); vtkSmartPointer container = vtkSmartPointer::New(); if (numPoints>1 && numPointsOriginal) { if (anyPoint) { for (int j=0; jGetPoint(j); itk::Point itkP; itkP[0] = p[0]; itkP[1] = p[1]; itkP[2] = p[2]; itk::Index<3> idx; mask->TransformPhysicalPointToIndex(itkP, idx); if ( mask->GetPixel(idx)>0 && mask->GetLargestPossibleRegion().IsInside(idx) ) { for (int k=0; kGetPoint(k); vtkIdType id = vtkNewPoints->InsertNextPoint(p); container->GetPointIds()->InsertNextId(id); } break; } } } else { double* start = pointsOriginal->GetPoint(0); itk::Point itkStart; itkStart[0] = start[0]; itkStart[1] = start[1]; itkStart[2] = start[2]; itk::Index<3> idxStart; mask->TransformPhysicalPointToIndex(itkStart, idxStart); double* end = pointsOriginal->GetPoint(numPointsOriginal-1); itk::Point itkEnd; itkEnd[0] = end[0]; itkEnd[1] = end[1]; itkEnd[2] = end[2]; itk::Index<3> idxEnd; mask->TransformPhysicalPointToIndex(itkEnd, idxEnd); if ( mask->GetPixel(idxStart)>0 && mask->GetPixel(idxEnd)>0 && mask->GetLargestPossibleRegion().IsInside(idxStart) && mask->GetLargestPossibleRegion().IsInside(idxEnd) ) { for (int j=0; jGetPoint(j); vtkIdType id = vtkNewPoints->InsertNextPoint(p); container->GetPointIds()->InsertNextId(id); } } } } vtkNewCells->InsertNextCell(container); } if (vtkNewCells->GetNumberOfCells()<=0) return NULL; vtkSmartPointer newPolyData = vtkSmartPointer::New(); newPolyData->SetPoints(vtkNewPoints); newPolyData->SetLines(vtkNewCells); return mitk::FiberBundleX::New(newPolyData); } +mitk::FiberBundleX::Pointer mitk::FiberBundleX::RemoveFibersOutside(ItkUcharImgType* mask, bool invert) +{ + float minSpacing = 1; + if(mask->GetSpacing()[0]GetSpacing()[1] && mask->GetSpacing()[0]GetSpacing()[2]) + minSpacing = mask->GetSpacing()[0]; + else if (mask->GetSpacing()[1] < mask->GetSpacing()[2]) + minSpacing = mask->GetSpacing()[1]; + else + minSpacing = mask->GetSpacing()[2]; + + mitk::FiberBundleX::Pointer fibCopy = this->GetDeepCopy(); + fibCopy->ResampleFibers(minSpacing/10); + vtkSmartPointer polyData =fibCopy->GetFiberPolyData(); + + vtkSmartPointer vtkNewPoints = vtkSmartPointer::New(); + vtkSmartPointer vtkNewCells = vtkSmartPointer::New(); + + MITK_INFO << "Cutting fibers"; + boost::progress_display disp(m_NumFibers); + for (int i=0; iGetCell(i); + int numPoints = cell->GetNumberOfPoints(); + vtkPoints* points = cell->GetPoints(); + + vtkSmartPointer container = vtkSmartPointer::New(); + if (numPoints>1) + { + int newNumPoints = 0; + for (int j=0; jGetPoint(j); + + itk::Point itkP; + itkP[0] = p[0]; itkP[1] = p[1]; itkP[2] = p[2]; + itk::Index<3> idx; + mask->TransformPhysicalPointToIndex(itkP, idx); + + if ( mask->GetPixel(idx)>0 && mask->GetLargestPossibleRegion().IsInside(idx) && !invert ) + { + vtkIdType id = vtkNewPoints->InsertNextPoint(p); + container->GetPointIds()->InsertNextId(id); + newNumPoints++; + } + else if ( (mask->GetPixel(idx)<=0 || !mask->GetLargestPossibleRegion().IsInside(idx)) && invert ) + { + vtkIdType id = vtkNewPoints->InsertNextPoint(p); + container->GetPointIds()->InsertNextId(id); + newNumPoints++; + } + else if (newNumPoints>0) + { + vtkNewCells->InsertNextCell(container); + + newNumPoints = 0; + container = vtkSmartPointer::New(); + } + } + + if (newNumPoints>0) + vtkNewCells->InsertNextCell(container); + } + + } + + if (vtkNewCells->GetNumberOfCells()<=0) + return NULL; + + vtkSmartPointer newPolyData = vtkSmartPointer::New(); + newPolyData->SetPoints(vtkNewPoints); + newPolyData->SetLines(vtkNewCells); + return mitk::FiberBundleX::New(newPolyData); +} + mitk::FiberBundleX::Pointer mitk::FiberBundleX::ExtractFiberSubset(mitk::PlanarFigure* pf) { if (pf==NULL) return NULL; std::vector tmp = ExtractFiberIdSubset(pf); if (tmp.size()<=0) return mitk::FiberBundleX::New(); vtkSmartPointer pTmp = GeneratePolyDataByIds(tmp); return mitk::FiberBundleX::New(pTmp); } std::vector mitk::FiberBundleX::ExtractFiberIdSubset(mitk::PlanarFigure* pf) { MITK_DEBUG << "Extracting fibers!"; // vector which is returned, contains all extracted FiberIds std::vector FibersInROI; if (pf==NULL) return FibersInROI; /* Handle type of planarfigure */ // if incoming pf is a pfc mitk::PlanarFigureComposite::Pointer pfcomp= dynamic_cast(pf); if (!pfcomp.IsNull()) { // process requested boolean operation of PFC switch (pfcomp->getOperationType()) { case 0: { MITK_DEBUG << "AND PROCESSING"; //AND //temporarly store results of the child in this vector, we need that to accumulate the std::vector childResults = this->ExtractFiberIdSubset(pfcomp->getChildAt(0)); MITK_DEBUG << "first roi got fibers in ROI: " << childResults.size(); MITK_DEBUG << "sorting..."; std::sort(childResults.begin(), childResults.end()); MITK_DEBUG << "sorting done"; std::vector AND_Assamblage(childResults.size()); //std::vector AND_Assamblage; fill(AND_Assamblage.begin(), AND_Assamblage.end(), -1); //AND_Assamblage.reserve(childResults.size()); //max size AND can reach anyway std::vector::iterator it; for (int i=1; igetNumberOfChildren(); ++i) { std::vector tmpChild = this->ExtractFiberIdSubset(pfcomp->getChildAt(i)); MITK_DEBUG << "ROI " << i << " has fibers in ROI: " << tmpChild.size(); sort(tmpChild.begin(), tmpChild.end()); it = std::set_intersection(childResults.begin(), childResults.end(), tmpChild.begin(), tmpChild.end(), AND_Assamblage.begin() ); } MITK_DEBUG << "resize Vector"; long i=0; while (i < AND_Assamblage.size() && AND_Assamblage[i] != -1){ //-1 represents a placeholder in the array ++i; } AND_Assamblage.resize(i); MITK_DEBUG << "returning AND vector, size: " << AND_Assamblage.size(); return AND_Assamblage; // break; } case 1: { //OR std::vector OR_Assamblage = this->ExtractFiberIdSubset(pfcomp->getChildAt(0)); std::vector::iterator it; MITK_DEBUG << OR_Assamblage.size(); for (int i=1; igetNumberOfChildren(); ++i) { it = OR_Assamblage.end(); std::vector tmpChild = this->ExtractFiberIdSubset(pfcomp->getChildAt(i)); OR_Assamblage.insert(it, tmpChild.begin(), tmpChild.end()); MITK_DEBUG << "ROI " << i << " has fibers in ROI: " << tmpChild.size() << " OR Assamblage: " << OR_Assamblage.size(); } sort(OR_Assamblage.begin(), OR_Assamblage.end()); it = unique(OR_Assamblage.begin(), OR_Assamblage.end()); OR_Assamblage.resize( it - OR_Assamblage.begin() ); MITK_DEBUG << "returning OR vector, size: " << OR_Assamblage.size(); return OR_Assamblage; } case 2: { //NOT //get IDs of all fibers std::vector childResults; childResults.reserve(this->GetNumFibers()); vtkSmartPointer idSet = m_FiberIdDataSet->GetCellData()->GetArray(FIBER_ID_ARRAY); MITK_DEBUG << "m_NumOfFib: " << this->GetNumFibers() << " cellIdNum: " << idSet->GetNumberOfTuples(); for(long i=0; iGetNumFibers(); i++) { MITK_DEBUG << "i: " << i << " idset: " << idSet->GetTuple(i)[0]; childResults.push_back(idSet->GetTuple(i)[0]); } std::sort(childResults.begin(), childResults.end()); std::vector NOT_Assamblage(childResults.size()); //fill it with -1, otherwise 0 will be stored and 0 can also be an ID of fiber! fill(NOT_Assamblage.begin(), NOT_Assamblage.end(), -1); std::vector::iterator it; for (long i=0; igetNumberOfChildren(); ++i) { std::vector tmpChild = ExtractFiberIdSubset(pfcomp->getChildAt(i)); sort(tmpChild.begin(), tmpChild.end()); it = std::set_difference(childResults.begin(), childResults.end(), tmpChild.begin(), tmpChild.end(), NOT_Assamblage.begin() ); } MITK_DEBUG << "resize Vector"; long i=0; while (NOT_Assamblage[i] != -1){ //-1 represents a placeholder in the array ++i; } NOT_Assamblage.resize(i); return NOT_Assamblage; } default: MITK_DEBUG << "we have an UNDEFINED composition... ERROR" ; break; } } else { mitk::Geometry2D::ConstPointer pfgeometry = pf->GetGeometry2D(); const mitk::PlaneGeometry* planeGeometry = dynamic_cast (pfgeometry.GetPointer()); Vector3D planeNormal = planeGeometry->GetNormal(); planeNormal.Normalize(); Point3D planeOrigin = planeGeometry->GetOrigin(); MITK_DEBUG << "planeOrigin: " << planeOrigin[0] << " | " << planeOrigin[1] << " | " << planeOrigin[2] << endl; MITK_DEBUG << "planeNormal: " << planeNormal[0] << " | " << planeNormal[1] << " | " << planeNormal[2] << endl; std::vector PointsOnPlane; // contains all pointIds which are crossing the cutting plane std::vector PointsInROI; // based on PointsOnPlane, all ROI relevant point IDs are stored here /* Define cutting plane by ROI (PlanarFigure) */ vtkSmartPointer plane = vtkSmartPointer::New(); plane->SetOrigin(planeOrigin[0],planeOrigin[1],planeOrigin[2]); plane->SetNormal(planeNormal[0],planeNormal[1],planeNormal[2]); /* get all points/fibers cutting the plane */ MITK_DEBUG << "start clipping"; vtkSmartPointer clipper = vtkSmartPointer::New(); clipper->SetInput(m_FiberIdDataSet); clipper->SetClipFunction(plane); clipper->GenerateClipScalarsOn(); clipper->GenerateClippedOutputOn(); vtkSmartPointer clipperout = clipper->GetClippedOutput(); MITK_DEBUG << "end clipping"; MITK_DEBUG << "init and update clipperoutput"; clipperout->GetPointData()->Initialize(); clipperout->Update(); MITK_DEBUG << "init and update clipperoutput completed"; MITK_DEBUG << "STEP 1: find all points which have distance 0 to the given plane"; /*======STEP 1====== * extract all points, which are crossing the plane */ // Scalar values describe the distance between each remaining point to the given plane. Values sorted by point index vtkSmartPointer distanceList = clipperout->GetPointData()->GetScalars(); vtkIdType sizeOfList = distanceList->GetNumberOfTuples(); PointsOnPlane.reserve(sizeOfList); /* use reserve for high-performant push_back, no hidden copy procedures are processed then! * size of list can be optimized by reducing allocation, but be aware of iterator and vector size*/ for (int i=0; iGetTuple(i); // check if point is on plane. // 0.01 due to some approximation errors when calculating distance if (distance[0] >= -0.01 && distance[0] <= 0.01) PointsOnPlane.push_back(i); } MITK_DEBUG << "Num Of points on plane: " << PointsOnPlane.size(); MITK_DEBUG << "Step 2: extract Interesting points with respect to given extraction planarFigure"; PointsInROI.reserve(PointsOnPlane.size()); /*=======STEP 2===== * extract ROI relevant pointIds */ mitk::PlanarCircle::Pointer circleName = mitk::PlanarCircle::New(); mitk::PlanarPolygon::Pointer polyName = mitk::PlanarPolygon::New(); if ( pf->GetNameOfClass() == circleName->GetNameOfClass() ) { //calculate circle radius mitk::Point3D V1w = pf->GetWorldControlPoint(0); //centerPoint mitk::Point3D V2w = pf->GetWorldControlPoint(1); //radiusPoint double distPF = V1w.EuclideanDistanceTo(V2w); for (int i=0; iGetPoint(PointsOnPlane[i])[0] - V1w[0]) * (clipperout->GetPoint(PointsOnPlane[i])[0] - V1w[0]) + (clipperout->GetPoint(PointsOnPlane[i])[1] - V1w[1]) * (clipperout->GetPoint(PointsOnPlane[i])[1] - V1w[1]) + (clipperout->GetPoint(PointsOnPlane[i])[2] - V1w[2]) * (clipperout->GetPoint(PointsOnPlane[i])[2] - V1w[2])) ; if( XdistPnt <= distPF) PointsInROI.push_back(PointsOnPlane[i]); } } else if ( pf->GetNameOfClass() == polyName->GetNameOfClass() ) { //create vtkPolygon using controlpoints from planarFigure polygon vtkSmartPointer polygonVtk = vtkSmartPointer::New(); //get the control points from pf and insert them to vtkPolygon unsigned int nrCtrlPnts = pf->GetNumberOfControlPoints(); for (int i=0; iGetPoints()->InsertNextPoint((double)pf->GetWorldControlPoint(i)[0], (double)pf->GetWorldControlPoint(i)[1], (double)pf->GetWorldControlPoint(i)[2] ); } //prepare everything for using pointInPolygon function double n[3]; polygonVtk->ComputeNormal(polygonVtk->GetPoints()->GetNumberOfPoints(), static_cast(polygonVtk->GetPoints()->GetData()->GetVoidPointer(0)), n); double bounds[6]; polygonVtk->GetPoints()->GetBounds(bounds); for (int i=0; iGetPoint(PointsOnPlane[i])[0], clipperout->GetPoint(PointsOnPlane[i])[1], clipperout->GetPoint(PointsOnPlane[i])[2]}; int isInPolygon = polygonVtk->PointInPolygon(checkIn, polygonVtk->GetPoints()->GetNumberOfPoints() , static_cast(polygonVtk->GetPoints()->GetData()->GetVoidPointer(0)), bounds, n); if( isInPolygon ) PointsInROI.push_back(PointsOnPlane[i]); } } MITK_DEBUG << "Step3: Identify fibers"; // we need to access the fiberId Array, so make sure that this array is available if (!clipperout->GetCellData()->HasArray(FIBER_ID_ARRAY)) { MITK_DEBUG << "ERROR: FiberID array does not exist, no correlation between points and fiberIds possible! Make sure calling GenerateFiberIds()"; return FibersInROI; // FibersInRoi is empty then } if (PointsInROI.size()<=0) return FibersInROI; // prepare a structure where each point id is represented as an indexId. // vector looks like: | pntId | fiberIdx | std::vector< long > pointindexFiberMap; // walk through the whole subline section and create an vector sorted by point index vtkCellArray *clipperlines = clipperout->GetLines(); clipperlines->InitTraversal(); long numOfLineCells = clipperlines->GetNumberOfCells(); long numofClippedPoints = clipperout->GetNumberOfPoints(); pointindexFiberMap.resize(numofClippedPoints); //prepare resulting vector FibersInROI.reserve(PointsInROI.size()); MITK_DEBUG << "\n===== Pointindex based structure initialized ======\n"; // go through resulting "sub"lines which are stored as cells, "i" corresponds to current line id. for (int i=0, ic=0 ; iGetCell(ic, npts, pts); // go through point ids in hosting subline, "j" corresponds to current pointindex in current line i. eg. idx[0]=45; idx[1]=46 for (long j=0; jGetCellData()->GetArray(FIBER_ID_ARRAY)->GetTuple(i)[0] << " to pointId: " << pts[j]; pointindexFiberMap[ pts[j] ] = clipperout->GetCellData()->GetArray(FIBER_ID_ARRAY)->GetTuple(i)[0]; // MITK_DEBUG << "in array: " << pointindexFiberMap[ pts[j] ]; } } MITK_DEBUG << "\n===== Pointindex based structure finalized ======\n"; // get all Points in ROI with according fiberID for (long k = 0; k < PointsInROI.size(); k++) { //MITK_DEBUG << "point " << PointsInROI[k] << " belongs to fiber " << pointindexFiberMap[ PointsInROI[k] ]; if (pointindexFiberMap[ PointsInROI[k] ]<=GetNumFibers() && pointindexFiberMap[ PointsInROI[k] ]>=0) FibersInROI.push_back(pointindexFiberMap[ PointsInROI[k] ]); else MITK_INFO << "ERROR in ExtractFiberIdSubset; impossible fiber id detected"; } m_PointsRoi = PointsInROI; } // detecting fiberId duplicates MITK_DEBUG << "check for duplicates"; sort(FibersInROI.begin(), FibersInROI.end()); bool hasDuplicats = false; for(long i=0; i::iterator it; it = unique (FibersInROI.begin(), FibersInROI.end()); FibersInROI.resize( it - FibersInROI.begin() ); } return FibersInROI; } void mitk::FiberBundleX::UpdateFiberGeometry() { vtkSmartPointer cleaner = vtkSmartPointer::New(); cleaner->SetInput(m_FiberPolyData); cleaner->PointMergingOff(); cleaner->Update(); m_FiberPolyData = cleaner->GetOutput(); m_FiberLengths.clear(); m_MeanFiberLength = 0; m_MedianFiberLength = 0; m_LengthStDev = 0; m_NumFibers = m_FiberPolyData->GetNumberOfCells(); if (m_NumFibers<=0) // no fibers present; apply default geometry { m_MinFiberLength = 0; m_MaxFiberLength = 0; mitk::Geometry3D::Pointer geometry = mitk::Geometry3D::New(); geometry->SetImageGeometry(true); float b[] = {0, 1, 0, 1, 0, 1}; geometry->SetFloatBounds(b); SetGeometry(geometry); return; } float min = itk::NumericTraits::NonpositiveMin(); float max = itk::NumericTraits::max(); float b[] = {max, min, max, min, max, min}; for (int i=0; iGetNumberOfCells(); i++) { vtkCell* cell = m_FiberPolyData->GetCell(i); int p = cell->GetNumberOfPoints(); vtkPoints* points = cell->GetPoints(); float length = 0; for (int j=0; jGetPoint(j, p1); if (p1[0]b[1]) b[1]=p1[0]; if (p1[1]b[3]) b[3]=p1[1]; if (p1[2]b[5]) b[5]=p1[2]; // calculate statistics if (jGetPoint(j+1, p2); float dist = std::sqrt((p1[0]-p2[0])*(p1[0]-p2[0])+(p1[1]-p2[1])*(p1[1]-p2[1])+(p1[2]-p2[2])*(p1[2]-p2[2])); length += dist; } } m_FiberLengths.push_back(length); m_MeanFiberLength += length; if (i==0) { m_MinFiberLength = length; m_MaxFiberLength = length; } else { if (lengthm_MaxFiberLength) m_MaxFiberLength = length; } } m_MeanFiberLength /= m_NumFibers; std::vector< float > sortedLengths = m_FiberLengths; std::sort(sortedLengths.begin(), sortedLengths.end()); for (int i=0; i1) m_LengthStDev /= (m_NumFibers-1); else m_LengthStDev = 0; m_LengthStDev = std::sqrt(m_LengthStDev); m_MedianFiberLength = sortedLengths.at(m_NumFibers/2); // provide some border margin for(int i=0; i<=4; i+=2) b[i] -=10; for(int i=1; i<=5; i+=2) b[i] +=10; mitk::Geometry3D::Pointer geometry = mitk::Geometry3D::New(); geometry->SetFloatBounds(b); this->SetGeometry(geometry); } -QStringList mitk::FiberBundleX::GetAvailableColorCodings() +std::vector mitk::FiberBundleX::GetAvailableColorCodings() { - QStringList availableColorCodings; + std::vector availableColorCodings; int numColors = m_FiberPolyData->GetPointData()->GetNumberOfArrays(); for(int i=0; iGetPointData()->GetArrayName(i)); + availableColorCodings.push_back(m_FiberPolyData->GetPointData()->GetArrayName(i)); } //this controlstructure shall be implemented by the calling method - if (availableColorCodings.isEmpty()) + if (availableColorCodings.empty()) MITK_DEBUG << "no colorcodings available in fiberbundleX"; return availableColorCodings; } char* mitk::FiberBundleX::GetCurrentColorCoding() { return m_CurrentColorCoding; } void mitk::FiberBundleX::SetColorCoding(const char* requestedColorCoding) { if (requestedColorCoding==NULL) return; MITK_DEBUG << "SetColorCoding:" << requestedColorCoding; if( strcmp (COLORCODING_ORIENTATION_BASED,requestedColorCoding) == 0 ) { this->m_CurrentColorCoding = (char*) COLORCODING_ORIENTATION_BASED; } else if( strcmp (COLORCODING_FA_BASED,requestedColorCoding) == 0 ) { this->m_CurrentColorCoding = (char*) COLORCODING_FA_BASED; } else if( strcmp (COLORCODING_CUSTOM,requestedColorCoding) == 0 ) { this->m_CurrentColorCoding = (char*) COLORCODING_CUSTOM; } else { MITK_DEBUG << "FIBERBUNDLE X: UNKNOWN COLORCODING in FIBERBUNDLEX Datastructure"; this->m_CurrentColorCoding = (char*) COLORCODING_CUSTOM; //will cause blank colorcoding of fibers } } void mitk::FiberBundleX::RotateAroundAxis(double x, double y, double z) { MITK_INFO << "Rotating fibers"; x = x*M_PI/180; y = y*M_PI/180; z = z*M_PI/180; vnl_matrix_fixed< double, 3, 3 > rotX; rotX.set_identity(); rotX[1][1] = cos(x); rotX[2][2] = rotX[1][1]; rotX[1][2] = -sin(x); rotX[2][1] = -rotX[1][2]; vnl_matrix_fixed< double, 3, 3 > rotY; rotY.set_identity(); rotY[0][0] = cos(y); rotY[2][2] = rotY[0][0]; rotY[0][2] = sin(y); rotY[2][0] = -rotY[0][2]; vnl_matrix_fixed< double, 3, 3 > rotZ; rotZ.set_identity(); rotZ[0][0] = cos(z); rotZ[1][1] = rotZ[0][0]; rotZ[0][1] = -sin(z); rotZ[1][0] = -rotZ[0][1]; mitk::Geometry3D::Pointer geom = this->GetGeometry(); mitk::Point3D center = geom->GetCenter(); boost::progress_display disp(m_NumFibers); vtkSmartPointer vtkNewPoints = vtkSmartPointer::New(); vtkSmartPointer vtkNewCells = vtkSmartPointer::New(); for (int i=0; iGetCell(i); int numPoints = cell->GetNumberOfPoints(); vtkPoints* points = cell->GetPoints(); vtkSmartPointer container = vtkSmartPointer::New(); for (int j=0; jGetPoint(j); vnl_vector_fixed< double, 3 > dir; dir[0] = p[0]-center[0]; dir[1] = p[1]-center[1]; dir[2] = p[2]-center[2]; dir = rotZ*rotY*rotX*dir; dir[0] += center[0]; dir[1] += center[1]; dir[2] += center[2]; vtkIdType id = vtkNewPoints->InsertNextPoint(dir.data_block()); container->GetPointIds()->InsertNextId(id); } vtkNewCells->InsertNextCell(container); } m_FiberPolyData = vtkSmartPointer::New(); m_FiberPolyData->SetPoints(vtkNewPoints); m_FiberPolyData->SetLines(vtkNewCells); UpdateColorCoding(); UpdateFiberGeometry(); } void mitk::FiberBundleX::ScaleFibers(double x, double y, double z) { MITK_INFO << "Scaling fibers"; boost::progress_display disp(m_NumFibers); mitk::Geometry3D* geom = this->GetGeometry(); mitk::Point3D c = geom->GetCenter(); vtkSmartPointer vtkNewPoints = vtkSmartPointer::New(); vtkSmartPointer vtkNewCells = vtkSmartPointer::New(); for (int i=0; iGetCell(i); int numPoints = cell->GetNumberOfPoints(); vtkPoints* points = cell->GetPoints(); vtkSmartPointer container = vtkSmartPointer::New(); for (int j=0; jGetPoint(j); p[0] -= c[0]; p[1] -= c[1]; p[2] -= c[2]; p[0] *= x; p[1] *= y; p[2] *= z; p[0] += c[0]; p[1] += c[1]; p[2] += c[2]; vtkIdType id = vtkNewPoints->InsertNextPoint(p); container->GetPointIds()->InsertNextId(id); } vtkNewCells->InsertNextCell(container); } m_FiberPolyData = vtkSmartPointer::New(); m_FiberPolyData->SetPoints(vtkNewPoints); m_FiberPolyData->SetLines(vtkNewCells); UpdateColorCoding(); UpdateFiberGeometry(); } void mitk::FiberBundleX::TranslateFibers(double x, double y, double z) { MITK_INFO << "Translating fibers"; boost::progress_display disp(m_NumFibers); vtkSmartPointer vtkNewPoints = vtkSmartPointer::New(); vtkSmartPointer vtkNewCells = vtkSmartPointer::New(); for (int i=0; iGetCell(i); int numPoints = cell->GetNumberOfPoints(); vtkPoints* points = cell->GetPoints(); vtkSmartPointer container = vtkSmartPointer::New(); for (int j=0; jGetPoint(j); p[0] += x; p[1] += y; p[2] += z; vtkIdType id = vtkNewPoints->InsertNextPoint(p); container->GetPointIds()->InsertNextId(id); } vtkNewCells->InsertNextCell(container); } m_FiberPolyData = vtkSmartPointer::New(); m_FiberPolyData->SetPoints(vtkNewPoints); m_FiberPolyData->SetLines(vtkNewCells); UpdateColorCoding(); UpdateFiberGeometry(); } void mitk::FiberBundleX::MirrorFibers(unsigned int axis) { if (axis>2) return; MITK_INFO << "Mirroring fibers"; boost::progress_display disp(m_NumFibers); vtkSmartPointer vtkNewPoints = vtkSmartPointer::New(); vtkSmartPointer vtkNewCells = vtkSmartPointer::New(); for (int i=0; iGetCell(i); int numPoints = cell->GetNumberOfPoints(); vtkPoints* points = cell->GetPoints(); vtkSmartPointer container = vtkSmartPointer::New(); for (int j=0; jGetPoint(j); p[axis] = -p[axis]; vtkIdType id = vtkNewPoints->InsertNextPoint(p); container->GetPointIds()->InsertNextId(id); } vtkNewCells->InsertNextCell(container); } m_FiberPolyData = vtkSmartPointer::New(); m_FiberPolyData->SetPoints(vtkNewPoints); m_FiberPolyData->SetLines(vtkNewCells); UpdateColorCoding(); UpdateFiberGeometry(); } bool mitk::FiberBundleX::ApplyCurvatureThreshold(float minRadius, bool deleteFibers) { if (minRadius<0) return true; vtkSmartPointer vtkNewPoints = vtkSmartPointer::New(); vtkSmartPointer vtkNewCells = vtkSmartPointer::New(); MITK_INFO << "Applying curvature threshold"; boost::progress_display disp(m_FiberPolyData->GetNumberOfCells()); for (int i=0; iGetNumberOfCells(); i++) { ++disp ; vtkCell* cell = m_FiberPolyData->GetCell(i); int numPoints = cell->GetNumberOfPoints(); vtkPoints* points = cell->GetPoints(); // calculate curvatures vtkSmartPointer container = vtkSmartPointer::New(); for (int j=0; jGetPoint(j, p1); double p2[3]; points->GetPoint(j+1, p2); double p3[3]; points->GetPoint(j+2, p3); vnl_vector_fixed< float, 3 > v1, v2, v3; v1[0] = p2[0]-p1[0]; v1[1] = p2[1]-p1[1]; v1[2] = p2[2]-p1[2]; v2[0] = p3[0]-p2[0]; v2[1] = p3[1]-p2[1]; v2[2] = p3[2]-p2[2]; v3[0] = p1[0]-p3[0]; v3[1] = p1[1]-p3[1]; v3[2] = p1[2]-p3[2]; float a = v1.magnitude(); float b = v2.magnitude(); float c = v3.magnitude(); float r = a*b*c/std::sqrt((a+b+c)*(a+b-c)*(b+c-a)*(a-b+c)); // radius of triangle via Heron's formula (area of triangle) vtkIdType id = vtkNewPoints->InsertNextPoint(p1); container->GetPointIds()->InsertNextId(id); if (deleteFibers && rInsertNextCell(container); container = vtkSmartPointer::New(); } else if (j==numPoints-3) { id = vtkNewPoints->InsertNextPoint(p2); container->GetPointIds()->InsertNextId(id); id = vtkNewPoints->InsertNextPoint(p3); container->GetPointIds()->InsertNextId(id); vtkNewCells->InsertNextCell(container); } } } if (vtkNewCells->GetNumberOfCells()<=0) return false; m_FiberPolyData = vtkSmartPointer::New(); m_FiberPolyData->SetPoints(vtkNewPoints); m_FiberPolyData->SetLines(vtkNewCells); UpdateColorCoding(); UpdateFiberGeometry(); return true; } bool mitk::FiberBundleX::RemoveShortFibers(float lengthInMM) { + MITK_INFO << "Removing short fibers"; if (lengthInMM<=0 || lengthInMMm_MaxFiberLength) // can't remove all fibers + { + MITK_WARN << "Process aborted. No fibers would be left!"; return false; + } vtkSmartPointer vtkNewPoints = vtkSmartPointer::New(); vtkSmartPointer vtkNewCells = vtkSmartPointer::New(); float min = m_MaxFiberLength; - MITK_INFO << "Removing short fibers"; boost::progress_display disp(m_NumFibers); for (int i=0; iGetCell(i); int numPoints = cell->GetNumberOfPoints(); vtkPoints* points = cell->GetPoints(); if (m_FiberLengths.at(i)>=lengthInMM) { vtkSmartPointer container = vtkSmartPointer::New(); for (int j=0; jGetPoint(j); vtkIdType id = vtkNewPoints->InsertNextPoint(p); container->GetPointIds()->InsertNextId(id); } vtkNewCells->InsertNextCell(container); if (m_FiberLengths.at(i)GetNumberOfCells()<=0) return false; m_FiberPolyData = vtkSmartPointer::New(); m_FiberPolyData->SetPoints(vtkNewPoints); m_FiberPolyData->SetLines(vtkNewCells); UpdateColorCoding(); UpdateFiberGeometry(); return true; } bool mitk::FiberBundleX::RemoveLongFibers(float lengthInMM) { if (lengthInMM<=0 || lengthInMM>m_MaxFiberLength) return true; if (lengthInMM vtkNewPoints = vtkSmartPointer::New(); vtkSmartPointer vtkNewCells = vtkSmartPointer::New(); MITK_INFO << "Removing long fibers"; boost::progress_display disp(m_NumFibers); for (int i=0; iGetCell(i); int numPoints = cell->GetNumberOfPoints(); vtkPoints* points = cell->GetPoints(); if (m_FiberLengths.at(i)<=lengthInMM) { vtkSmartPointer container = vtkSmartPointer::New(); for (int j=0; jGetPoint(j); vtkIdType id = vtkNewPoints->InsertNextPoint(p); container->GetPointIds()->InsertNextId(id); } vtkNewCells->InsertNextCell(container); } } if (vtkNewCells->GetNumberOfCells()<=0) return false; m_FiberPolyData = vtkSmartPointer::New(); m_FiberPolyData->SetPoints(vtkNewPoints); m_FiberPolyData->SetLines(vtkNewCells); UpdateColorCoding(); UpdateFiberGeometry(); return true; } -void mitk::FiberBundleX::DoFiberSmoothing(int pointsPerCm, double tension, double continuity, double bias ) +void mitk::FiberBundleX::DoFiberSmoothing(float pointDistance, double tension, double continuity, double bias ) { + if (pointDistance<=0) + return; + vtkSmartPointer vtkSmoothPoints = vtkSmartPointer::New(); //in smoothpoints the interpolated points representing a fiber are stored. //in vtkcells all polylines are stored, actually all id's of them are stored vtkSmartPointer vtkSmoothCells = vtkSmartPointer::New(); //cellcontainer for smoothed lines vtkIdType pointHelperCnt = 0; - MITK_INFO << "Resampling fibers"; + MITK_INFO << "Smoothing fibers"; boost::progress_display disp(m_NumFibers); for (int i=0; iGetCell(i); int numPoints = cell->GetNumberOfPoints(); vtkPoints* points = cell->GetPoints(); vtkSmartPointer newPoints = vtkSmartPointer::New(); for (int j=0; jInsertNextPoint(points->GetPoint(j)); float length = m_FiberLengths.at(i); - length /=10; - int sampling = pointsPerCm*length; + int sampling = std::ceil(length/pointDistance); vtkSmartPointer xSpline = vtkSmartPointer::New(); vtkSmartPointer ySpline = vtkSmartPointer::New(); vtkSmartPointer zSpline = vtkSmartPointer::New(); xSpline->SetDefaultBias(bias); xSpline->SetDefaultTension(tension); xSpline->SetDefaultContinuity(continuity); ySpline->SetDefaultBias(bias); ySpline->SetDefaultTension(tension); ySpline->SetDefaultContinuity(continuity); zSpline->SetDefaultBias(bias); zSpline->SetDefaultTension(tension); zSpline->SetDefaultContinuity(continuity); vtkSmartPointer spline = vtkSmartPointer::New(); spline->SetXSpline(xSpline); spline->SetYSpline(ySpline); spline->SetZSpline(zSpline); spline->SetPoints(newPoints); vtkSmartPointer functionSource = vtkSmartPointer::New(); functionSource->SetParametricFunction(spline); functionSource->SetUResolution(sampling); functionSource->SetVResolution(sampling); functionSource->SetWResolution(sampling); functionSource->Update(); vtkPolyData* outputFunction = functionSource->GetOutput(); vtkPoints* tmpSmoothPnts = outputFunction->GetPoints(); //smoothPoints of current fiber vtkSmartPointer smoothLine = vtkSmartPointer::New(); smoothLine->GetPointIds()->SetNumberOfIds(tmpSmoothPnts->GetNumberOfPoints()); for (int j=0; jGetNumberOfPoints(); j++) { smoothLine->GetPointIds()->SetId(j, j+pointHelperCnt); vtkSmoothPoints->InsertNextPoint(tmpSmoothPnts->GetPoint(j)); } vtkSmoothCells->InsertNextCell(smoothLine); pointHelperCnt += tmpSmoothPnts->GetNumberOfPoints(); } m_FiberPolyData = vtkSmartPointer::New(); m_FiberPolyData->SetPoints(vtkSmoothPoints); m_FiberPolyData->SetLines(vtkSmoothCells); UpdateColorCoding(); UpdateFiberGeometry(); - m_FiberSampling = pointsPerCm; + m_FiberSampling = 10/pointDistance; } -void mitk::FiberBundleX::DoFiberSmoothing(int pointsPerCm) +void mitk::FiberBundleX::DoFiberSmoothing(float pointDistance) { - DoFiberSmoothing(pointsPerCm, 0, 0, 0 ); + DoFiberSmoothing(pointDistance, 0, 0, 0 ); } // Resample fiber to get equidistant points void mitk::FiberBundleX::ResampleFibers(float pointDistance) { if (pointDistance<=0.00001) return; vtkSmartPointer newPoly = vtkSmartPointer::New(); vtkSmartPointer newCellArray = vtkSmartPointer::New(); vtkSmartPointer newPoints = vtkSmartPointer::New(); int numberOfLines = m_NumFibers; MITK_INFO << "Resampling fibers"; boost::progress_display disp(m_NumFibers); for (int i=0; iGetCell(i); int numPoints = cell->GetNumberOfPoints(); vtkPoints* points = cell->GetPoints(); vtkSmartPointer container = vtkSmartPointer::New(); double* point = points->GetPoint(0); vtkIdType pointId = newPoints->InsertNextPoint(point); container->GetPointIds()->InsertNextId(pointId); float dtau = 0; int cur_p = 1; itk::Vector dR; float normdR = 0; for (;;) { while (dtau <= pointDistance && cur_p < numPoints) { itk::Vector v1; point = points->GetPoint(cur_p-1); v1[0] = point[0]; v1[1] = point[1]; v1[2] = point[2]; itk::Vector v2; point = points->GetPoint(cur_p); v2[0] = point[0]; v2[1] = point[1]; v2[2] = point[2]; dR = v2 - v1; normdR = std::sqrt(dR.GetSquaredNorm()); dtau += normdR; cur_p++; } if (dtau >= pointDistance) { itk::Vector v1; point = points->GetPoint(cur_p-1); v1[0] = point[0]; v1[1] = point[1]; v1[2] = point[2]; itk::Vector v2 = v1 - dR*( (dtau-pointDistance)/normdR ); pointId = newPoints->InsertNextPoint(v2.GetDataPointer()); container->GetPointIds()->InsertNextId(pointId); } else { point = points->GetPoint(numPoints-1); pointId = newPoints->InsertNextPoint(point); container->GetPointIds()->InsertNextId(pointId); break; } dtau = dtau-pointDistance; } newCellArray->InsertNextCell(container); } newPoly->SetPoints(newPoints); newPoly->SetLines(newCellArray); m_FiberPolyData = newPoly; UpdateFiberGeometry(); UpdateColorCoding(); m_FiberSampling = 10/pointDistance; } // reapply selected colorcoding in case polydata structure has changed void mitk::FiberBundleX::UpdateColorCoding() { char* cc = GetCurrentColorCoding(); if( strcmp (COLORCODING_ORIENTATION_BASED,cc) == 0 ) DoColorCodingOrientationBased(); else if( strcmp (COLORCODING_FA_BASED,cc) == 0 ) DoColorCodingFaBased(); } // reapply selected colorcoding in case polydata structure has changed bool mitk::FiberBundleX::Equals(mitk::FiberBundleX* fib) { if (fib==NULL) return false; mitk::FiberBundleX::Pointer tempFib = this->SubtractBundle(fib); mitk::FiberBundleX::Pointer tempFib2 = fib->SubtractBundle(this); if (tempFib.IsNull() && tempFib2.IsNull()) return true; return false; } /* ESSENTIAL IMPLEMENTATION OF SUPERCLASS METHODS */ void mitk::FiberBundleX::UpdateOutputInformation() { } void mitk::FiberBundleX::SetRequestedRegionToLargestPossibleRegion() { } bool mitk::FiberBundleX::RequestedRegionIsOutsideOfTheBufferedRegion() { return false; } bool mitk::FiberBundleX::VerifyRequestedRegion() { return true; } void mitk::FiberBundleX::SetRequestedRegion(const itk::DataObject *data ) { } diff --git a/Modules/DiffusionImaging/FiberTracking/IODataStructures/FiberBundleX/mitkFiberBundleX.h b/Modules/DiffusionImaging/FiberTracking/IODataStructures/FiberBundleX/mitkFiberBundleX.h index aae49e042f..b98c70f376 100644 --- a/Modules/DiffusionImaging/FiberTracking/IODataStructures/FiberBundleX/mitkFiberBundleX.h +++ b/Modules/DiffusionImaging/FiberTracking/IODataStructures/FiberBundleX/mitkFiberBundleX.h @@ -1,157 +1,158 @@ /*=================================================================== 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. ===================================================================*/ #ifndef _MITK_FiberBundleX_H #define _MITK_FiberBundleX_H //includes for MITK datastructure #include #include "FiberTrackingExports.h" #include //includes storing fiberdata #include //may be replaced by class precompile argument #include // may be replaced by class #include // my be replaced by class #include -#include +//#include #include namespace mitk { /** * \brief Base Class for Fiber Bundles; */ class FiberTracking_EXPORT FiberBundleX : public BaseData { public: typedef itk::Image ItkUcharImgType; // fiber colorcodings static const char* COLORCODING_ORIENTATION_BASED; static const char* COLORCODING_FA_BASED; static const char* COLORCODING_CUSTOM; static const char* FIBER_ID_ARRAY; virtual void UpdateOutputInformation(); virtual void SetRequestedRegionToLargestPossibleRegion(); virtual bool RequestedRegionIsOutsideOfTheBufferedRegion(); virtual bool VerifyRequestedRegion(); virtual void SetRequestedRegion(const itk::DataObject *data ); mitkClassMacro( FiberBundleX, BaseData ) itkNewMacro( Self ) mitkNewMacro1Param(Self, vtkSmartPointer) // custom constructor // colorcoding related methods void SetColorCoding(const char*); void SetFAMap(mitk::Image::Pointer); void DoColorCodingOrientationBased(); void DoColorCodingFaBased(); void DoUseFaFiberOpacity(); void ResetFiberOpacity(); // fiber smoothing/resampling void ResampleFibers(float pointDistance = 1); - void DoFiberSmoothing(int pointsPerCm); - void DoFiberSmoothing(int pointsPerCm, double tension, double continuity, double bias ); + void DoFiberSmoothing(float pointDistance); + void DoFiberSmoothing(float pointDistance, double tension, double continuity, double bias ); bool RemoveShortFibers(float lengthInMM); bool RemoveLongFibers(float lengthInMM); bool ApplyCurvatureThreshold(float minRadius, bool deleteFibers); void MirrorFibers(unsigned int axis); void RotateAroundAxis(double x, double y, double z); void TranslateFibers(double x, double y, double z); void ScaleFibers(double x, double y, double z); // add/subtract fibers FiberBundleX::Pointer AddBundle(FiberBundleX* fib); FiberBundleX::Pointer SubtractBundle(FiberBundleX* fib); // fiber subset extraction FiberBundleX::Pointer ExtractFiberSubset(PlanarFigure *pf); std::vector ExtractFiberIdSubset(PlanarFigure* pf); FiberBundleX::Pointer ExtractFiberSubset(ItkUcharImgType* mask, bool anyPoint); + FiberBundleX::Pointer RemoveFibersOutside(ItkUcharImgType* mask, bool invert=false); vtkSmartPointer GeneratePolyDataByIds( std::vector ); // TODO: make protected void GenerateFiberIds(); // TODO: make protected // get/set data void SetFiberPolyData(vtkSmartPointer, bool updateGeometry = true); vtkSmartPointer GetFiberPolyData(); - QStringList GetAvailableColorCodings(); + std::vector< std::string > GetAvailableColorCodings(); char* GetCurrentColorCoding(); itkGetMacro( NumFibers, int) itkGetMacro( FiberSampling, int) itkGetMacro( MinFiberLength, float ) itkGetMacro( MaxFiberLength, float ) itkGetMacro( MeanFiberLength, float ) itkGetMacro( MedianFiberLength, float ) itkGetMacro( LengthStDev, float ) std::vector GetPointsRoi() { return m_PointsRoi; } // copy fiber bundle mitk::FiberBundleX::Pointer GetDeepCopy(); // compare fiber bundles bool Equals(FiberBundleX* fib); protected: FiberBundleX( vtkPolyData* fiberPolyData = NULL ); virtual ~FiberBundleX(); itk::Point GetItkPoint(double point[3]); // calculate geometry from fiber extent void UpdateFiberGeometry(); // calculate colorcoding values according to m_CurrentColorCoding void UpdateColorCoding(); private: // actual fiber container vtkSmartPointer m_FiberPolyData; // contains fiber ids vtkSmartPointer m_FiberIdDataSet; char* m_CurrentColorCoding; int m_NumFibers; std::vector< float > m_FiberLengths; float m_MinFiberLength; float m_MaxFiberLength; float m_MeanFiberLength; float m_MedianFiberLength; float m_LengthStDev; int m_FiberSampling; std::vector m_PointsRoi; // this global variable needs to be refactored }; } // namespace mitk #endif /* _MITK_FiberBundleX_H */ diff --git a/Modules/DiffusionImaging/FiberTracking/IODataStructures/mitkFiberTrackingObjectFactory.cpp b/Modules/DiffusionImaging/FiberTracking/IODataStructures/mitkFiberTrackingObjectFactory.cpp index 7ff0166236..442fcbf642 100644 --- a/Modules/DiffusionImaging/FiberTracking/IODataStructures/mitkFiberTrackingObjectFactory.cpp +++ b/Modules/DiffusionImaging/FiberTracking/IODataStructures/mitkFiberTrackingObjectFactory.cpp @@ -1,124 +1,124 @@ #include "mitkFiberTrackingObjectFactory.h" mitk::FiberTrackingObjectFactory::FiberTrackingObjectFactory(bool /*registerSelf*/) :CoreObjectFactoryBase() { static bool alreadyDone = false; if (!alreadyDone) { MITK_DEBUG << "FiberTrackingObjectFactory c'tor" << std::endl; RegisterIOFactories(); mitk::FiberBundleXIOFactory::RegisterOneFactory(); //modernized mitk::FiberBundleXWriterFactory::RegisterOneFactory();//modernized m_FileWriters.push_back( mitk::FiberBundleXWriter::New().GetPointer() );//modernized mitk::CoreObjectFactory::GetInstance()->RegisterExtraFactory(this); CreateFileExtensionsMap(); alreadyDone = true; } } mitk::Mapper::Pointer mitk::FiberTrackingObjectFactory::CreateMapper(mitk::DataNode* node, MapperSlotId id) { mitk::Mapper::Pointer newMapper=NULL; if ( id == mitk::BaseRenderer::Standard2D ) { std::string classname("FiberBundleX"); if(node->GetData() && classname.compare(node->GetData()->GetNameOfClass())==0) { newMapper = mitk::FiberBundleXMapper2D::New(); newMapper->SetDataNode(node); } } else if ( id == mitk::BaseRenderer::Standard3D ) { std::string classname("FiberBundleX"); if(node->GetData() && classname.compare(node->GetData()->GetNameOfClass())==0) { newMapper = mitk::FiberBundleXMapper3D::New(); newMapper->SetDataNode(node); } - classname = "FiberBundleXThreadMonitor"; - if(node->GetData() && classname.compare(node->GetData()->GetNameOfClass())==0) - { - newMapper = mitk::FiberBundleXThreadMonitorMapper3D::New(); - newMapper->SetDataNode(node); - } +// classname = "FiberBundleXThreadMonitor"; +// if(node->GetData() && classname.compare(node->GetData()->GetNameOfClass())==0) +// { +// newMapper = mitk::FiberBundleXThreadMonitorMapper3D::New(); +// newMapper->SetDataNode(node); +// } } return newMapper; } void mitk::FiberTrackingObjectFactory::SetDefaultProperties(mitk::DataNode* node) { std::string classname("FiberBundleX"); if(node->GetData() && classname.compare(node->GetData()->GetNameOfClass())==0) { mitk::FiberBundleXMapper3D::SetDefaultProperties(node); mitk::FiberBundleXMapper2D::SetDefaultProperties(node); } - classname = "FiberBundleXThreadMonitor"; - if(node->GetData() && classname.compare(node->GetData()->GetNameOfClass())==0) - { - mitk::FiberBundleXThreadMonitorMapper3D::SetDefaultProperties(node); - } +// classname = "FiberBundleXThreadMonitor"; +// if(node->GetData() && classname.compare(node->GetData()->GetNameOfClass())==0) +// { +// mitk::FiberBundleXThreadMonitorMapper3D::SetDefaultProperties(node); +// } } const char* mitk::FiberTrackingObjectFactory::GetFileExtensions() { std::string fileExtension; this->CreateFileExtensions(m_FileExtensionsMap, fileExtension); return fileExtension.c_str(); } mitk::CoreObjectFactoryBase::MultimapType mitk::FiberTrackingObjectFactory::GetFileExtensionsMap() { return m_FileExtensionsMap; } const char* mitk::FiberTrackingObjectFactory::GetSaveFileExtensions() { std::string fileExtension; this->CreateFileExtensions(m_SaveFileExtensionsMap, fileExtension); return fileExtension.c_str(); } mitk::CoreObjectFactoryBase::MultimapType mitk::FiberTrackingObjectFactory::GetSaveFileExtensionsMap() { return m_SaveFileExtensionsMap; } void mitk::FiberTrackingObjectFactory::CreateFileExtensionsMap() { m_FileExtensionsMap.insert(std::pair("*.fib", "Fiber Bundle")); m_FileExtensionsMap.insert(std::pair("*.vtk", "Fiber Bundle")); m_SaveFileExtensionsMap.insert(std::pair("*.fib", "Fiber Bundle")); m_SaveFileExtensionsMap.insert(std::pair("*.vtk", "Fiber Bundle")); } void mitk::FiberTrackingObjectFactory::RegisterIOFactories() { } void RegisterFiberTrackingObjectFactory() { static bool oneFiberTrackingObjectFactoryRegistered = false; if ( ! oneFiberTrackingObjectFactoryRegistered ) { MITK_DEBUG << "Registering FiberTrackingObjectFactory..." << std::endl; mitk::CoreObjectFactory::GetInstance()->RegisterExtraFactory(mitk::FiberTrackingObjectFactory::New()); oneFiberTrackingObjectFactoryRegistered = true; } -} \ No newline at end of file +} diff --git a/Modules/DiffusionImaging/FiberTracking/IODataStructures/mitkFiberTrackingObjectFactory.h b/Modules/DiffusionImaging/FiberTracking/IODataStructures/mitkFiberTrackingObjectFactory.h index 3ba7a4b04b..c0a1f715fb 100644 --- a/Modules/DiffusionImaging/FiberTracking/IODataStructures/mitkFiberTrackingObjectFactory.h +++ b/Modules/DiffusionImaging/FiberTracking/IODataStructures/mitkFiberTrackingObjectFactory.h @@ -1,54 +1,54 @@ #ifndef MITKFIBERTRACKINGOBJECTFACTORY_H #define MITKFIBERTRACKINGOBJECTFACTORY_H #include "mitkCoreObjectFactory.h" #include "FiberTrackingExports.h" //modernized fiberbundle datastrucutre #include "mitkFiberBundleX.h" #include "mitkFiberBundleXIOFactory.h" #include "mitkFiberBundleXWriterFactory.h" #include "mitkFiberBundleXWriter.h" #include "mitkFiberBundleXMapper3D.h" #include "mitkFiberBundleXMapper2D.h" -#include "mitkFiberBundleXThreadMonitorMapper3D.h" -#include "mitkFiberBundleXThreadMonitor.h" +//#include "mitkFiberBundleXThreadMonitorMapper3D.h" +//#include "mitkFiberBundleXThreadMonitor.h" #include "mitkPlanarFigureMapper3D.h" namespace mitk { class FiberTracking_EXPORT FiberTrackingObjectFactory : public CoreObjectFactoryBase { public: mitkClassMacro(FiberTrackingObjectFactory,CoreObjectFactoryBase); itkNewMacro(FiberTrackingObjectFactory); virtual Mapper::Pointer CreateMapper(mitk::DataNode* node, MapperSlotId slotId); virtual void SetDefaultProperties(mitk::DataNode* node); virtual const char* GetFileExtensions(); virtual mitk::CoreObjectFactoryBase::MultimapType GetFileExtensionsMap(); virtual const char* GetSaveFileExtensions(); virtual mitk::CoreObjectFactoryBase::MultimapType GetSaveFileExtensionsMap(); void RegisterIOFactories(); protected: FiberTrackingObjectFactory(bool registerSelf = true); private: void CreateFileExtensionsMap(); std::string m_ExternalFileExtensions; std::string m_InternalFileExtensions; std::string m_SaveFileExtensions; MultimapType m_FileExtensionsMap; MultimapType m_SaveFileExtensionsMap; }; } // global declaration for simple call by // applications void FiberTracking_EXPORT RegisterFiberTrackingObjectFactory(); #endif // MITKFIBERTRACKINGOBJECTFACTORY_H diff --git a/Modules/DiffusionImaging/FiberTracking/Interactions/mitkFiberBundleInteractor.cpp b/Modules/DiffusionImaging/FiberTracking/Interactions/mitkFiberBundleInteractor.cpp index 997b91b1a4..7ed8619e19 100644 --- a/Modules/DiffusionImaging/FiberTracking/Interactions/mitkFiberBundleInteractor.cpp +++ b/Modules/DiffusionImaging/FiberTracking/Interactions/mitkFiberBundleInteractor.cpp @@ -1,274 +1,274 @@ /*=================================================================== 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 "mitkFiberBundleInteractor.h" #include #include #include #include #include #include #include #include #include #include #include #include #include "mitkBaseRenderer.h" #include #include #include #include #include #include -#include +// #include mitk::FiberBundleInteractor::FiberBundleInteractor(const char * type, DataNode* dataNode) : Interactor(type, dataNode), m_LastPosition(0) { m_LastPoint.Fill(0); } mitk::FiberBundleInteractor::~FiberBundleInteractor() {} void mitk::FiberBundleInteractor::SelectFiber(int position) { MITK_INFO << "mitk::FiberBundleInteractor::SelectFiber " << position; mitk::PointSet* pointSet = dynamic_cast(m_DataNode->GetData()); if (pointSet == NULL) return; if (pointSet->GetSize()<=0)//if List is empty, then no select of a point can be done! return; mitk::Point3D noPoint;//dummyPoint... not needed anyway noPoint.Fill(0); mitk::PointOperation* doOp = new mitk::PointOperation(OpSELECTPOINT, noPoint, position); if (m_UndoEnabled) { mitk::PointOperation* undoOp = new mitk::PointOperation(OpDESELECTPOINT, noPoint, position); OperationEvent *operationEvent = new OperationEvent(pointSet, doOp, undoOp); m_UndoController->SetOperationEvent(operationEvent); } pointSet->ExecuteOperation(doOp); } void mitk::FiberBundleInteractor::DeselectAllFibers() { MITK_INFO << "mitk::FiberBundleInteractor::DeselectAllFibers "; mitk::PointSet* pointSet = dynamic_cast(m_DataNode->GetData()); if (pointSet == NULL) return; mitk::PointSet::DataType *itkPointSet = pointSet->GetPointSet(); mitk::PointSet::PointsContainer::Iterator it, end; end = itkPointSet->GetPoints()->End(); for (it = itkPointSet->GetPoints()->Begin(); it != end; it++) { int position = it->Index(); PointSet::PointDataType pointData = {0, false, PTUNDEFINED}; itkPointSet->GetPointData(position, &pointData); if ( pointData.selected )//then declare an operation which unselects this point; UndoOperation as well! { mitk::Point3D noPoint; noPoint.Fill(0); mitk::PointOperation* doOp = new mitk::PointOperation(OpDESELECTPOINT, noPoint, position); if (m_UndoEnabled) { mitk::PointOperation* undoOp = new mitk::PointOperation(OpSELECTPOINT, noPoint, position); OperationEvent *operationEvent = new OperationEvent(pointSet, doOp, undoOp); m_UndoController->SetOperationEvent(operationEvent); } pointSet->ExecuteOperation(doOp); } } } float mitk::FiberBundleInteractor::CanHandleEvent(StateEvent const* stateEvent) const //go through all points and check, if the given Point lies near a line { float returnValue = 0; mitk::PositionEvent const *posEvent = dynamic_cast (stateEvent->GetEvent()); //checking if a keyevent can be handled: if (posEvent == NULL) { //check, if the current state has a transition waiting for that key event. if (this->GetCurrentState()->GetTransition(stateEvent->GetId())!=NULL) { return 0.5; } else { return 0; } } //Mouse event handling: //on MouseMove do nothing! reimplement if needed differently if (stateEvent->GetEvent()->GetType() == mitk::Type_MouseMove) { return 0; } //if the event can be understood and if there is a transition waiting for that event if (this->GetCurrentState()->GetTransition(stateEvent->GetId())!=NULL) { returnValue = 0.5;//it can be understood } //check on the right data-type mitk::FiberBundleX* bundle = dynamic_cast(m_DataNode->GetData()); if (bundle == NULL) return 0; return 0.5; } bool mitk::FiberBundleInteractor::ExecuteAction( Action* action, mitk::StateEvent const* stateEvent ) { bool ok = false;//for return type bool //checking corresponding Data; has to be a PointSet or a subclass mitk::FiberBundleX* bundle = dynamic_cast(m_DataNode->GetData()); if (bundle == NULL) return false; // Get Event and extract renderer const Event *event = stateEvent->GetEvent(); BaseRenderer *renderer = NULL; vtkRenderWindow *renderWindow = NULL; vtkRenderWindowInteractor *renderWindowInteractor = NULL; vtkRenderer *currentVtkRenderer = NULL; vtkCamera *camera = NULL; if ( event != NULL ) { renderer = event->GetSender(); if ( renderer != NULL ) { renderWindow = renderer->GetRenderWindow(); if ( renderWindow != NULL ) { renderWindowInteractor = renderWindow->GetInteractor(); if ( renderWindowInteractor != NULL ) { currentVtkRenderer = renderWindowInteractor ->GetInteractorStyle()->GetCurrentRenderer(); if ( currentVtkRenderer != NULL ) { camera = currentVtkRenderer->GetActiveCamera(); } } } } } /*Each case must watch the type of the event!*/ switch (action->GetActionId()) { case AcCHECKHOVERING: { - QApplication::restoreOverrideCursor(); +// QApplication::restoreOverrideCursor(); // Re-enable VTK interactor (may have been disabled previously) if ( renderWindowInteractor != NULL ) { renderWindowInteractor->Enable(); } const DisplayPositionEvent *dpe = dynamic_cast< const DisplayPositionEvent * >( stateEvent->GetEvent() ); // Check if we have a DisplayPositionEvent if ( dpe != NULL ) { // Check if an object is present at the current mouse position DataNode *pickedNode = dpe->GetPickedObjectNode(); if ( pickedNode != m_DataNode ) { // if(pickedNode == 0) // MITK_INFO << "picked node is NULL, no hovering"; // else // MITK_INFO << "wrong node: " << pickedNode; this->HandleEvent( new StateEvent( EIDNOFIGUREHOVER ) ); ok = true; break; } m_CurrentPickedPoint = dpe->GetWorldPosition(); m_CurrentPickedDisplayPoint = dpe->GetDisplayPosition(); - QApplication::setOverrideCursor(Qt::UpArrowCursor); +// QApplication::setOverrideCursor(Qt::UpArrowCursor); this->HandleEvent( new StateEvent( EIDFIGUREHOVER ) ); } ok = true; break; } break; // case AcSELECTPICKEDOBJECT: // MITK_INFO << "FiberBundleInteractor AcSELECTPICKEDOBJECT"; // break; // case AcDESELECTALL: // MITK_INFO << "FiberBundleInteractor AcDESELECTALL"; // break; case AcREMOVE: { MITK_INFO << "picking fiber at " << m_CurrentPickedPoint; // QmitkStdMultiWidgetEditor::Pointer multiWidgetEditor; // multiWidgetEditor->GetStdMultiWidget()->GetRenderWindow1()->GetRenderer()->GetSliceNavigationController()->SelectSliceByPoint( // m_CurrentPickedPoint); BaseRenderer* renderer = mitk::BaseRenderer::GetByName("stdmulti.widget1"); renderer->GetSliceNavigationController()->SelectSliceByPoint( m_CurrentPickedPoint); renderer = mitk::BaseRenderer::GetByName("stdmulti.widget2"); renderer->GetSliceNavigationController()->SelectSliceByPoint( m_CurrentPickedPoint); renderer = mitk::BaseRenderer::GetByName("stdmulti.widget3"); renderer->GetSliceNavigationController()->SelectSliceByPoint( m_CurrentPickedPoint); // mitk::RenderingManager::GetInstance()->RequestUpdateAll(); } break; default: return Superclass::ExecuteAction( action, stateEvent ); } return ok; } diff --git a/Modules/DiffusionImaging/FiberTracking/MiniApps/CMakeLists.txt b/Modules/DiffusionImaging/FiberTracking/MiniApps/CMakeLists.txt index 8e7361bdee..d8ab51b688 100755 --- a/Modules/DiffusionImaging/FiberTracking/MiniApps/CMakeLists.txt +++ b/Modules/DiffusionImaging/FiberTracking/MiniApps/CMakeLists.txt @@ -1,49 +1,51 @@ OPTION(BUILD_FiberTrackingMiniApps "Build commandline tools for fiber tracking" OFF) IF(BUILD_FiberTrackingMiniApps) # include necessary modules here MitkExt QmitkExt MITK_CHECK_MODULE(_RESULT DiffusionCore FiberTracking ) IF(_RESULT) MESSAGE("Warning: FiberTrackingMiniApps is missing ${_RESULT}") ELSE(_RESULT) MITK_USE_MODULE( DiffusionCore FiberTracking ) # needed include directories INCLUDE_DIRECTORIES( ${CMAKE_CURRENT_SOURCE_DIR} ${CMAKE_CURRENT_BINARY_DIR} ${ALL_INCLUDE_DIRECTORIES}) PROJECT( mitkFiberTrackingMiniApps ) # fill in the standalone executables here SET(FIBERTRACKINGMINIAPPS mitkFiberTrackingMiniApps ) # set additional files here SET(FIBERTRACKING_ADDITIONAL_FILES MiniAppManager.cpp GibbsTracking.cpp StreamlineTracking.cpp + FiberProcessing.cpp + PeakExtraction.cpp TractometerAngularErrorTool.cpp ) # create an executable foreach tool (only one at the moment) FOREACH(tool ${FIBERTRACKINGMINIAPPS}) ADD_EXECUTABLE( ${tool} ${tool}.cpp ${FIBERTRACKING_ADDITIONAL_FILES} ) TARGET_LINK_LIBRARIES( ${tool} ${ALL_LIBRARIES} ) ENDFOREACH(tool) ENDIF() MITK_INSTALL_TARGETS(EXECUTABLES mitkFiberTrackingMiniApps ) ENDIF(BUILD_FiberTrackingMiniApps) diff --git a/Modules/DiffusionImaging/FiberTracking/Testing/mitkFiberProcessing.cpp b/Modules/DiffusionImaging/FiberTracking/MiniApps/FiberProcessing.cpp similarity index 50% rename from Modules/DiffusionImaging/FiberTracking/Testing/mitkFiberProcessing.cpp rename to Modules/DiffusionImaging/FiberTracking/MiniApps/FiberProcessing.cpp index 866dc7b9fc..ac38ea21eb 100644 --- a/Modules/DiffusionImaging/FiberTracking/Testing/mitkFiberProcessing.cpp +++ b/Modules/DiffusionImaging/FiberTracking/MiniApps/FiberProcessing.cpp @@ -1,131 +1,160 @@ /*=================================================================== 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 "mitkTestingMacros.h" +#include "MiniAppManager.h" #include #include #include #include #include #include #include #include #include #include #include #include #include #include #include #include -#include #include #include #include +#include "ctkCommandLineParser.h" +#include /** * Short program to average redundant gradients in dwi-files */ mitk::FiberBundleX::Pointer LoadFib(std::string filename) { const std::string s1="", s2=""; std::vector fibInfile = mitk::BaseDataIO::LoadBaseDataFromFile( filename, s1, s2, false ); if( fibInfile.empty() ) MITK_INFO << "File " << filename << " could not be read!"; mitk::BaseData::Pointer baseData = fibInfile.at(0); return dynamic_cast(baseData.GetPointer()); } -int mitkFiberProcessing(int argc, char* argv[]) +int FiberProcessing(int argc, char* argv[]) { - MITK_TEST_BEGIN("mitkFiberBundleXTest"); - - if ( argc<6 ) - { - std::cout << argv[0] << " " << std::endl; - std::cout << std::endl; + ctkCommandLineParser parser; + parser.setArgumentPrefix("--", "-"); + parser.addArgument("input", "i", ctkCommandLineParser::String, "input fiber bundle (.fib)", mitk::Any(), false); + parser.addArgument("outFile", "o", ctkCommandLineParser::String, "output fiber bundle (.fib)", mitk::Any(), false); + + parser.addArgument("resample", "r", ctkCommandLineParser::Float, "Resample fiber with the given point distance (in mm)"); + parser.addArgument("smooth", "s", ctkCommandLineParser::Float, "Smooth fiber with the given point distance (in mm)"); + parser.addArgument("minLength", "l", ctkCommandLineParser::Float, "Minimum fiber length (in mm)"); + parser.addArgument("maxLength", "m", ctkCommandLineParser::Float, "Maximum fiber length (in mm)"); + parser.addArgument("minCurv", "a", ctkCommandLineParser::Float, "Minimum curvature radius (in mm)"); + parser.addArgument("mirror", "p", ctkCommandLineParser::Int, "Invert fiber coordinates XYZ (e.g. 010 to invert y-coordinate of each fiber point)"); + + map parsedArgs = parser.parseArguments(argc, argv); + if (parsedArgs.size()==0) return EXIT_FAILURE; - } + + float pointDist = -1; + if (parsedArgs.count("resample")) + pointDist = mitk::any_cast(parsedArgs["resample"]); + + float smoothDist = -1; + if (parsedArgs.count("smooth")) + smoothDist = mitk::any_cast(parsedArgs["smooth"]); + + float minFiberLength = -1; + if (parsedArgs.count("minLength")) + minFiberLength = mitk::any_cast(parsedArgs["minLength"]); + + float maxFiberLength = -1; + if (parsedArgs.count("maxLength")) + maxFiberLength = mitk::any_cast(parsedArgs["maxLength"]); + + float curvThres = -1; + if (parsedArgs.count("minCurv")) + curvThres = mitk::any_cast(parsedArgs["minCurv"]); + + int axis = 0; + if (parsedArgs.count("mirror")) + axis = mitk::any_cast(parsedArgs["mirror"]); + + string inFileName = mitk::any_cast(parsedArgs["input"]); + string outFileName = mitk::any_cast(parsedArgs["outFile"]); try { RegisterDiffusionCoreObjectFactory(); RegisterFiberTrackingObjectFactory(); - mitk::FiberBundleX::Pointer fib = LoadFib(argv[1]); - int pointDist = QString(argv[2]).toFloat(); - float lenThres = QString(argv[3]).toFloat(); - float curvThres = QString(argv[4]).toFloat(); + mitk::FiberBundleX::Pointer fib = LoadFib(inFileName); - std::string outfilename; - if (argc==7) - outfilename = argv[6]; - else - outfilename = argv[1]; + if (minFiberLength>0) + fib->RemoveShortFibers(minFiberLength); - if (lenThres>0) - fib->RemoveShortFibers(lenThres); + if (maxFiberLength>0) + fib->RemoveLongFibers(maxFiberLength); if (curvThres>0) fib->ApplyCurvatureThreshold(curvThres, false); if (pointDist>0) fib->ResampleFibers(pointDist); - int axis = QString(argv[5]).toInt(); + if (smoothDist>0) + fib->DoFiberSmoothing(smoothDist); + if (axis/100==1) fib->MirrorFibers(0); if ((axis%100)/10==1) fib->MirrorFibers(1); if (axis%10==1) fib->MirrorFibers(2); mitk::CoreObjectFactory::FileWriterList fileWriters = mitk::CoreObjectFactory::GetInstance()->GetFileWriters(); for (mitk::CoreObjectFactory::FileWriterList::iterator it = fileWriters.begin() ; it != fileWriters.end() ; ++it) { if ( (*it)->CanWriteBaseDataType(fib.GetPointer()) ) { - MITK_INFO << "writing " << outfilename; - (*it)->SetFileName( outfilename.c_str() ); + MITK_INFO << "writing " << outFileName; + (*it)->SetFileName( outFileName.c_str() ); (*it)->DoWrite( fib.GetPointer() ); } } } catch (itk::ExceptionObject e) { MITK_INFO << e; return EXIT_FAILURE; } catch (std::exception e) { MITK_INFO << e.what(); return EXIT_FAILURE; } catch (...) { MITK_INFO << "ERROR!?!"; return EXIT_FAILURE; } - MITK_INFO << "DONE"; - - MITK_TEST_END(); } +RegisterFiberTrackingMiniApp(FiberProcessing); diff --git a/Modules/DiffusionImaging/FiberTracking/MiniApps/GibbsTracking.cpp b/Modules/DiffusionImaging/FiberTracking/MiniApps/GibbsTracking.cpp index f15d2bb328..6b5ed9a955 100755 --- a/Modules/DiffusionImaging/FiberTracking/MiniApps/GibbsTracking.cpp +++ b/Modules/DiffusionImaging/FiberTracking/MiniApps/GibbsTracking.cpp @@ -1,217 +1,215 @@ /*=================================================================== 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 "MiniAppManager.h" #include #include #include #include #include #include #include #include #include #include #include #include #include "ctkCommandLineParser.h" +#include template typename itk::ShCoefficientImageImporter< float, shOrder >::QballImageType::Pointer TemplatedConvertShCoeffs(mitk::Image* mitkImg, int toolkit) { typedef itk::ShCoefficientImageImporter< float, shOrder > FilterType; typedef mitk::ImageToItk< itk::Image< float, 4 > > CasterType; CasterType::Pointer caster = CasterType::New(); caster->SetInput(mitkImg); caster->Update(); typename FilterType::Pointer filter = FilterType::New(); - switch (toolkit) { case 0: filter->SetToolkit(FilterType::FSL); break; case 1: filter->SetToolkit(FilterType::MRTRIX); break; default: filter->SetToolkit(FilterType::FSL); } - filter->SetInputImage(caster->GetOutput()); filter->GenerateData(); return filter->GetQballImage(); } int GibbsTracking(int argc, char* argv[]) { ctkCommandLineParser parser; parser.setArgumentPrefix("--", "-"); parser.addArgument("input", "i", ctkCommandLineParser::String, "input image (tensor, Q-ball or FSL/MRTrix SH-coefficient image)", mitk::Any(), false); parser.addArgument("parameters", "p", ctkCommandLineParser::String, "parameter file (.gtp)", mitk::Any(), false); parser.addArgument("mask", "m", ctkCommandLineParser::String, "binary mask image"); - parser.addArgument("shConvention", "s", ctkCommandLineParser::String, "sh coefficient convention (FSL, MRtrix) (default = FSL)"); + parser.addArgument("shConvention", "s", ctkCommandLineParser::String, "sh coefficient convention (FSL, MRtrix)", string("FSL"), true); parser.addArgument("outFile", "o", ctkCommandLineParser::String, "output fiber bundle (.fib)", mitk::Any(), false); map parsedArgs = parser.parseArguments(argc, argv); if (parsedArgs.size()==0) return EXIT_FAILURE; string inFileName = mitk::any_cast(parsedArgs["input"]); string paramFileName = mitk::any_cast(parsedArgs["parameters"]); string outFileName = mitk::any_cast(parsedArgs["outFile"]); try { RegisterDiffusionCoreObjectFactory(); RegisterFiberTrackingObjectFactory(); // instantiate gibbs tracker typedef itk::Vector OdfVectorType; typedef itk::Image ItkQballImageType; typedef itk::GibbsTrackingFilter GibbsTrackingFilterType; GibbsTrackingFilterType::Pointer gibbsTracker = GibbsTrackingFilterType::New(); // load input image const std::string s1="", s2=""; std::vector infile = mitk::BaseDataIO::LoadBaseDataFromFile( inFileName, s1, s2, false ); // try to cast to qball image - QString inImageName(inFileName.c_str()); - if( inImageName.endsWith(".qbi") ) + if( boost::algorithm::ends_with(inFileName, ".qbi") ) { MITK_INFO << "Loading qball image ..."; mitk::QBallImage::Pointer mitkQballImage = dynamic_cast(infile.at(0).GetPointer()); ItkQballImageType::Pointer itk_qbi = ItkQballImageType::New(); mitk::CastToItkImage(mitkQballImage, itk_qbi); gibbsTracker->SetQBallImage(itk_qbi.GetPointer()); } - else if( inImageName.endsWith(".dti") ) + else if( boost::algorithm::ends_with(inFileName, ".dti") ) { MITK_INFO << "Loading tensor image ..."; typedef itk::Image< itk::DiffusionTensor3D, 3 > ItkTensorImage; mitk::TensorImage::Pointer mitkTensorImage = dynamic_cast(infile.at(0).GetPointer()); ItkTensorImage::Pointer itk_dti = ItkTensorImage::New(); mitk::CastToItkImage(mitkTensorImage, itk_dti); gibbsTracker->SetTensorImage(itk_dti); } - else if ( inImageName.endsWith(".nii") ) + else if ( boost::algorithm::ends_with(inFileName, ".nii") ) { MITK_INFO << "Loading sh-coefficient image ..."; mitk::Image::Pointer mitkImage = dynamic_cast(infile.at(0).GetPointer()); int nrCoeffs = mitkImage->GetLargestPossibleRegion().GetSize()[3]; int c=3, d=2-2*nrCoeffs; double D = c*c-4*d; int shOrder; if (D>0) { shOrder = (-c+sqrt(D))/2.0; if (shOrder<0) shOrder = (-c-sqrt(D))/2.0; } else if (D==0) shOrder = -c/2.0; MITK_INFO << "using SH-order " << shOrder; int toolkitConvention = 0; if (parsedArgs.count("shConvention")) { - QString convention(mitk::any_cast(parsedArgs["shConvention"]).c_str()); - if ( convention.compare("MRtrix", Qt::CaseInsensitive)==0 ) + string convention = mitk::any_cast(parsedArgs["shConvention"]).c_str(); + + if ( boost::algorithm::equals(convention, "MRtrix") ) { toolkitConvention = 1; MITK_INFO << "Using MRtrix style sh-coefficient convention"; } else MITK_INFO << "Using FSL style sh-coefficient convention"; } else MITK_INFO << "Using FSL style sh-coefficient convention"; switch (shOrder) { case 4: gibbsTracker->SetQBallImage(TemplatedConvertShCoeffs<4>(mitkImage, toolkitConvention)); break; case 6: gibbsTracker->SetQBallImage(TemplatedConvertShCoeffs<6>(mitkImage, toolkitConvention)); break; case 8: gibbsTracker->SetQBallImage(TemplatedConvertShCoeffs<8>(mitkImage, toolkitConvention)); break; case 10: gibbsTracker->SetQBallImage(TemplatedConvertShCoeffs<10>(mitkImage, toolkitConvention)); break; case 12: gibbsTracker->SetQBallImage(TemplatedConvertShCoeffs<12>(mitkImage, toolkitConvention)); break; default: MITK_INFO << "SH-order " << shOrder << " not supported"; } } else return EXIT_FAILURE; // global tracking if (parsedArgs.count("mask")) { typedef itk::Image MaskImgType; mitk::Image::Pointer mitkMaskImage = mitk::IOUtil::LoadImage(mitk::any_cast(parsedArgs["mask"])); MaskImgType::Pointer itk_mask = MaskImgType::New(); mitk::CastToItkImage(mitkMaskImage, itk_mask); gibbsTracker->SetMaskImage(itk_mask); } gibbsTracker->SetDuplicateImage(false); gibbsTracker->SetLoadParameterFile( paramFileName ); // gibbsTracker->SetLutPath( "" ); gibbsTracker->Update(); mitk::FiberBundleX::Pointer mitkFiberBundle = mitk::FiberBundleX::New(gibbsTracker->GetFiberBundle()); mitk::CoreObjectFactory::FileWriterList fileWriters = mitk::CoreObjectFactory::GetInstance()->GetFileWriters(); for (mitk::CoreObjectFactory::FileWriterList::iterator it = fileWriters.begin() ; it != fileWriters.end() ; ++it) { if ( (*it)->CanWriteBaseDataType(mitkFiberBundle.GetPointer()) ) { (*it)->SetFileName( outFileName.c_str() ); (*it)->DoWrite( mitkFiberBundle.GetPointer() ); } } } catch (itk::ExceptionObject e) { MITK_INFO << e; return EXIT_FAILURE; } catch (std::exception e) { MITK_INFO << e.what(); return EXIT_FAILURE; } catch (...) { MITK_INFO << "ERROR!?!"; return EXIT_FAILURE; } - MITK_INFO << "DONE"; return EXIT_SUCCESS; } RegisterFiberTrackingMiniApp(GibbsTracking); diff --git a/Modules/DiffusionImaging/FiberTracking/MiniApps/PeakExtraction.cpp b/Modules/DiffusionImaging/FiberTracking/MiniApps/PeakExtraction.cpp new file mode 100755 index 0000000000..21d387709e --- /dev/null +++ b/Modules/DiffusionImaging/FiberTracking/MiniApps/PeakExtraction.cpp @@ -0,0 +1,351 @@ +/*=================================================================== + +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 "MiniAppManager.h" + +#include +#include +#include + +#include +#include +#include +#include +#include +#include + +#include +#include +#include +#include "ctkCommandLineParser.h" +#include +#include +#include +#include +#include +#include + + +mitk::Image::Pointer LoadData(std::string filename) +{ + if( filename.empty() ) + return NULL; + + const std::string s1="", s2=""; + std::vector infile = mitk::BaseDataIO::LoadBaseDataFromFile( filename, s1, s2, false ); + if( infile.empty() ) + { + MITK_INFO << "File " << filename << " could not be read!"; + return NULL; + } + + mitk::BaseData::Pointer baseData = infile.at(0); + return dynamic_cast(baseData.GetPointer()); +} + +int PeakExtraction(int argc, char* argv[]) +{ + ctkCommandLineParser parser; + parser.setArgumentPrefix("--", "-"); + parser.addArgument("image", "i", ctkCommandLineParser::String, "sh coefficient image", mitk::Any(), false); + parser.addArgument("outroot", "o", ctkCommandLineParser::String, "output root", mitk::Any(), false); + parser.addArgument("mask", "m", ctkCommandLineParser::String, "mask image"); + parser.addArgument("normalization", "n", ctkCommandLineParser::Int, "0=no norm, 1=max norm, 2=single vec norm", 1, true); + parser.addArgument("numpeaks", "p", ctkCommandLineParser::Int, "maximum number of extracted peaks", 2, true); + parser.addArgument("peakthres", "r", ctkCommandLineParser::Float, "peak threshold relative to largest peak", 0.4, true); + parser.addArgument("abspeakthres", "a", ctkCommandLineParser::Float, "absolute peak threshold weighted with local GFA value", 0.06, true); + parser.addArgument("shConvention", "s", ctkCommandLineParser::String, "use specified SH-basis (MITK, FSL, MRtrix)", string("MITK"), true); + parser.addArgument("noFlip", "f", ctkCommandLineParser::Bool, "do not flip input image to match MITK coordinate convention"); + + map parsedArgs = parser.parseArguments(argc, argv); + if (parsedArgs.size()==0) + return EXIT_FAILURE; + + // mandatory arguments + string imageName = mitk::any_cast(parsedArgs["image"]); + string outRoot = mitk::any_cast(parsedArgs["outroot"]); + + // optional arguments + string maskImageName(""); + if (parsedArgs.count("mask")) + maskImageName = mitk::any_cast(parsedArgs["mask"]); + + int normalization = 1; + if (parsedArgs.count("normalization")) + normalization = mitk::any_cast(parsedArgs["normalization"]); + + int numPeaks = 2; + if (parsedArgs.count("numpeaks")) + numPeaks = mitk::any_cast(parsedArgs["numpeaks"]); + + float peakThres = 0.4; + if (parsedArgs.count("peakthres")) + peakThres = mitk::any_cast(parsedArgs["peakthres"]); + + float absPeakThres = 0.06; + if (parsedArgs.count("abspeakthres")) + absPeakThres = mitk::any_cast(parsedArgs["abspeakthres"]); + + bool noFlip = false; + if (parsedArgs.count("noFlip")) + noFlip = mitk::any_cast(parsedArgs["noFlip"]); + + MITK_INFO << "image: " << imageName; + MITK_INFO << "outroot: " << outRoot; + if (!maskImageName.empty()) + MITK_INFO << "mask: " << maskImageName; + else + MITK_INFO << "no mask image selected"; + MITK_INFO << "numpeaks: " << numPeaks; + MITK_INFO << "peakthres: " << peakThres; + MITK_INFO << "abspeakthres: " << absPeakThres; + + try + { + mitk::CoreObjectFactory::GetInstance(); + + RegisterDiffusionCoreObjectFactory(); + + mitk::Image::Pointer image = LoadData(imageName); + mitk::Image::Pointer mask = LoadData(maskImageName); + + typedef itk::Image ItkUcharImgType; + typedef itk::FiniteDiffOdfMaximaExtractionFilter< float, 4, 20242 > MaximaExtractionFilterType; + MaximaExtractionFilterType::Pointer filter = MaximaExtractionFilterType::New(); + + int toolkitConvention = 0; + + if (parsedArgs.count("shConvention")) + { + string convention = mitk::any_cast(parsedArgs["shConvention"]).c_str(); + if ( boost::algorithm::equals(convention, "FSL") ) + { + toolkitConvention = 1; + MITK_INFO << "Using FSL SH-basis"; + } + else if ( boost::algorithm::equals(convention, "MRtrix") ) + { + toolkitConvention = 2; + MITK_INFO << "Using MRtrix SH-basis"; + } + else + MITK_INFO << "Using MITK SH-basis"; + } + else + MITK_INFO << "Using MITK SH-basis"; + + ItkUcharImgType::Pointer itkMaskImage = NULL; + if (mask.IsNotNull()) + { + try{ + itkMaskImage = ItkUcharImgType::New(); + mitk::CastToItkImage(mask, itkMaskImage); + filter->SetMaskImage(itkMaskImage); + } + catch(...) + { + + } + } + + if (toolkitConvention>0) + { + MITK_INFO << "Converting coefficient image to MITK format"; + typedef itk::ShCoefficientImageImporter< float, 4 > ConverterType; + typedef mitk::ImageToItk< itk::Image< float, 4 > > CasterType; + CasterType::Pointer caster = CasterType::New(); + caster->SetInput(image); + caster->Update(); + itk::Image< float, 4 >::Pointer itkImage = caster->GetOutput(); + + ConverterType::Pointer converter = ConverterType::New(); + + if (noFlip) + { + converter->SetInputImage(itkImage); + } + else + { + itk::FixedArray flipAxes; + flipAxes[0] = true; + flipAxes[1] = true; + flipAxes[2] = false; + flipAxes[3] = false; + itk::FlipImageFilter< itk::Image< float, 4 > >::Pointer flipper = itk::FlipImageFilter< itk::Image< float, 4 > >::New(); + flipper->SetInput(itkImage); + flipper->SetFlipAxes(flipAxes); + flipper->Update(); + itk::Image< float, 4 >::Pointer flipped = flipper->GetOutput(); + flipped->SetDirection(itkImage->GetDirection()); + flipped->SetOrigin(itkImage->GetOrigin()); + + converter->SetInputImage(flipped); + } + + switch (toolkitConvention) + { + case 1: + converter->SetToolkit(ConverterType::FSL); + filter->SetToolkit(MaximaExtractionFilterType::FSL); + break; + case 2: + converter->SetToolkit(ConverterType::MRTRIX); + filter->SetToolkit(MaximaExtractionFilterType::MRTRIX); + break; + default: + converter->SetToolkit(ConverterType::FSL); + filter->SetToolkit(MaximaExtractionFilterType::FSL); + break; + } + converter->GenerateData(); + filter->SetInput(converter->GetCoefficientImage()); + + // write qbi + ConverterType::QballImageType::Pointer itkQbi = converter->GetQballImage(); + + if (itkMaskImage.IsNotNull()) + { + itkQbi->SetDirection(itkMaskImage->GetDirection()); + itkQbi->SetOrigin(itkMaskImage->GetOrigin()); + } + + mitk::QBallImage::Pointer mitkQbi = mitk::QBallImage::New(); + mitkQbi->InitializeByItk( itkQbi.GetPointer() ); + mitkQbi->SetVolume( itkQbi->GetBufferPointer() ); + + string outfilename = outRoot; + outfilename.append("_QBI.qbi"); + MITK_INFO << "writing " << outfilename; + + mitk::NrrdQBallImageWriter::Pointer writer = mitk::NrrdQBallImageWriter::New(); + writer->SetFileName(outfilename.c_str()); + writer->DoWrite(mitkQbi.GetPointer()); + } + else + { + try{ + typedef mitk::ImageToItk< MaximaExtractionFilterType::CoefficientImageType > CasterType; + CasterType::Pointer caster = CasterType::New(); + caster->SetInput(image); + caster->Update(); + filter->SetInput(caster->GetOutput()); + } + catch(...) + { + MITK_INFO << "wrong image type"; + return EXIT_FAILURE; + } + } + + filter->SetMaxNumPeaks(numPeaks); + filter->SetPeakThreshold(peakThres); + filter->SetAbsolutePeakThreshold(absPeakThres); + filter->SetAngularThreshold(1); + + switch (normalization) + { + case 0: + filter->SetNormalizationMethod(MaximaExtractionFilterType::NO_NORM); + break; + case 1: + filter->SetNormalizationMethod(MaximaExtractionFilterType::MAX_VEC_NORM); + break; + case 2: + filter->SetNormalizationMethod(MaximaExtractionFilterType::SINGLE_VEC_NORM); + break; + } + + filter->Update(); + + // write direction images + { + typedef MaximaExtractionFilterType::ItkDirectionImageContainer ItkDirectionImageContainer; + ItkDirectionImageContainer::Pointer container = filter->GetDirectionImageContainer(); + for (int i=0; iSize(); i++) + { + MaximaExtractionFilterType::ItkDirectionImage::Pointer itkImg = container->GetElement(i); + + if (itkMaskImage.IsNotNull()) + { + itkImg->SetDirection(itkMaskImage->GetDirection()); + itkImg->SetOrigin(itkMaskImage->GetOrigin()); + } + + string outfilename = outRoot; + outfilename.append("_DIRECTION_"); + outfilename.append(boost::lexical_cast(i)); + outfilename.append(".nrrd"); + + MITK_INFO << "writing " << outfilename; + typedef itk::ImageFileWriter< MaximaExtractionFilterType::ItkDirectionImage > WriterType; + WriterType::Pointer writer = WriterType::New(); + writer->SetFileName(outfilename); + writer->SetInput(itkImg); + writer->Update(); + } + } + + // write num directions image + { + ItkUcharImgType::Pointer numDirImage = filter->GetNumDirectionsImage(); + + if (itkMaskImage.IsNotNull()) + { + numDirImage->SetDirection(itkMaskImage->GetDirection()); + numDirImage->SetOrigin(itkMaskImage->GetOrigin()); + } + + string outfilename = outRoot.c_str(); + outfilename.append("_NUM_DIRECTIONS.nrrd"); + MITK_INFO << "writing " << outfilename; + typedef itk::ImageFileWriter< ItkUcharImgType > WriterType; + WriterType::Pointer writer = WriterType::New(); + writer->SetFileName(outfilename); + writer->SetInput(numDirImage); + writer->Update(); + } + + // write vector field + { + mitk::FiberBundleX::Pointer directions = filter->GetOutputFiberBundle(); + + string outfilename = outRoot.c_str(); + outfilename.append("_VECTOR_FIELD.fib"); + + mitk::FiberBundleXWriter::Pointer fibWriter = mitk::FiberBundleXWriter::New(); + fibWriter->SetFileName(outfilename.c_str()); + fibWriter->DoWrite(directions.GetPointer()); + } + } + catch (itk::ExceptionObject e) + { + MITK_INFO << e; + return EXIT_FAILURE; + } + catch (std::exception e) + { + MITK_INFO << e.what(); + return EXIT_FAILURE; + } + catch (...) + { + MITK_INFO << "ERROR!?!"; + return EXIT_FAILURE; + } + MITK_INFO << "DONE"; + return EXIT_SUCCESS; +} +RegisterFiberTrackingMiniApp(PeakExtraction); diff --git a/Modules/DiffusionImaging/FiberTracking/MiniApps/TractometerAngularErrorTool.cpp b/Modules/DiffusionImaging/FiberTracking/MiniApps/TractometerAngularErrorTool.cpp index 00996996dd..b7f099d30e 100755 --- a/Modules/DiffusionImaging/FiberTracking/MiniApps/TractometerAngularErrorTool.cpp +++ b/Modules/DiffusionImaging/FiberTracking/MiniApps/TractometerAngularErrorTool.cpp @@ -1,247 +1,264 @@ /*=================================================================== 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 "MiniAppManager.h" #include #include #include #include #include #include #include #include #include "ctkCommandLineParser.h" #include "ctkCommandLineParser.cpp" #include #include -#include -#include -#include #include #include +#include +#include +#include #define _USE_MATH_DEFINES #include int TractometerAngularErrorTool(int argc, char* argv[]) { ctkCommandLineParser parser; parser.setArgumentPrefix("--", "-"); parser.addArgument("input", "i", ctkCommandLineParser::String, "input tractogram (.fib, vtk ascii file format)", mitk::Any(), false); parser.addArgument("reference", "r", ctkCommandLineParser::StringList, "reference direction images", mitk::Any(), false); parser.addArgument("out", "o", ctkCommandLineParser::String, "output root", mitk::Any(), false); parser.addArgument("mask", "m", ctkCommandLineParser::String, "mask image"); parser.addArgument("athresh", "a", ctkCommandLineParser::Float, "angular threshold in degrees. closer fiber directions are regarded as one direction and clustered together.", 25, true); parser.addArgument("verbose", "v", ctkCommandLineParser::Bool, "output optional and intermediate calculation results"); + parser.addArgument("ignore", "n", ctkCommandLineParser::Bool, "don't increase error for missing or too many directions"); map parsedArgs = parser.parseArguments(argc, argv); if (parsedArgs.size()==0) return EXIT_FAILURE; ctkCommandLineParser::StringContainerType referenceImages = mitk::any_cast(parsedArgs["reference"]); string fibFile = mitk::any_cast(parsedArgs["input"]); string maskImage(""); if (parsedArgs.count("mask")) maskImage = mitk::any_cast(parsedArgs["mask"]); float angularThreshold = 25; if (parsedArgs.count("athresh")) angularThreshold = mitk::any_cast(parsedArgs["athresh"]); string outRoot = mitk::any_cast(parsedArgs["out"]); bool verbose = false; if (parsedArgs.count("verbose")) verbose = mitk::any_cast(parsedArgs["verbose"]); + bool ignore = false; + if (parsedArgs.count("ignore")) + ignore = mitk::any_cast(parsedArgs["ignore"]); + try { RegisterDiffusionCoreObjectFactory(); RegisterFiberTrackingObjectFactory(); typedef itk::Image ItkUcharImgType; typedef itk::Image< itk::Vector< float, 3>, 3 > ItkDirectionImage3DType; typedef itk::VectorContainer< int, ItkDirectionImage3DType::Pointer > ItkDirectionImageContainerType; typedef itk::EvaluateDirectionImagesFilter< float > EvaluationFilterType; // load fiber bundle mitk::FiberBundleX::Pointer inputTractogram = dynamic_cast(mitk::IOUtil::LoadDataNode(fibFile)->GetData()); // load reference directions ItkDirectionImageContainerType::Pointer referenceImageContainer = ItkDirectionImageContainerType::New(); for (int i=0; i(mitk::IOUtil::LoadDataNode(referenceImages.at(i))->GetData()); typedef mitk::ImageToItk< ItkDirectionImage3DType > CasterType; CasterType::Pointer caster = CasterType::New(); caster->SetInput(img); caster->Update(); ItkDirectionImage3DType::Pointer itkImg = caster->GetOutput(); referenceImageContainer->InsertElement(referenceImageContainer->Size(),itkImg); } catch(...){ MITK_INFO << "could not load: " << referenceImages.at(i); } } // load/create mask image ItkUcharImgType::Pointer itkMaskImage = ItkUcharImgType::New(); if (maskImage.compare("")==0) { ItkDirectionImage3DType::Pointer dirImg = referenceImageContainer->GetElement(0); itkMaskImage->SetSpacing( dirImg->GetSpacing() ); itkMaskImage->SetOrigin( dirImg->GetOrigin() ); itkMaskImage->SetDirection( dirImg->GetDirection() ); itkMaskImage->SetLargestPossibleRegion( dirImg->GetLargestPossibleRegion() ); itkMaskImage->SetBufferedRegion( dirImg->GetLargestPossibleRegion() ); itkMaskImage->SetRequestedRegion( dirImg->GetLargestPossibleRegion() ); itkMaskImage->Allocate(); itkMaskImage->FillBuffer(1); } else { mitk::Image::Pointer mitkMaskImage = dynamic_cast(mitk::IOUtil::LoadDataNode(maskImage)->GetData()); CastToItkImage(mitkMaskImage, itkMaskImage); } // extract directions from fiber bundle itk::TractsToVectorImageFilter::Pointer fOdfFilter = itk::TractsToVectorImageFilter::New(); fOdfFilter->SetFiberBundle(inputTractogram); fOdfFilter->SetMaskImage(itkMaskImage); fOdfFilter->SetAngularThreshold(cos(angularThreshold*M_PI/180)); fOdfFilter->SetNormalizeVectors(true); fOdfFilter->SetUseWorkingCopy(false); fOdfFilter->Update(); ItkDirectionImageContainerType::Pointer directionImageContainer = fOdfFilter->GetDirectionImageContainer(); if (verbose) { // write vector field mitk::FiberBundleX::Pointer directions = fOdfFilter->GetOutputFiberBundle(); mitk::CoreObjectFactory::FileWriterList fileWriters = mitk::CoreObjectFactory::GetInstance()->GetFileWriters(); for (mitk::CoreObjectFactory::FileWriterList::iterator it = fileWriters.begin() ; it != fileWriters.end() ; ++it) { if ( (*it)->CanWriteBaseDataType(directions.GetPointer()) ) { - QString outfilename(outRoot.c_str()); - outfilename += "_VECTOR_FIELD.fib"; - (*it)->SetFileName( outfilename.toStdString().c_str() ); + string outfilename = outRoot; + outfilename.append("_VECTOR_FIELD.fib"); + (*it)->SetFileName( outfilename.c_str() ); (*it)->DoWrite( directions.GetPointer() ); } } // write direction images for (int i=0; iSize(); i++) { itk::TractsToVectorImageFilter::ItkDirectionImageType::Pointer itkImg = directionImageContainer->GetElement(i); typedef itk::ImageFileWriter< itk::TractsToVectorImageFilter::ItkDirectionImageType > WriterType; WriterType::Pointer writer = WriterType::New(); - QString outfilename(outRoot.c_str()); - outfilename += "_DIRECTION_"; - outfilename += QString::number(i); - outfilename += ".nrrd"; - MITK_INFO << "writing " << outfilename.toStdString(); - writer->SetFileName(outfilename.toStdString().c_str()); + + string outfilename = outRoot; + outfilename.append("_DIRECTION_"); + outfilename.append(boost::lexical_cast(i)); + outfilename.append(".nrrd"); + + MITK_INFO << "writing " << outfilename; + writer->SetFileName(outfilename.c_str()); writer->SetInput(itkImg); writer->Update(); } // write num direction image { ItkUcharImgType::Pointer numDirImage = fOdfFilter->GetNumDirectionsImage(); typedef itk::ImageFileWriter< ItkUcharImgType > WriterType; WriterType::Pointer writer = WriterType::New(); - QString outfilename(outRoot.c_str()); - outfilename += "_NUM_DIRECTIONS.nrrd"; - MITK_INFO << "writing " << outfilename.toStdString(); - writer->SetFileName(outfilename.toStdString().c_str()); + + string outfilename = outRoot; + outfilename.append("_NUM_DIRECTIONS.nrrd"); + + MITK_INFO << "writing " << outfilename; + writer->SetFileName(outfilename.c_str()); writer->SetInput(numDirImage); writer->Update(); } } // evaluate directions EvaluationFilterType::Pointer evaluationFilter = EvaluationFilterType::New(); evaluationFilter->SetImageSet(directionImageContainer); evaluationFilter->SetReferenceImageSet(referenceImageContainer); evaluationFilter->SetMaskImage(itkMaskImage); + evaluationFilter->SetIgnoreMissingDirections(ignore); evaluationFilter->Update(); if (verbose) { EvaluationFilterType::OutputImageType::Pointer angularErrorImage = evaluationFilter->GetOutput(0); typedef itk::ImageFileWriter< EvaluationFilterType::OutputImageType > WriterType; WriterType::Pointer writer = WriterType::New(); - QString outfilename(outRoot.c_str()); - outfilename += "_ERROR_IMAGE.nrrd"; - writer->SetFileName(outfilename.toStdString().c_str()); + + string outfilename = outRoot; + outfilename.append("_ERROR_IMAGE.nrrd"); + + MITK_INFO << "writing " << outfilename; + writer->SetFileName(outfilename.c_str()); writer->SetInput(angularErrorImage); writer->Update(); } - QString logFile(outRoot.c_str()); logFile += "_ANGULAR_ERROR.csv"; - QFile file(logFile); - file.open(QIODevice::WriteOnly | QIODevice::Text); - QTextStream out(&file); - QString sens = QString("Mean:"); - sens += ","; - sens += QString::number(evaluationFilter->GetMeanAngularError()); - sens += ";"; - - sens += QString("Median:"); - sens += ","; - sens += QString::number(evaluationFilter->GetMedianAngularError()); - sens += ";"; - - sens += QString("Maximum:"); - sens += ","; - sens += QString::number(evaluationFilter->GetMaxAngularError()); - sens += ";"; - - sens += QString("Minimum:"); - sens += ","; - sens += QString::number(evaluationFilter->GetMinAngularError()); - sens += ";"; - - sens += QString("STDEV:"); - sens += ","; - sens += QString::number(std::sqrt(evaluationFilter->GetVarAngularError())); - sens += ";"; - - out << sens; + string logFile = outRoot; + logFile.append("_ANGULAR_ERROR.csv"); + + ofstream file; + file.open (logFile.c_str()); + + string sens = "Mean:"; + sens.append(","); + sens.append(boost::lexical_cast(evaluationFilter->GetMeanAngularError())); + sens.append(";\n"); + + sens.append("Median:"); + sens.append(","); + sens.append(boost::lexical_cast(evaluationFilter->GetMedianAngularError())); + sens.append(";\n"); + + sens.append("Maximum:"); + sens.append(","); + sens.append(boost::lexical_cast(evaluationFilter->GetMaxAngularError())); + sens.append(";\n"); + + sens.append("Minimum:"); + sens.append(","); + sens.append(boost::lexical_cast(evaluationFilter->GetMinAngularError())); + sens.append(";\n"); + + sens.append("STDEV:"); + sens.append(","); + sens.append(boost::lexical_cast(std::sqrt(evaluationFilter->GetVarAngularError()))); + sens.append(";\n"); + + file << sens; + + file.close(); MITK_INFO << "DONE"; } catch (itk::ExceptionObject e) { MITK_INFO << e; return EXIT_FAILURE; } catch (std::exception e) { MITK_INFO << e.what(); return EXIT_FAILURE; } catch (...) { MITK_INFO << "ERROR!?!"; return EXIT_FAILURE; } return EXIT_SUCCESS; } RegisterFiberTrackingMiniApp(TractometerAngularErrorTool); diff --git a/Modules/DiffusionImaging/FiberTracking/Rendering/mitkFiberBundleXMapper3D.cpp b/Modules/DiffusionImaging/FiberTracking/Rendering/mitkFiberBundleXMapper3D.cpp index 75c540a01e..72e7d4c7e1 100644 --- a/Modules/DiffusionImaging/FiberTracking/Rendering/mitkFiberBundleXMapper3D.cpp +++ b/Modules/DiffusionImaging/FiberTracking/Rendering/mitkFiberBundleXMapper3D.cpp @@ -1,202 +1,202 @@ /*=================================================================== 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 "mitkFiberBundleXMapper3D.h" #include //#include //#include #include #include #include #include //not essential for mapper -#include +// #include mitk::FiberBundleXMapper3D::FiberBundleXMapper3D() { m_lut = vtkLookupTable::New(); m_lut->Build(); } mitk::FiberBundleXMapper3D::~FiberBundleXMapper3D() { } const mitk::FiberBundleX* mitk::FiberBundleXMapper3D::GetInput() { return static_cast ( GetDataNode()->GetData() ); } /* This method is called once the mapper gets new input, for UI rotation or changes in colorcoding this method is NOT called */ void mitk::FiberBundleXMapper3D::GenerateData(mitk::BaseRenderer *renderer) { //MITK_INFO << "GENERATE DATA FOR FBX :)"; //=====timer measurement==== - QTime myTimer; - myTimer.start(); +// QTime myTimer; +// myTimer.start(); //========================== mitk::FiberBundleX* FBX = dynamic_cast (GetDataNode()->GetData()); if (FBX == NULL) return; vtkSmartPointer FiberData = FBX->GetFiberPolyData(); if (FiberData == NULL) return; FBXLocalStorage3D *localStorage = m_LSH.GetLocalStorage(renderer); localStorage->m_FiberMapper->SetInput(FiberData); if ( FiberData->GetPointData()->GetNumberOfArrays() > 0 ) localStorage->m_FiberMapper->SelectColorArray( FBX->GetCurrentColorCoding() ); localStorage->m_FiberMapper->ScalarVisibilityOn(); localStorage->m_FiberMapper->SetScalarModeToUsePointFieldData(); localStorage->m_FiberActor->SetMapper(localStorage->m_FiberMapper); localStorage->m_FiberMapper->SetLookupTable(m_lut); // set Opacity float tmpopa; this->GetDataNode()->GetOpacity(tmpopa, NULL); localStorage->m_FiberActor->GetProperty()->SetOpacity((double) tmpopa); // set color if (FBX->GetCurrentColorCoding() != NULL){ // localStorage->m_FiberMapper->SelectColorArray(""); localStorage->m_FiberMapper->SelectColorArray(FBX->GetCurrentColorCoding()); MITK_DEBUG << "MapperFBX: " << FBX->GetCurrentColorCoding(); if(FBX->GetCurrentColorCoding() == FBX->COLORCODING_CUSTOM) { float temprgb[3]; this->GetDataNode()->GetColor( temprgb, NULL ); double trgb[3] = { (double) temprgb[0], (double) temprgb[1], (double) temprgb[2] }; localStorage->m_FiberActor->GetProperty()->SetColor(trgb); } } localStorage->m_FiberAssembly->AddPart(localStorage->m_FiberActor); localStorage->m_LastUpdateTime.Modified(); //since this method is called after generating all necessary data for fiber visualization, all modifications are represented so far. } void mitk::FiberBundleXMapper3D::GenerateDataForRenderer( mitk::BaseRenderer *renderer ) { bool visible = true; GetDataNode()->GetVisibility(visible, renderer, "visible"); if ( !visible ) return; // Calculate time step of the input data for the specified renderer (integer value) // this method is implemented in mitkMapper this->CalculateTimeStep( renderer ); //check if updates occured in the node or on the display FBXLocalStorage3D *localStorage = m_LSH.GetLocalStorage(renderer); const DataNode *node = this->GetDataNode(); if ( (localStorage->m_LastUpdateTime < node->GetMTime()) || (localStorage->m_LastUpdateTime < node->GetPropertyList()->GetMTime()) //was a property modified? || (localStorage->m_LastUpdateTime < node->GetPropertyList(renderer)->GetMTime()) ) { MITK_DEBUG << "UPDATE NEEDED FOR _ " << renderer->GetName(); this->GenerateData(renderer); } } void mitk::FiberBundleXMapper3D::SetDefaultProperties(mitk::DataNode* node, mitk::BaseRenderer* renderer, bool overwrite) { // MITK_INFO << "FiberBundleXxXXMapper3D()SetDefaultProperties"; //MITK_INFO << "FiberBundleMapperX3D SetDefault Properties(...)"; // node->AddProperty( "DisplayChannel", mitk::IntProperty::New( true ), renderer, overwrite ); node->AddProperty( "LineWidth", mitk::IntProperty::New( true ), renderer, overwrite ); node->AddProperty( "opacity", mitk::FloatProperty::New( 1.0 ), renderer, overwrite); // node->AddProperty( "VertexOpacity_1", mitk::BoolProperty::New( false ), renderer, overwrite); // node->AddProperty( "Set_FA_VertexAlpha", mitk::BoolProperty::New( false ), renderer, overwrite); // node->AddProperty( "pointSize", mitk::FloatProperty::New(0.5), renderer, overwrite); // node->AddProperty( "setShading", mitk::IntProperty::New(1), renderer, overwrite); // node->AddProperty( "Xmove", mitk::IntProperty::New( 0 ), renderer, overwrite); // node->AddProperty( "Ymove", mitk::IntProperty::New( 0 ), renderer, overwrite); // node->AddProperty( "Zmove", mitk::IntProperty::New( 0 ), renderer, overwrite); // node->AddProperty( "RepPoints", mitk::BoolProperty::New( false ), renderer, overwrite); // node->AddProperty( "TubeSides", mitk::IntProperty::New( 8 ), renderer, overwrite); // node->AddProperty( "TubeRadius", mitk::FloatProperty::New( 0.15 ), renderer, overwrite); // node->AddProperty( "TubeOpacity", mitk::FloatProperty::New( 1.0 ), renderer, overwrite); node->AddProperty( "pickable", mitk::BoolProperty::New( true ), renderer, overwrite); Superclass::SetDefaultProperties(node, renderer, overwrite); } vtkProp* mitk::FiberBundleXMapper3D::GetVtkProp(mitk::BaseRenderer *renderer) { //MITK_INFO << "FiberBundleXxXXMapper3D()GetVTKProp"; //this->GenerateData(); return m_LSH.GetLocalStorage(renderer)->m_FiberAssembly; } void mitk::FiberBundleXMapper3D::ApplyProperties(mitk::BaseRenderer* renderer) { } void mitk::FiberBundleXMapper3D::UpdateVtkObjects() { } void mitk::FiberBundleXMapper3D::SetVtkMapperImmediateModeRendering(vtkMapper *) { } mitk::FiberBundleXMapper3D::FBXLocalStorage3D::FBXLocalStorage3D() { m_FiberActor = vtkSmartPointer::New(); m_FiberMapper = vtkSmartPointer::New(); m_FiberAssembly = vtkSmartPointer::New(); } diff --git a/Modules/DiffusionImaging/FiberTracking/SignalModels/mitkAstroStickModel.cpp b/Modules/DiffusionImaging/FiberTracking/SignalModels/mitkAstroStickModel.cpp index 753b8b9f20..d2b317c8a9 100644 --- a/Modules/DiffusionImaging/FiberTracking/SignalModels/mitkAstroStickModel.cpp +++ b/Modules/DiffusionImaging/FiberTracking/SignalModels/mitkAstroStickModel.cpp @@ -1,88 +1,88 @@ /*=================================================================== 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 #include template< class ScalarType > AstroStickModel< ScalarType >::AstroStickModel() : m_Diffusivity(0.001) , m_BValue(1000) , m_NumSticks(42) , m_RandomizeSticks(false) { m_RandGen = ItkRandGenType::New(); - vnl_matrix_fixed* sticks = itk::PointShell<42, vnl_matrix_fixed >::DistributePointShell(); + vnl_matrix_fixed* sticks = itk::PointShell<42, vnl_matrix_fixed >::DistributePointShell(); for (int i=0; iget(0,i); stick[1] = sticks->get(1,i); stick[2] = sticks->get(2,i); stick.Normalize(); m_Sticks.push_back(stick); } } template< class ScalarType > AstroStickModel< ScalarType >::~AstroStickModel() { } template< class ScalarType > typename AstroStickModel< ScalarType >::GradientType AstroStickModel< ScalarType >::GetRandomDirection() { GradientType vec; vec[0] = m_RandGen->GetNormalVariate(); vec[1] = m_RandGen->GetNormalVariate(); vec[2] = m_RandGen->GetNormalVariate(); vec.Normalize(); return vec; } template< class ScalarType > typename AstroStickModel< ScalarType >::PixelType AstroStickModel< ScalarType >::SimulateMeasurement() { PixelType signal; signal.SetSize(this->m_GradientList.size()); - double b = -m_BValue*m_Diffusivity; + ScalarType b = -m_BValue*m_Diffusivity; if (m_RandomizeSticks) m_NumSticks = 30 + m_RandGen->GetIntegerVariate()%31; for( unsigned int i=0; im_GradientList.size(); i++) { GradientType g = this->m_GradientList[i]; - double bVal = g.GetNorm(); bVal *= bVal; + ScalarType bVal = g.GetNorm(); bVal *= bVal; if (bVal>0.0001) { for (int j=0; j #include namespace mitk { /** * \brief Generates the diffusion signal using an idealised cylinder with zero radius: e^(-bd(ng)²) * */ template< class ScalarType > class AstroStickModel : public DiffusionSignalModel< ScalarType > { public: AstroStickModel(); ~AstroStickModel(); typedef typename DiffusionSignalModel< ScalarType >::PixelType PixelType; typedef typename DiffusionSignalModel< ScalarType >::GradientType GradientType; typedef typename DiffusionSignalModel< ScalarType >::GradientListType GradientListType; typedef itk::Statistics::MersenneTwisterRandomVariateGenerator ItkRandGenType; /** Actual signal generation **/ PixelType SimulateMeasurement(); void SetRandomizeSticks(bool randomize=true){ m_RandomizeSticks=randomize; } - void SetBvalue(float bValue) { m_BValue = bValue; } ///< b-value used to generate the artificial signal - void SetDiffusivity(float diffusivity) { m_Diffusivity = diffusivity; } ///< Scalar diffusion constant + void SetBvalue(ScalarType bValue) { m_BValue = bValue; } ///< b-value used to generate the artificial signal + void SetDiffusivity(ScalarType diffusivity) { m_Diffusivity = diffusivity; } ///< Scalar diffusion constant void SetNumSticks(unsigned int order) { vnl_matrix sticks; switch (order) { case 1: m_NumSticks = 12; sticks = itk::PointShell<12, vnl_matrix_fixed >::DistributePointShell()->as_matrix(); break; case 2: m_NumSticks = 42; sticks = itk::PointShell<42, vnl_matrix_fixed >::DistributePointShell()->as_matrix(); break; case 3: m_NumSticks = 92; sticks = itk::PointShell<92, vnl_matrix_fixed >::DistributePointShell()->as_matrix(); break; case 4: m_NumSticks = 162; sticks = itk::PointShell<162, vnl_matrix_fixed >::DistributePointShell()->as_matrix(); break; case 5: m_NumSticks = 252; sticks = itk::PointShell<252, vnl_matrix_fixed >::DistributePointShell()->as_matrix(); break; default: m_NumSticks = 42; sticks = itk::PointShell<42, vnl_matrix_fixed >::DistributePointShell()->as_matrix(); break; } for (int i=0; i #include template< class ScalarType > BallModel< ScalarType >::BallModel() : m_Diffusivity(0.001) , m_BValue(1000) { } template< class ScalarType > BallModel< ScalarType >::~BallModel() { } template< class ScalarType > typename BallModel< ScalarType >::PixelType BallModel< ScalarType >::SimulateMeasurement() { PixelType signal; signal.SetSize(this->m_GradientList.size()); for( unsigned int i=0; im_GradientList.size(); i++) { GradientType g = this->m_GradientList[i]; - double bVal = g.GetNorm(); bVal *= bVal; + ScalarType bVal = g.GetNorm(); bVal *= bVal; if (bVal>0.0001) signal[i] = exp( -m_BValue * bVal * m_Diffusivity ); else signal[i] = 1; } return signal; } diff --git a/Modules/DiffusionImaging/FiberTracking/SignalModels/mitkBallModel.h b/Modules/DiffusionImaging/FiberTracking/SignalModels/mitkBallModel.h index 0a6daad1aa..a2a832740c 100644 --- a/Modules/DiffusionImaging/FiberTracking/SignalModels/mitkBallModel.h +++ b/Modules/DiffusionImaging/FiberTracking/SignalModels/mitkBallModel.h @@ -1,58 +1,58 @@ /*=================================================================== 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. ===================================================================*/ #ifndef _MITK_BallModel_H #define _MITK_BallModel_H #include namespace mitk { /** * \brief Generates direction independent diffusion measurement employing a scalar diffusion constant d: e^(-bd) * */ template< class ScalarType > class BallModel : public DiffusionSignalModel< ScalarType > { public: BallModel(); ~BallModel(); typedef typename DiffusionSignalModel< ScalarType >::PixelType PixelType; typedef typename DiffusionSignalModel< ScalarType >::GradientType GradientType; /** Actual signal generation **/ PixelType SimulateMeasurement(); - void SetDiffusivity(float D) { m_Diffusivity = D; } - void SetBvalue(float bValue) { m_BValue = bValue; } + void SetDiffusivity(ScalarType D) { m_Diffusivity = D; } + void SetBvalue(ScalarType bValue) { m_BValue = bValue; } protected: - float m_Diffusivity; ///< Scalar diffusion constant - float m_BValue; ///< b-value used to generate the artificial signal + ScalarType m_Diffusivity; ///< Scalar diffusion constant + ScalarType m_BValue; ///< b-value used to generate the artificial signal }; } #include "mitkBallModel.cpp" #endif diff --git a/Modules/DiffusionImaging/FiberTracking/SignalModels/mitkStickModel.cpp b/Modules/DiffusionImaging/FiberTracking/SignalModels/mitkStickModel.cpp index 10222ae7c1..4bd3a68891 100644 --- a/Modules/DiffusionImaging/FiberTracking/SignalModels/mitkStickModel.cpp +++ b/Modules/DiffusionImaging/FiberTracking/SignalModels/mitkStickModel.cpp @@ -1,55 +1,55 @@ /*=================================================================== 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 #include template< class ScalarType > StickModel< ScalarType >::StickModel() : m_Diffusivity(0.001) , m_BValue(1000) { } template< class ScalarType > StickModel< ScalarType >::~StickModel() { } template< class ScalarType > typename StickModel< ScalarType >::PixelType StickModel< ScalarType >::SimulateMeasurement() { this->m_FiberDirection.Normalize(); PixelType signal; signal.SetSize(this->m_GradientList.size()); for( unsigned int i=0; im_GradientList.size(); i++) { GradientType g = this->m_GradientList[i]; - double bVal = g.GetNorm(); bVal *= bVal; + ScalarType bVal = g.GetNorm(); bVal *= bVal; if (bVal>0.0001) { - double dot = this->m_FiberDirection*g; + ScalarType dot = this->m_FiberDirection*g; signal[i] = exp( -m_BValue * bVal * m_Diffusivity*dot*dot ); } else signal[i] = 1; } return signal; } diff --git a/Modules/DiffusionImaging/FiberTracking/SignalModels/mitkStickModel.h b/Modules/DiffusionImaging/FiberTracking/SignalModels/mitkStickModel.h index f4aaff92af..7452b65f3d 100644 --- a/Modules/DiffusionImaging/FiberTracking/SignalModels/mitkStickModel.h +++ b/Modules/DiffusionImaging/FiberTracking/SignalModels/mitkStickModel.h @@ -1,57 +1,57 @@ /*=================================================================== 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. ===================================================================*/ #ifndef _MITK_StickModel_H #define _MITK_StickModel_H #include namespace mitk { /** * \brief Generates the diffusion signal using an idealised cylinder with zero radius: e^(-bd(ng)²) * */ template< class ScalarType > class StickModel : public DiffusionSignalModel< ScalarType > { public: StickModel(); ~StickModel(); typedef typename DiffusionSignalModel< ScalarType >::PixelType PixelType; typedef typename DiffusionSignalModel< ScalarType >::GradientType GradientType; /** Actual signal generation **/ PixelType SimulateMeasurement(); - void SetBvalue(float bValue) { m_BValue = bValue; } ///< b-value used to generate the artificial signal - void SetDiffusivity(float diffusivity) { m_Diffusivity = diffusivity; } ///< Scalar diffusion constant + void SetBvalue(ScalarType bValue) { m_BValue = bValue; } ///< b-value used to generate the artificial signal + void SetDiffusivity(ScalarType diffusivity) { m_Diffusivity = diffusivity; } ///< Scalar diffusion constant protected: - float m_BValue; ///< b-value used to generate the artificial signal - float m_Diffusivity; ///< Scalar diffusion constant + ScalarType m_BValue; ///< b-value used to generate the artificial signal + ScalarType m_Diffusivity; ///< Scalar diffusion constant }; } #include "mitkStickModel.cpp" #endif diff --git a/Modules/DiffusionImaging/FiberTracking/SignalModels/mitkTensorModel.cpp b/Modules/DiffusionImaging/FiberTracking/SignalModels/mitkTensorModel.cpp index 28ee1cb38c..67a1662cf4 100644 --- a/Modules/DiffusionImaging/FiberTracking/SignalModels/mitkTensorModel.cpp +++ b/Modules/DiffusionImaging/FiberTracking/SignalModels/mitkTensorModel.cpp @@ -1,80 +1,80 @@ /*=================================================================== 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 #include template< class ScalarType > TensorModel< ScalarType >::TensorModel() : m_BValue(1000) { m_KernelDirection[0]=1; m_KernelDirection[1]=0; m_KernelDirection[2]=0; m_KernelTensorMatrix.fill(0.0); m_KernelTensorMatrix[0][0] = 0.002; m_KernelTensorMatrix[1][1] = 0.0005; m_KernelTensorMatrix[2][2] = 0.0005; } template< class ScalarType > TensorModel< ScalarType >::~TensorModel() { } template< class ScalarType > typename TensorModel< ScalarType >::PixelType TensorModel< ScalarType >::SimulateMeasurement() { PixelType signal; signal.SetSize(this->m_GradientList.size()); signal.Fill(0.0); ItkTensorType tensor; tensor.Fill(0.0); this->m_FiberDirection.Normalize(); vnl_vector_fixed axis = itk::CrossProduct(m_KernelDirection, this->m_FiberDirection).GetVnlVector(); axis.normalize(); vnl_quaternion rotation(axis, acos(m_KernelDirection*this->m_FiberDirection)); rotation.normalize(); vnl_matrix_fixed matrix = rotation.rotation_matrix_transpose(); vnl_matrix_fixed tensorMatrix = matrix.transpose()*m_KernelTensorMatrix*matrix; tensor[0] = tensorMatrix[0][0]; tensor[1] = tensorMatrix[0][1]; tensor[2] = tensorMatrix[0][2]; tensor[3] = tensorMatrix[1][1]; tensor[4] = tensorMatrix[1][2]; tensor[5] = tensorMatrix[2][2]; for( unsigned int i=0; im_GradientList.size(); i++) { GradientType g = this->m_GradientList[i]; - double bVal = g.GetNorm(); bVal *= bVal; + ScalarType bVal = g.GetNorm(); bVal *= bVal; if (bVal>0.0001) { - itk::DiffusionTensor3D S; + itk::DiffusionTensor3D< ScalarType > S; S[0] = g[0]*g[0]; S[1] = g[1]*g[0]; S[2] = g[2]*g[0]; S[3] = g[1]*g[1]; S[4] = g[2]*g[1]; S[5] = g[2]*g[2]; - double D = tensor[0]*S[0] + tensor[1]*S[1] + tensor[2]*S[2] + - tensor[1]*S[1] + tensor[3]*S[3] + tensor[4]*S[4] + - tensor[2]*S[2] + tensor[4]*S[4] + tensor[5]*S[5]; + ScalarType D = tensor[0]*S[0] + tensor[1]*S[1] + tensor[2]*S[2] + + tensor[1]*S[1] + tensor[3]*S[3] + tensor[4]*S[4] + + tensor[2]*S[2] + tensor[4]*S[4] + tensor[5]*S[5]; // check for corrupted tensor and generate signal if (D>=0) signal[i] = exp ( -m_BValue * bVal * D ); } else signal[i] = 1; } return signal; } diff --git a/Modules/DiffusionImaging/FiberTracking/SignalModels/mitkTensorModel.h b/Modules/DiffusionImaging/FiberTracking/SignalModels/mitkTensorModel.h index 0a94e5b860..fba519de02 100644 --- a/Modules/DiffusionImaging/FiberTracking/SignalModels/mitkTensorModel.h +++ b/Modules/DiffusionImaging/FiberTracking/SignalModels/mitkTensorModel.h @@ -1,64 +1,64 @@ /*=================================================================== 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. ===================================================================*/ #ifndef _MITK_TensorModel_H #define _MITK_TensorModel_H #include #include namespace mitk { /** * \brief Generates diffusion measurement employing a second rank tensor model: e^(-bg^TDg) * */ template< class ScalarType > class TensorModel : public DiffusionSignalModel< ScalarType > { public: TensorModel(); ~TensorModel(); typedef typename DiffusionSignalModel< ScalarType >::PixelType PixelType; - typedef itk::DiffusionTensor3D< float > ItkTensorType; + typedef itk::DiffusionTensor3D< ScalarType > ItkTensorType; typedef typename DiffusionSignalModel< ScalarType >::GradientType GradientType; /** Actual signal generation **/ PixelType SimulateMeasurement(); - void SetBvalue(float bValue) { m_BValue = bValue; } + void SetBvalue(ScalarType bValue) { m_BValue = bValue; } void SetDiffusivity1(ScalarType d1){ m_KernelTensorMatrix[0][0] = d1; } void SetDiffusivity2(ScalarType d2){ m_KernelTensorMatrix[1][1] = d2; } void SetDiffusivity3(ScalarType d3){ m_KernelTensorMatrix[2][2] = d3; } protected: /** Calculates tensor matrix from FA and ADC **/ void UpdateKernelTensor(); GradientType m_KernelDirection; ///< Direction of the kernel tensors principal eigenvector vnl_matrix_fixed m_KernelTensorMatrix; ///< 3x3 matrix containing the kernel tensor values - float m_BValue; ///< b-value used to generate the artificial signal + ScalarType m_BValue; ///< b-value used to generate the artificial signal }; } #include "mitkTensorModel.cpp" #endif diff --git a/Modules/DiffusionImaging/FiberTracking/Testing/files.cmake b/Modules/DiffusionImaging/FiberTracking/Testing/files.cmake index affeb8469e..b5d52ea256 100644 --- a/Modules/DiffusionImaging/FiberTracking/Testing/files.cmake +++ b/Modules/DiffusionImaging/FiberTracking/Testing/files.cmake @@ -1,8 +1,7 @@ SET(MODULE_CUSTOM_TESTS mitkFiberBundleXReaderWriterTest.cpp mitkFiberBundleXTest.cpp mitkGibbsTrackingTest.cpp - mitkFiberProcessing.cpp ) diff --git a/Modules/DiffusionImaging/FiberTracking/files.cmake b/Modules/DiffusionImaging/FiberTracking/files.cmake index 912c88e510..641f614cee 100644 --- a/Modules/DiffusionImaging/FiberTracking/files.cmake +++ b/Modules/DiffusionImaging/FiberTracking/files.cmake @@ -1,105 +1,105 @@ set(CPP_FILES MiniApps/ctkCommandLineParser.h # DataStructures -> FiberBundleX IODataStructures/FiberBundleX/mitkFiberBundleX.cpp IODataStructures/FiberBundleX/mitkFiberBundleXWriter.cpp IODataStructures/FiberBundleX/mitkFiberBundleXReader.cpp IODataStructures/FiberBundleX/mitkFiberBundleXIOFactory.cpp IODataStructures/FiberBundleX/mitkFiberBundleXWriterFactory.cpp IODataStructures/FiberBundleX/mitkFiberBundleXSerializer.cpp - IODataStructures/FiberBundleX/mitkFiberBundleXThreadMonitor.cpp +# IODataStructures/FiberBundleX/mitkFiberBundleXThreadMonitor.cpp # DataStructures -> PlanarFigureComposite IODataStructures/PlanarFigureComposite/mitkPlanarFigureComposite.cpp # DataStructures IODataStructures/mitkFiberTrackingObjectFactory.cpp # Rendering Rendering/mitkFiberBundleXMapper2D.cpp Rendering/mitkFiberBundleXMapper3D.cpp - Rendering/mitkFiberBundleXThreadMonitorMapper3D.cpp +# Rendering/mitkFiberBundleXThreadMonitorMapper3D.cpp #Rendering/mitkPlanarFigureMapper3D.cpp # Interactions Interactions/mitkFiberBundleInteractor.cpp # Tractography Algorithms/GibbsTracking/mitkParticleGrid.cpp Algorithms/GibbsTracking/mitkMetropolisHastingsSampler.cpp Algorithms/GibbsTracking/mitkEnergyComputer.cpp Algorithms/GibbsTracking/mitkGibbsEnergyComputer.cpp Algorithms/GibbsTracking/mitkFiberBuilder.cpp Algorithms/GibbsTracking/mitkSphereInterpolator.cpp ) set(H_FILES MiniApps/ctkCommandLineParser.h # Rendering Rendering/mitkFiberBundleXMapper3D.h Rendering/mitkFiberBundleXMapper2D.h - Rendering/mitkFiberBundleXThreadMonitorMapper3D.h +# Rendering/mitkFiberBundleXThreadMonitorMapper3D.h #Rendering/mitkPlanarFigureMapper3D.h # DataStructures -> FiberBundleX IODataStructures/FiberBundleX/mitkFiberBundleX.h IODataStructures/FiberBundleX/mitkFiberBundleXWriter.h IODataStructures/FiberBundleX/mitkFiberBundleXReader.h IODataStructures/FiberBundleX/mitkFiberBundleXIOFactory.h IODataStructures/FiberBundleX/mitkFiberBundleXWriterFactory.h IODataStructures/FiberBundleX/mitkFiberBundleXSerializer.h - IODataStructures/FiberBundleX/mitkFiberBundleXThreadMonitor.h +# IODataStructures/FiberBundleX/mitkFiberBundleXThreadMonitor.h IODataStructures/mitkFiberTrackingObjectFactory.h # Algorithms Algorithms/itkTractDensityImageFilter.h Algorithms/itkTractsToFiberEndingsImageFilter.h Algorithms/itkTractsToRgbaImageFilter.h Algorithms/itkElectrostaticRepulsionDiffusionGradientReductionFilter.h Algorithms/itkFibersFromPlanarFiguresFilter.h Algorithms/itkTractsToDWIImageFilter.h Algorithms/itkTractsToVectorImageFilter.h Algorithms/itkKspaceImageFilter.h Algorithms/itkDftImageFilter.h Algorithms/itkAddArtifactsToDwiImageFilter.h Algorithms/itkFieldmapGeneratorFilter.h Algorithms/itkEvaluateDirectionImagesFilter.h # (old) Tractography Algorithms/itkGibbsTrackingFilter.h Algorithms/itkStochasticTractographyFilter.h Algorithms/itkStreamlineTrackingFilter.h Algorithms/GibbsTracking/mitkParticle.h Algorithms/GibbsTracking/mitkParticleGrid.h Algorithms/GibbsTracking/mitkMetropolisHastingsSampler.h Algorithms/GibbsTracking/mitkSimpSamp.h Algorithms/GibbsTracking/mitkEnergyComputer.h Algorithms/GibbsTracking/mitkGibbsEnergyComputer.h Algorithms/GibbsTracking/mitkSphereInterpolator.h Algorithms/GibbsTracking/mitkFiberBuilder.h # Signal Models SignalModels/mitkDiffusionSignalModel.h SignalModels/mitkTensorModel.h SignalModels/mitkBallModel.h SignalModels/mitkDotModel.h SignalModels/mitkAstroStickModel.h SignalModels/mitkStickModel.h SignalModels/mitkDiffusionNoiseModel.h SignalModels/mitkRicianNoiseModel.h SignalModels/mitkKspaceArtifact.h ) set(RESOURCE_FILES # Binary directory resources FiberTrackingLUTBaryCoords.bin FiberTrackingLUTIndices.bin # Shaders Shaders/mitkShaderFiberClipping.xml ) diff --git a/Modules/DiffusionImaging/Quantification/CMakeLists.txt b/Modules/DiffusionImaging/Quantification/CMakeLists.txt index 71d73e4220..1b5239a874 100644 --- a/Modules/DiffusionImaging/Quantification/CMakeLists.txt +++ b/Modules/DiffusionImaging/Quantification/CMakeLists.txt @@ -1,9 +1,9 @@ #DiffusionImaging/Quantification MITK_CREATE_MODULE( Quantification SUBPROJECTS MITK-DTI INCLUDE_DIRS Algorithms IODataStructures IODataStructures/TbssImages Rendering ${CMAKE_CURRENT_BINARY_DIR} - DEPENDS DiffusionCore FiberTracking MitkGraphAlgorithms + DEPENDS DiffusionCore FiberTracking MitkGraphAlgorithms QmitkExt ) add_subdirectory(Testing) diff --git a/Plugins/org.mitk.gui.qt.diffusionimaging/documentation/UserManual/QmitkFiberfoxViewUserManual.dox b/Plugins/org.mitk.gui.qt.diffusionimaging/documentation/UserManual/QmitkFiberfoxViewUserManual.dox index 6c04946775..1361a54a73 100644 --- a/Plugins/org.mitk.gui.qt.diffusionimaging/documentation/UserManual/QmitkFiberfoxViewUserManual.dox +++ b/Plugins/org.mitk.gui.qt.diffusionimaging/documentation/UserManual/QmitkFiberfoxViewUserManual.dox @@ -1,109 +1,111 @@ /** \page org_mitk_views_fiberfoxview Fiberfox This view provides the user interface for Fiberfox [1], an interactive simulation tool for defining artificial white matter fibers and generating corresponding diffusion weighted images. Arbitrary fiber configurations like bent, crossing, kissing, twisting, and fanning bundles can be intuitively defined by positioning only a few 3D waypoints to trigger the automated generation of synthetic fibers. From these fibers a diffusion weighted signal is simulated using a flexible combination of various diffusion models. It can be modified using specified acquisition settings such as gradient direction, b-value, signal-to-noise ratio, image size, and resolution. Available sections: - \ref QmitkFiberfoxViewUserManualFiberDefinition - \ref QmitkFiberfoxViewUserManualSignalGeneration - \ref QmitkFiberfoxViewUserManualKnownIssues - \ref QmitkFiberfoxViewUserManualReferences \image html Fiberfox.png Fig. 1: Screenshot of the Fiberfox framework. The four render windows display an axial (top left), sagittal (top right) and coronal (bottom left) 2D cut as well as a 3D view of a synthetic fiber helix and the fiducials used to define its shape. In the 2D views the helix is superimposing the baseline volume of the corresponding diffusion weighted image. The sagittal render window shows a close-up view on one of the circular fiducials. \section QmitkFiberfoxViewUserManualFiberDefinition Fiber Definition Fiber strands are defined simply by placing markers in a 3D image volume. The fibers are then interpolated between these fiducials. Example: \li Chose an image volume to place the markers used to define the fiber pathway. If you don't have such an image available switch to the "Signal Generation" tab, define the size and spacing of the desired image and click "Generate Image". If no fiber bundle is selected, this will generate a dummy image that can be used to place the fiducials. \li Start placing fiducials at the desired positions to define the fiber pathway. To do that, click on the button with the circle pictogram, then click at the desired position and plane in the image volume and drag your mouse while keeping the button pressed to generate a circular shape. Adjust the shape using the control points (Fig. 2). The position of control point D introduces a twist of the fibers between two successive fiducials. The actual fiber generation is triggered automatically as soon as you place the second control point. \li In some cases the fibers are entangled in a way that can't be resolved by introducing an additional fiber twist. Fiberfox tries to avoid these situations, which arise from different normal orientations of succeeding fiducials, automatically. In rare cases this is not successful. Use the double-arrow button to flip the fiber positions of the selected fiducial in one dimension. Either the problem is resolved now or you can resolve it manually by adjusting the twist-control point. +\li To create non elliptical fiber profile shapes switch to the Fiber Extraction View. This view provides tools to extract subesets of fibers from fiber bundles and enables to cut out arbitrary polygonal fiber shapes from existing bundles. \image html Fiberfox-Fiducial.png Fig. 2: Control points defining the actual shape of the fiducial. A specifies the fiducials position in space, B and C the two ellipse radii and D the twisting angle between two successive fiducials. Fiber Options: \li Real Time Fibers: If checked, each parameter adjustment (fiducial position, number of fibers, ...) will be directly applied to the selected fiber bundle. If unchecked, the fibers will only be generated if the corresponding button "Generate Fibers" is clicked. \li Advanced Options: Show/hide advanced options \li #Fibers: Specifies the number of fibers that will be generated for the selected bundle. -\li Fiber Sampling: Adjusts the number of points per cm that make up the fiber. A higher sampling rate is needed if high curvatures are modeled. +\li Fiber Sampling: Adjusts the distenace of the fiber sampling points (in mm). A higher sampling rate is needed if high curvatures are modeled. \li Tension, Continuity, Bias: Parameters controlling the shape of the splines interpolation the fiducials. See Wikipedia for details. Fiducial Options: \li Use Constant Fiducial Radius: If checked, all fiducials are treated as circles with the same radius. The first fiducial of the bundle defines the radius of all other fiducials. \li Align with grid: Click to shift all fiducial center points to the next voxel center. Operations: \li Rotation: Define the rotation of the selected fiber bundle around each axis (in degree). \li Translation: Define the translation of the selected fiber bundle along each axis (in mm). \li Scaling: Define a scaling factor for the selected fiber bundle in each dimension. \li Transform Selection: Apply specified rotation, translation and scaling to the selected Bundle/Fiducial \li Copy Bundles: Add copies of the selected fiber bundles to the datamanager. \li Join Bundles: Add new bundle to the datamanager that contains all fibers from the selected bundles. \li Include Fiducials: If checked, the specified transformation is also applied to the fiducials belonging to the selected fiber bundle and the fiducials are also copied. \image html FiberfoxExamples.png Fig. 3: Examples of artificial crossing (a,b), fanning (c,d), highly curved (e,f), kissing (g,h) and twisting (i,j) fibers as well as of the corresponding tensor images generated with Fiberfox. \section QmitkFiberfoxViewUserManualSignalGeneration Signal Generation To generate an artificial signal from the input fibers we follow the concepts recently presented by Panagiotaki et al. in a review and taxonomy of different compartment models [2]: a flexible model combining multiple compartments is used to simulate the anisotropic diffusion inside (intra-axonal compartment) and between axons (inter-axonal compartment), isotropic diffusion outside of the axons (extra-axonal compartment 1) and the restricted diffusion in other cell types (extra-axonal compartment 2) weighted according to their respective volume fraction. A diffusion weighted image is generated from the fibers by selecting the according fiber bundle in the datamanager and clicking "Generate Image". If some other diffusion weighted image is selected together with the fiber bundle, Fiberfox directly uses the parameters of the selected image (size, spacing, gradient directions, b-values) for the signal generation process. Additionally a binary image can be selected that defines the tissue area. Voxels outside of this mask will contain no signal, only noise. Basic Image Settings: \li Image Dimensions: Specifies actual image size (number of voxels in each dimension). \li Image Spacing: Specifies voxel size in mm. Beware that changing the voxel size also changes the signal strength, e.g. increasing the resolution from 2x2x2 mm to 1x1x1 mm decreases the signal obtained for each voxel by a factor 8. \li Gradient Directions: Number of gradients directions distributed equally over the half sphere. 10% baseline images are automatically added. \li b-Value: Diffusion weighting in s/mm². If an existing diffusion weighted image is used to set the basic parameters, the b-value is defined by the gradient direction magnitudes of this image, which also enables the use of multiple b-values. Advanced Image Settings (activate checkbox "Advanced Options"): \li Repetitions: Specifies the number of averages used for the acquisition to reduce noise. \li Signal Scale: Additional scaling factor for the signal in each voxel. The default value of 125 results in a maximum signal amplitude of 1000 for 2x2x2 mm voxels. Beware that changing this value without changing the noise variance results in a changed SNR. Adjustment of this value might be needed if the overall signal values are much too high or much too low (depends on a variety of factors like voxel size and relaxation times). \li Echo Time TE: Time between the 90° excitation pulse and the first spin echo. Increasing this time results in a stronger T2-relaxation effect (Wikipedia). \li Line Readout Time: Time to read one line in k-space. Increasing this time results in a stronger T2* effect which causes an attenuation of the higher frequencies in phase direction (here along y-axis) which again results in a blurring effect of sharp edges perpendicular to the phase direction. \li Tinhom Relaxation: Time constant specifying the signal decay due to magnetic field inhomogeneities (also called T2'). Together with the tissue specific relaxation time constant T2 this defines the T2* decay constant: T2*=(T2 T2')/(T2+T2') \li Fiber Radius (in µm): Used to calculate the volume fractions of the used compartments (fiber, water, etc.). If set to 0 (default) the fiber radius is set automatically so that the voxel containing the most fibers is filled completely. A realistic axon radius ranges from about 5 to 20 microns. Using the automatic estimation the resulting value might very well be much larger or smaller than this range. \li Interpolation Shrink: The signal generated at each position along the fibers is distributed on the surrounding voxels using an interpolation scheme shaped like an arctangent function. Large values result in a steeper interpolation scheme approximating a nearest neighbor interpolation. Very small values result in an almost linear interpolation. \li Simulate Signal Relaxation: If checked, the relaxation induced signal decay is simulated, other wise the parameters TE, Line Readout Time, Tinhom, and T2 are ignored. \li Disable Partial Volume Effects: If checked, the actual volume fractions of the single compartments are ignored. A voxel will either be filled by the intra axonal compartment completely or will contain no fiber at all. \li Output k-Space Image: Some of the effects simulated in our framework are modeled in the k-space representation of the actual image. Checking this box will output this frequency representation (amplitude spectrum). Compartment Settings: The group-boxes "Intra-axonal Compartment", "Inter-axonal Compartment" and "Extra-axonal Compartments" allow the specification which model to use and the corresponding model parameters. Currently the following models are implemented: \li Stick: The “stick” model describes diffusion in an idealized cylinder with zero radius. Parameter: Diffusivity d \li Zeppelin: Cylindrically symmetric diffusion tensor. Parameters: Parallel diffusivity d|| and perpendicular diffusivity d⊥ \li Tensor: Full diffusion tensor. Parameters: Parallel diffusivity d|| and perpendicular diffusivity constants d⊥1 and d⊥2 \li Ball: Isotropic compartment. Parameter: Diffusivity d \li Astrosticks: Consists of multiple stick models pointing in different directions. The single stick orientations can either be distributed equally over the sphere or are sampled randomly. The model represents signal coming from a type of glial cell called astrocytes, or populations of axons with arbitrary orientation. Parameters: randomization of the stick orientations and diffusivity of the sticks d. \li Dot: Isotropically restricted compartment. No parameter. For a detailed description of the single models, please refer to Panagiotaki et al. "Compartment models of the diffusion MR signal in brain white matter: A taxonomy and comparison."[2]. Additionally to the model parameters, each compartment has its own T2 signal relaxation constant (in ms). Noise and Artifacts: \li Rician Noise: Add Rician noise with the specified variance to the signal. \li N/2 Ghosts: Specify the offset between successive lines in k-space. This offset causes ghost images in distance N/2 in phase direction due to the alternating EPI readout directions. \li Distortions: Simulate distortions due to magnetic field inhomogeneities. This is achieved by adding an additional phase during the readout process. The input is a frequency map specifying the inhomogeneities. +\li Eddy Currents: EXPERIMENTAL! This feature is currently being tested and might not yet behave as expected! \li Gibbs Ringing: Ringing artifacts occurring on edges in the image due to the frequency low-pass filtering caused by the limited size of the k-space. The higher the oversampling factor, the larger the distance from the corresponding edge in which the ringing is still visible. Keep in mind that increasing the oversampling factor results in a quadratic increase of computation time. \section QmitkFiberfoxViewUserManualKnownIssues Known Issues \li If fiducials are created in one of the marginal slices of the underlying image, a position change of the fiducial can be observed upon selection/deselection. If the fiducial is created in any other slice this bug does not occur. \li If a scaling factor is applied to the selcted fiber bundle, the corresponding fiducials are not scaled accordingly. \li In some cases the automatic update of the selected fiber bundle is not triggered even if "Real Time Fibers" is checked, e.g. if a fiducial is deleted. If this happens on can always force an update by pressing the "Generate Fibers" button. If any other issues or feature requests arises during the use of Fiberfox, please don't hesitate to send us an e-mail or directly report the issue in our bugtracker: http://bugs.mitk.org/ \section QmitkFiberfoxViewUserManualReferences References [1] Peter F. Neher, Bram Stieltjes, Frederik B. Laun, Hans-Peter Meinzer, and Klaus H. Fritzsche: Fiberfox: A novel tool to generate software phantoms of complex fiber geometries. In proceedings: ISMRM 2013 [2] Panagiotaki, E., Schneider, T., Siow, B., Hall, M.G., Lythgoe, M.F., Alexander, D.C.: Compartment models of the diffusion mr signal in brain white matter: A taxonomy and comparison. Neuroimage 59 (2012) 2241–2254 */ diff --git a/Plugins/org.mitk.gui.qt.diffusionimaging/files.cmake b/Plugins/org.mitk.gui.qt.diffusionimaging/files.cmake index 090612aff9..0c3fa25393 100644 --- a/Plugins/org.mitk.gui.qt.diffusionimaging/files.cmake +++ b/Plugins/org.mitk.gui.qt.diffusionimaging/files.cmake @@ -1,173 +1,173 @@ set(SRC_CPP_FILES QmitkODFDetailsWidget.cpp QmitkODFRenderWidget.cpp QmitkPartialVolumeAnalysisWidget.cpp QmitkIVIMWidget.cpp QmitkTbssRoiAnalysisWidget.cpp QmitkResidualAnalysisWidget.cpp QmitkResidualViewWidget.cpp QmitkTensorModelParametersWidget.cpp QmitkZeppelinModelParametersWidget.cpp QmitkStickModelParametersWidget.cpp QmitkDotModelParametersWidget.cpp QmitkBallModelParametersWidget.cpp QmitkAstrosticksModelParametersWidget.cpp ) set(INTERNAL_CPP_FILES mitkPluginActivator.cpp QmitkQBallReconstructionView.cpp QmitkPreprocessingView.cpp QmitkDiffusionDicomImportView.cpp QmitkDiffusionQuantificationView.cpp QmitkTensorReconstructionView.cpp QmitkDiffusionImagingPublicPerspective.cpp QmitkControlVisualizationPropertiesView.cpp QmitkODFDetailsView.cpp QmitkGibbsTrackingView.cpp QmitkStochasticFiberTrackingView.cpp QmitkStreamlineTrackingView.cpp QmitkFiberProcessingView.cpp - QmitkFiberBundleDeveloperView.cpp +# QmitkFiberBundleDeveloperView.cpp QmitkPartialVolumeAnalysisView.cpp QmitkIVIMView.cpp QmitkTractbasedSpatialStatisticsView.cpp QmitkTbssTableModel.cpp QmitkTbssMetaTableModel.cpp QmitkTbssSkeletonizationView.cpp Connectomics/QmitkConnectomicsDataView.cpp Connectomics/QmitkConnectomicsNetworkOperationsView.cpp Connectomics/QmitkConnectomicsStatisticsView.cpp Connectomics/QmitkNetworkHistogramCanvas.cpp QmitkDwiSoftwarePhantomView.cpp QmitkOdfMaximaExtractionView.cpp QmitkFiberfoxView.cpp QmitkFiberExtractionView.cpp QmitkFieldmapGeneratorView.cpp ) set(UI_FILES src/internal/QmitkQBallReconstructionViewControls.ui src/internal/QmitkPreprocessingViewControls.ui src/internal/QmitkDiffusionDicomImportViewControls.ui src/internal/QmitkDiffusionQuantificationViewControls.ui src/internal/QmitkTensorReconstructionViewControls.ui src/internal/QmitkControlVisualizationPropertiesViewControls.ui src/internal/QmitkODFDetailsViewControls.ui src/internal/QmitkGibbsTrackingViewControls.ui src/internal/QmitkStochasticFiberTrackingViewControls.ui src/internal/QmitkStreamlineTrackingViewControls.ui src/internal/QmitkFiberProcessingViewControls.ui - src/internal/QmitkFiberBundleDeveloperViewControls.ui +# src/internal/QmitkFiberBundleDeveloperViewControls.ui src/internal/QmitkPartialVolumeAnalysisViewControls.ui src/internal/QmitkIVIMViewControls.ui src/internal/QmitkTractbasedSpatialStatisticsViewControls.ui src/internal/QmitkTbssSkeletonizationViewControls.ui src/internal/Connectomics/QmitkConnectomicsDataViewControls.ui src/internal/Connectomics/QmitkConnectomicsNetworkOperationsViewControls.ui src/internal/Connectomics/QmitkConnectomicsStatisticsViewControls.ui src/internal/QmitkDwiSoftwarePhantomViewControls.ui src/internal/QmitkOdfMaximaExtractionViewControls.ui src/internal/QmitkFiberfoxViewControls.ui src/internal/QmitkFiberExtractionViewControls.ui src/QmitkTensorModelParametersWidgetControls.ui src/QmitkZeppelinModelParametersWidgetControls.ui src/QmitkStickModelParametersWidgetControls.ui src/QmitkDotModelParametersWidgetControls.ui src/QmitkBallModelParametersWidgetControls.ui src/QmitkAstrosticksModelParametersWidgetControls.ui src/internal/QmitkFieldmapGeneratorViewControls.ui ) set(MOC_H_FILES src/internal/mitkPluginActivator.h src/internal/QmitkQBallReconstructionView.h src/internal/QmitkPreprocessingView.h src/internal/QmitkDiffusionDicomImportView.h src/internal/QmitkDiffusionImagingPublicPerspective.h src/internal/QmitkDiffusionQuantificationView.h src/internal/QmitkTensorReconstructionView.h src/internal/QmitkControlVisualizationPropertiesView.h src/internal/QmitkODFDetailsView.h src/QmitkODFRenderWidget.h src/QmitkODFDetailsWidget.h src/internal/QmitkGibbsTrackingView.h src/internal/QmitkStochasticFiberTrackingView.h src/internal/QmitkStreamlineTrackingView.h src/internal/QmitkFiberProcessingView.h - src/internal/QmitkFiberBundleDeveloperView.h +# src/internal/QmitkFiberBundleDeveloperView.h src/internal/QmitkPartialVolumeAnalysisView.h src/QmitkPartialVolumeAnalysisWidget.h src/internal/QmitkIVIMView.h src/internal/QmitkTractbasedSpatialStatisticsView.h src/internal/QmitkTbssSkeletonizationView.h src/QmitkTbssRoiAnalysisWidget.h src/QmitkResidualAnalysisWidget.h src/QmitkResidualViewWidget.h src/internal/Connectomics/QmitkConnectomicsDataView.h src/internal/Connectomics/QmitkConnectomicsNetworkOperationsView.h src/internal/Connectomics/QmitkConnectomicsStatisticsView.h src/internal/Connectomics/QmitkNetworkHistogramCanvas.h src/internal/QmitkDwiSoftwarePhantomView.h src/internal/QmitkOdfMaximaExtractionView.h src/internal/QmitkFiberfoxView.h src/internal/QmitkFiberExtractionView.h src/QmitkTensorModelParametersWidget.h src/QmitkZeppelinModelParametersWidget.h src/QmitkStickModelParametersWidget.h src/QmitkDotModelParametersWidget.h src/QmitkBallModelParametersWidget.h src/QmitkAstrosticksModelParametersWidget.h src/internal/QmitkFieldmapGeneratorView.h ) set(CACHED_RESOURCE_FILES # list of resource files which can be used by the plug-in # system without loading the plug-ins shared library, # for example the icon used in the menu and tabs for the # plug-in views in the workbench plugin.xml resources/preprocessing.png resources/dwiimport.png resources/quantification.png resources/reconodf.png resources/recontensor.png resources/vizControls.png resources/OdfDetails.png resources/GibbsTracking.png resources/FiberBundleOperations.png resources/PartialVolumeAnalysis_24.png resources/IVIM_48.png resources/stochFB.png resources/tbss.png resources/connectomics/QmitkConnectomicsDataViewIcon_48.png resources/connectomics/QmitkConnectomicsNetworkOperationsViewIcon_48.png resources/connectomics/QmitkConnectomicsStatisticsViewIcon_48.png resources/arrow.png resources/qball_peaks.png resources/phantom.png resources/tensor.png resources/qball.png resources/StreamlineTracking.png resources/dwi2.png resources/odf.png resources/refresh.xpm ) set(QRC_FILES # uncomment the following line if you want to use Qt resources resources/QmitkDiffusionImaging.qrc #resources/QmitkTractbasedSpatialStatisticsView.qrc ) set(CPP_FILES ) foreach(file ${SRC_CPP_FILES}) set(CPP_FILES ${CPP_FILES} src/${file}) endforeach(file ${SRC_CPP_FILES}) foreach(file ${INTERNAL_CPP_FILES}) set(CPP_FILES ${CPP_FILES} src/internal/${file}) endforeach(file ${INTERNAL_CPP_FILES}) diff --git a/Plugins/org.mitk.gui.qt.diffusionimaging/src/internal/QmitkFiberExtractionView.cpp b/Plugins/org.mitk.gui.qt.diffusionimaging/src/internal/QmitkFiberExtractionView.cpp index 75fc7e4735..07bb33374b 100644 --- a/Plugins/org.mitk.gui.qt.diffusionimaging/src/internal/QmitkFiberExtractionView.cpp +++ b/Plugins/org.mitk.gui.qt.diffusionimaging/src/internal/QmitkFiberExtractionView.cpp @@ -1,1370 +1,1434 @@ /*=================================================================== 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. ===================================================================*/ // Blueberry #include #include // Qmitk #include "QmitkFiberExtractionView.h" #include // Qt #include // MITK #include #include #include #include #include #include #include #include #include #include #include #include // ITK #include #include #include #include #include #include #include #include const std::string QmitkFiberExtractionView::VIEW_ID = "org.mitk.views.fiberextraction"; const std::string id_DataManager = "org.mitk.views.datamanager"; using namespace mitk; QmitkFiberExtractionView::QmitkFiberExtractionView() : QmitkFunctionality() , m_Controls( 0 ) , m_MultiWidget( NULL ) , m_CircleCounter(0) , m_PolygonCounter(0) , m_UpsamplingFactor(5) { } // Destructor QmitkFiberExtractionView::~QmitkFiberExtractionView() { } void QmitkFiberExtractionView::CreateQtPartControl( QWidget *parent ) { // build up qt view, unless already done if ( !m_Controls ) { // create GUI widgets from the Qt Designer's .ui file m_Controls = new Ui::QmitkFiberExtractionViewControls; m_Controls->setupUi( parent ); m_Controls->doExtractFibersButton->setDisabled(true); m_Controls->PFCompoANDButton->setDisabled(true); m_Controls->PFCompoORButton->setDisabled(true); m_Controls->PFCompoNOTButton->setDisabled(true); m_Controls->m_PlanarFigureButtonsFrame->setEnabled(false); m_Controls->m_RectangleButton->setVisible(false); connect( m_Controls->m_CircleButton, SIGNAL( clicked() ), this, SLOT( OnDrawCircle() ) ); connect( m_Controls->m_PolygonButton, SIGNAL( clicked() ), this, SLOT( OnDrawPolygon() ) ); connect(m_Controls->PFCompoANDButton, SIGNAL(clicked()), this, SLOT(GenerateAndComposite()) ); connect(m_Controls->PFCompoORButton, SIGNAL(clicked()), this, SLOT(GenerateOrComposite()) ); connect(m_Controls->PFCompoNOTButton, SIGNAL(clicked()), this, SLOT(GenerateNotComposite()) ); connect(m_Controls->m_JoinBundles, SIGNAL(clicked()), this, SLOT(JoinBundles()) ); connect(m_Controls->m_SubstractBundles, SIGNAL(clicked()), this, SLOT(SubstractBundles()) ); connect(m_Controls->m_GenerateRoiImage, SIGNAL(clicked()), this, SLOT(GenerateRoiImage()) ); connect(m_Controls->m_Extract3dButton, SIGNAL(clicked()), this, SLOT(ExtractPassingMask())); connect( m_Controls->m_ExtractMask, SIGNAL(clicked()), this, SLOT(ExtractEndingInMask()) ); connect( m_Controls->doExtractFibersButton, SIGNAL(clicked()), this, SLOT(DoFiberExtraction()) ); + + connect( m_Controls->m_RemoveOutsideMaskButton, SIGNAL(clicked()), this, SLOT(DoRemoveOutsideMask())); + connect( m_Controls->m_RemoveInsideMaskButton, SIGNAL(clicked()), this, SLOT(DoRemoveInsideMask())); + } +} + +void QmitkFiberExtractionView::DoRemoveInsideMask() +{ + if (m_MaskImageNode.IsNull()) + return; + + mitk::Image::Pointer mitkMask = dynamic_cast(m_MaskImageNode->GetData()); + for (int i=0; i(m_SelectedFB.at(i)->GetData()); + QString name(m_SelectedFB.at(i)->GetName().c_str()); + + itkUCharImageType::Pointer mask = itkUCharImageType::New(); + mitk::CastToItkImage(mitkMask, mask); + mitk::FiberBundleX::Pointer newFib = fib->RemoveFibersOutside(mask, true); + if (newFib->GetNumFibers()<=0) + { + QMessageBox::information(NULL, "No output generated:", "The resulting fiber bundle contains no fibers."); + continue; + } + DataNode::Pointer newNode = DataNode::New(); + newNode->SetData(newFib); + name += "_Cut"; + newNode->SetName(name.toStdString()); + GetDefaultDataStorage()->Add(newNode); + m_SelectedFB.at(i)->SetVisibility(false); + } +} + +void QmitkFiberExtractionView::DoRemoveOutsideMask() +{ + if (m_MaskImageNode.IsNull()) + return; + + mitk::Image::Pointer mitkMask = dynamic_cast(m_MaskImageNode->GetData()); + for (int i=0; i(m_SelectedFB.at(i)->GetData()); + QString name(m_SelectedFB.at(i)->GetName().c_str()); + + itkUCharImageType::Pointer mask = itkUCharImageType::New(); + mitk::CastToItkImage(mitkMask, mask); + mitk::FiberBundleX::Pointer newFib = fib->RemoveFibersOutside(mask); + if (newFib->GetNumFibers()<=0) + { + QMessageBox::information(NULL, "No output generated:", "The resulting fiber bundle contains no fibers."); + continue; + } + DataNode::Pointer newNode = DataNode::New(); + newNode->SetData(newFib); + name += "_Cut"; + newNode->SetName(name.toStdString()); + GetDefaultDataStorage()->Add(newNode); + m_SelectedFB.at(i)->SetVisibility(false); } } void QmitkFiberExtractionView::ExtractEndingInMask() { if (m_MaskImageNode.IsNull()) return; mitk::Image::Pointer mitkMask = dynamic_cast(m_MaskImageNode->GetData()); for (int i=0; i(m_SelectedFB.at(i)->GetData()); QString name(m_SelectedFB.at(i)->GetName().c_str()); itkUCharImageType::Pointer mask = itkUCharImageType::New(); mitk::CastToItkImage(mitkMask, mask); mitk::FiberBundleX::Pointer newFib = fib->ExtractFiberSubset(mask, false); if (newFib->GetNumFibers()<=0) { QMessageBox::information(NULL, "No output generated:", "The resulting fiber bundle contains no fibers."); continue; } DataNode::Pointer newNode = DataNode::New(); newNode->SetData(newFib); name += "_ending-in-mask"; newNode->SetName(name.toStdString()); GetDefaultDataStorage()->Add(newNode); m_SelectedFB.at(i)->SetVisibility(false); } } void QmitkFiberExtractionView::ExtractPassingMask() { if (m_MaskImageNode.IsNull()) return; mitk::Image::Pointer mitkMask = dynamic_cast(m_MaskImageNode->GetData()); for (int i=0; i(m_SelectedFB.at(i)->GetData()); QString name(m_SelectedFB.at(i)->GetName().c_str()); itkUCharImageType::Pointer mask = itkUCharImageType::New(); mitk::CastToItkImage(mitkMask, mask); mitk::FiberBundleX::Pointer newFib = fib->ExtractFiberSubset(mask, true); if (newFib->GetNumFibers()<=0) { QMessageBox::information(NULL, "No output generated:", "The resulting fiber bundle contains no fibers."); continue; } DataNode::Pointer newNode = DataNode::New(); newNode->SetData(newFib); name += "_passing-mask"; newNode->SetName(name.toStdString()); GetDefaultDataStorage()->Add(newNode); m_SelectedFB.at(i)->SetVisibility(false); } } + void QmitkFiberExtractionView::GenerateRoiImage(){ if (m_SelectedPF.empty()) return; mitk::Geometry3D::Pointer geometry; if (!m_SelectedFB.empty()) { mitk::FiberBundleX::Pointer fib = dynamic_cast(m_SelectedFB.front()->GetData()); geometry = fib->GetGeometry(); } else return; itk::Vector spacing = geometry->GetSpacing(); spacing /= m_UpsamplingFactor; mitk::Point3D newOrigin = geometry->GetOrigin(); mitk::Geometry3D::BoundsArrayType bounds = geometry->GetBounds(); newOrigin[0] += bounds.GetElement(0); newOrigin[1] += bounds.GetElement(2); newOrigin[2] += bounds.GetElement(4); itk::Matrix direction; itk::ImageRegion<3> imageRegion; for (int i=0; i<3; i++) for (int j=0; j<3; j++) direction[j][i] = geometry->GetMatrixColumn(i)[j]/spacing[j]; imageRegion.SetSize(0, geometry->GetExtent(0)*m_UpsamplingFactor); imageRegion.SetSize(1, geometry->GetExtent(1)*m_UpsamplingFactor); imageRegion.SetSize(2, geometry->GetExtent(2)*m_UpsamplingFactor); m_PlanarFigureImage = itkUCharImageType::New(); m_PlanarFigureImage->SetSpacing( spacing ); // Set the image spacing m_PlanarFigureImage->SetOrigin( newOrigin ); // Set the image origin m_PlanarFigureImage->SetDirection( direction ); // Set the image direction m_PlanarFigureImage->SetRegions( imageRegion ); m_PlanarFigureImage->Allocate(); m_PlanarFigureImage->FillBuffer( 0 ); Image::Pointer tmpImage = Image::New(); tmpImage->InitializeByItk(m_PlanarFigureImage.GetPointer()); tmpImage->SetVolume(m_PlanarFigureImage->GetBufferPointer()); for (int i=0; iInitializeByItk(m_PlanarFigureImage.GetPointer()); tmpImage->SetVolume(m_PlanarFigureImage->GetBufferPointer()); node->SetData(tmpImage); node->SetName("ROI Image"); this->GetDefaultDataStorage()->Add(node); } void QmitkFiberExtractionView::CompositeExtraction(mitk::DataNode::Pointer node, mitk::Image* image) { if (dynamic_cast(node.GetPointer()->GetData()) && !dynamic_cast(node.GetPointer()->GetData())) { m_PlanarFigure = dynamic_cast(node.GetPointer()->GetData()); AccessFixedDimensionByItk_2( image, InternalReorientImagePlane, 3, m_PlanarFigure->GetGeometry(), -1); AccessFixedDimensionByItk_2( m_InternalImage, InternalCalculateMaskFromPlanarFigure, 3, 2, node->GetName() ); } } template < typename TPixel, unsigned int VImageDimension > void QmitkFiberExtractionView::InternalReorientImagePlane( const itk::Image< TPixel, VImageDimension > *image, mitk::Geometry3D* planegeo3D, int additionalIndex ) { MITK_DEBUG << "InternalReorientImagePlane() start"; typedef itk::Image< TPixel, VImageDimension > ImageType; typedef itk::Image< float, VImageDimension > FloatImageType; typedef itk::ResampleImageFilter ResamplerType; typename ResamplerType::Pointer resampler = ResamplerType::New(); mitk::PlaneGeometry* planegeo = dynamic_cast(planegeo3D); float upsamp = m_UpsamplingFactor; float gausssigma = 0.5; // Spacing typename ResamplerType::SpacingType spacing = planegeo->GetSpacing(); spacing[0] = image->GetSpacing()[0] / upsamp; spacing[1] = image->GetSpacing()[1] / upsamp; spacing[2] = image->GetSpacing()[2]; resampler->SetOutputSpacing( spacing ); // Size typename ResamplerType::SizeType size; size[0] = planegeo->GetParametricExtentInMM(0) / spacing[0]; size[1] = planegeo->GetParametricExtentInMM(1) / spacing[1]; size[2] = 1; resampler->SetSize( size ); // Origin typename mitk::Point3D orig = planegeo->GetOrigin(); typename mitk::Point3D corrorig; planegeo3D->WorldToIndex(orig,corrorig); corrorig[0] += 0.5/upsamp; corrorig[1] += 0.5/upsamp; corrorig[2] += 0; planegeo3D->IndexToWorld(corrorig,corrorig); resampler->SetOutputOrigin(corrorig ); // Direction typename ResamplerType::DirectionType direction; typename mitk::AffineTransform3D::MatrixType matrix = planegeo->GetIndexToWorldTransform()->GetMatrix(); for(int c=0; cSetOutputDirection( direction ); // Gaussian interpolation if(gausssigma != 0) { double sigma[3]; for( unsigned int d = 0; d < 3; d++ ) { sigma[d] = gausssigma * image->GetSpacing()[d]; } double alpha = 2.0; typedef itk::GaussianInterpolateImageFunction GaussianInterpolatorType; typename GaussianInterpolatorType::Pointer interpolator = GaussianInterpolatorType::New(); interpolator->SetInputImage( image ); interpolator->SetParameters( sigma, alpha ); resampler->SetInterpolator( interpolator ); } else { // typedef typename itk::BSplineInterpolateImageFunction // InterpolatorType; typedef typename itk::LinearInterpolateImageFunction InterpolatorType; typename InterpolatorType::Pointer interpolator = InterpolatorType::New(); interpolator->SetInputImage( image ); resampler->SetInterpolator( interpolator ); } // Other resampling options resampler->SetInput( image ); resampler->SetDefaultPixelValue(0); MITK_DEBUG << "Resampling requested image plane ... "; resampler->Update(); MITK_DEBUG << " ... done"; if(additionalIndex < 0) { this->m_InternalImage = mitk::Image::New(); this->m_InternalImage->InitializeByItk( resampler->GetOutput() ); this->m_InternalImage->SetVolume( resampler->GetOutput()->GetBufferPointer() ); } } template < typename TPixel, unsigned int VImageDimension > void QmitkFiberExtractionView::InternalCalculateMaskFromPlanarFigure( itk::Image< TPixel, VImageDimension > *image, unsigned int axis, std::string nodeName ) { MITK_DEBUG << "InternalCalculateMaskFromPlanarFigure() start"; typedef itk::Image< TPixel, VImageDimension > ImageType; typedef itk::CastImageFilter< ImageType, itkUCharImageType > CastFilterType; // Generate mask image as new image with same header as input image and // initialize with "1". itkUCharImageType::Pointer newMaskImage = itkUCharImageType::New(); newMaskImage->SetSpacing( image->GetSpacing() ); // Set the image spacing newMaskImage->SetOrigin( image->GetOrigin() ); // Set the image origin newMaskImage->SetDirection( image->GetDirection() ); // Set the image direction newMaskImage->SetRegions( image->GetLargestPossibleRegion() ); newMaskImage->Allocate(); newMaskImage->FillBuffer( 1 ); // Generate VTK polygon from (closed) PlanarFigure polyline // (The polyline points are shifted by -0.5 in z-direction to make sure // that the extrusion filter, which afterwards elevates all points by +0.5 // in z-direction, creates a 3D object which is cut by the the plane z=0) const Geometry2D *planarFigureGeometry2D = m_PlanarFigure->GetGeometry2D(); const PlanarFigure::PolyLineType planarFigurePolyline = m_PlanarFigure->GetPolyLine( 0 ); const Geometry3D *imageGeometry3D = m_InternalImage->GetGeometry( 0 ); vtkPolyData *polyline = vtkPolyData::New(); polyline->Allocate( 1, 1 ); // Determine x- and y-dimensions depending on principal axis int i0, i1; switch ( axis ) { case 0: i0 = 1; i1 = 2; break; case 1: i0 = 0; i1 = 2; break; case 2: default: i0 = 0; i1 = 1; break; } // Create VTK polydata object of polyline contour vtkPoints *points = vtkPoints::New(); PlanarFigure::PolyLineType::const_iterator it; std::vector indices; unsigned int numberOfPoints = 0; for ( it = planarFigurePolyline.begin(); it != planarFigurePolyline.end(); ++it ) { Point3D point3D; // Convert 2D point back to the local index coordinates of the selected // image Point2D point2D = it->Point; planarFigureGeometry2D->WorldToIndex(point2D, point2D); point2D[0] -= 0.5/m_UpsamplingFactor; point2D[1] -= 0.5/m_UpsamplingFactor; planarFigureGeometry2D->IndexToWorld(point2D, point2D); planarFigureGeometry2D->Map( point2D, point3D ); // Polygons (partially) outside of the image bounds can not be processed // further due to a bug in vtkPolyDataToImageStencil if ( !imageGeometry3D->IsInside( point3D ) ) { float bounds[2] = {0,0}; bounds[0] = this->m_InternalImage->GetLargestPossibleRegion().GetSize().GetElement(i0); bounds[1] = this->m_InternalImage->GetLargestPossibleRegion().GetSize().GetElement(i1); imageGeometry3D->WorldToIndex( point3D, point3D ); // if (point3D[i0]<0) // point3D[i0] = 0.5; // else if (point3D[i0]>bounds[0]) // point3D[i0] = bounds[0]-0.5; // if (point3D[i1]<0) // point3D[i1] = 0.5; // else if (point3D[i1]>bounds[1]) // point3D[i1] = bounds[1]-0.5; if (point3D[i0]<0) point3D[i0] = 0.0; else if (point3D[i0]>bounds[0]) point3D[i0] = bounds[0]-0.001; if (point3D[i1]<0) point3D[i1] = 0.0; else if (point3D[i1]>bounds[1]) point3D[i1] = bounds[1]-0.001; points->InsertNextPoint( point3D[i0], point3D[i1], -0.5 ); numberOfPoints++; } else { imageGeometry3D->WorldToIndex( point3D, point3D ); // Add point to polyline array points->InsertNextPoint( point3D[i0], point3D[i1], -0.5 ); numberOfPoints++; } } polyline->SetPoints( points ); points->Delete(); vtkIdType *ptIds = new vtkIdType[numberOfPoints]; for ( vtkIdType i = 0; i < numberOfPoints; ++i ) { ptIds[i] = i; } polyline->InsertNextCell( VTK_POLY_LINE, numberOfPoints, ptIds ); // Extrude the generated contour polygon vtkLinearExtrusionFilter *extrudeFilter = vtkLinearExtrusionFilter::New(); extrudeFilter->SetInput( polyline ); extrudeFilter->SetScaleFactor( 1 ); extrudeFilter->SetExtrusionTypeToNormalExtrusion(); extrudeFilter->SetVector( 0.0, 0.0, 1.0 ); // Make a stencil from the extruded polygon vtkPolyDataToImageStencil *polyDataToImageStencil = vtkPolyDataToImageStencil::New(); polyDataToImageStencil->SetInput( extrudeFilter->GetOutput() ); // Export from ITK to VTK (to use a VTK filter) typedef itk::VTKImageImport< itkUCharImageType > ImageImportType; typedef itk::VTKImageExport< itkUCharImageType > ImageExportType; typename ImageExportType::Pointer itkExporter = ImageExportType::New(); itkExporter->SetInput( newMaskImage ); vtkImageImport *vtkImporter = vtkImageImport::New(); this->ConnectPipelines( itkExporter, vtkImporter ); vtkImporter->Update(); // Apply the generated image stencil to the input image vtkImageStencil *imageStencilFilter = vtkImageStencil::New(); imageStencilFilter->SetInputConnection( vtkImporter->GetOutputPort() ); imageStencilFilter->SetStencil( polyDataToImageStencil->GetOutput() ); imageStencilFilter->ReverseStencilOff(); imageStencilFilter->SetBackgroundValue( 0 ); imageStencilFilter->Update(); // Export from VTK back to ITK vtkImageExport *vtkExporter = vtkImageExport::New(); vtkExporter->SetInputConnection( imageStencilFilter->GetOutputPort() ); vtkExporter->Update(); typename ImageImportType::Pointer itkImporter = ImageImportType::New(); this->ConnectPipelines( vtkExporter, itkImporter ); itkImporter->Update(); // calculate cropping bounding box m_InternalImageMask3D = itkImporter->GetOutput(); m_InternalImageMask3D->SetDirection(image->GetDirection()); itk::ImageRegionConstIterator itmask(m_InternalImageMask3D, m_InternalImageMask3D->GetLargestPossibleRegion()); itk::ImageRegionIterator itimage(image, image->GetLargestPossibleRegion()); itmask = itmask.Begin(); itimage = itimage.Begin(); typename ImageType::SizeType lowersize = {{9999999999,9999999999,9999999999}}; typename ImageType::SizeType uppersize = {{0,0,0}}; while( !itmask.IsAtEnd() ) { if(itmask.Get() == 0) { itimage.Set(0); } else { typename ImageType::IndexType index = itimage.GetIndex(); typename ImageType::SizeType signedindex; signedindex[0] = index[0]; signedindex[1] = index[1]; signedindex[2] = index[2]; lowersize[0] = signedindex[0] < lowersize[0] ? signedindex[0] : lowersize[0]; lowersize[1] = signedindex[1] < lowersize[1] ? signedindex[1] : lowersize[1]; lowersize[2] = signedindex[2] < lowersize[2] ? signedindex[2] : lowersize[2]; uppersize[0] = signedindex[0] > uppersize[0] ? signedindex[0] : uppersize[0]; uppersize[1] = signedindex[1] > uppersize[1] ? signedindex[1] : uppersize[1]; uppersize[2] = signedindex[2] > uppersize[2] ? signedindex[2] : uppersize[2]; } ++itmask; ++itimage; } typename ImageType::IndexType index; index[0] = lowersize[0]; index[1] = lowersize[1]; index[2] = lowersize[2]; typename ImageType::SizeType size; size[0] = uppersize[0] - lowersize[0] + 1; size[1] = uppersize[1] - lowersize[1] + 1; size[2] = uppersize[2] - lowersize[2] + 1; itk::ImageRegion<3> cropRegion = itk::ImageRegion<3>(index, size); // crop internal mask typedef itk::RegionOfInterestImageFilter< itkUCharImageType, itkUCharImageType > ROIMaskFilterType; typename ROIMaskFilterType::Pointer roi2 = ROIMaskFilterType::New(); roi2->SetRegionOfInterest(cropRegion); roi2->SetInput(m_InternalImageMask3D); roi2->Update(); m_InternalImageMask3D = roi2->GetOutput(); Image::Pointer tmpImage = Image::New(); tmpImage->InitializeByItk(m_InternalImageMask3D.GetPointer()); tmpImage->SetVolume(m_InternalImageMask3D->GetBufferPointer()); Image::Pointer tmpImage2 = Image::New(); tmpImage2->InitializeByItk(m_PlanarFigureImage.GetPointer()); const Geometry3D *pfImageGeometry3D = tmpImage2->GetGeometry( 0 ); const Geometry3D *intImageGeometry3D = tmpImage->GetGeometry( 0 ); typedef itk::ImageRegionIteratorWithIndex IteratorType; IteratorType imageIterator (m_InternalImageMask3D, m_InternalImageMask3D->GetRequestedRegion()); imageIterator.GoToBegin(); while ( !imageIterator.IsAtEnd() ) { unsigned char val = imageIterator.Value(); if (val>0) { itk::Index<3> index = imageIterator.GetIndex(); Point3D point; point[0] = index[0]; point[1] = index[1]; point[2] = index[2]; intImageGeometry3D->IndexToWorld(point, point); pfImageGeometry3D->WorldToIndex(point, point); point[i0] += 0.5; point[i1] += 0.5; index[0] = point[0]; index[1] = point[1]; index[2] = point[2]; if (pfImageGeometry3D->IsIndexInside(index)) m_PlanarFigureImage->SetPixel(index, 1); } ++imageIterator; } // Clean up VTK objects polyline->Delete(); extrudeFilter->Delete(); polyDataToImageStencil->Delete(); vtkImporter->Delete(); imageStencilFilter->Delete(); //vtkExporter->Delete(); // TODO: crashes when outcommented; memory leak?? delete[] ptIds; } void QmitkFiberExtractionView::StdMultiWidgetAvailable (QmitkStdMultiWidget &stdMultiWidget) { m_MultiWidget = &stdMultiWidget; } void QmitkFiberExtractionView::StdMultiWidgetNotAvailable() { m_MultiWidget = NULL; } /* OnSelectionChanged is registered to SelectionService, therefore no need to implement SelectionService Listener explicitly */ void QmitkFiberExtractionView::UpdateGui() { m_Controls->m_Extract3dButton->setEnabled(false); m_Controls->m_ExtractMask->setEnabled(false); + m_Controls->m_RemoveOutsideMaskButton->setEnabled(false); + m_Controls->m_RemoveInsideMaskButton->setEnabled(false); // are fiber bundles selected? if ( m_SelectedFB.empty() ) { m_Controls->m_InputData->setTitle("Please Select Input Data"); m_Controls->m_JoinBundles->setEnabled(false); m_Controls->m_SubstractBundles->setEnabled(false); m_Controls->doExtractFibersButton->setEnabled(false); m_Controls->m_PlanarFigureButtonsFrame->setEnabled(false); } else { m_Controls->m_InputData->setTitle("Input Data"); m_Controls->m_PlanarFigureButtonsFrame->setEnabled(true); // one bundle and one planar figure needed to extract fibers if (!m_SelectedPF.empty()) m_Controls->doExtractFibersButton->setEnabled(true); // more than two bundles needed to join/subtract if (m_SelectedFB.size() > 1) { m_Controls->m_JoinBundles->setEnabled(true); m_Controls->m_SubstractBundles->setEnabled(true); } else { m_Controls->m_JoinBundles->setEnabled(false); m_Controls->m_SubstractBundles->setEnabled(false); } if (m_MaskImageNode.IsNotNull()) { m_Controls->m_Extract3dButton->setEnabled(true); m_Controls->m_ExtractMask->setEnabled(true); + m_Controls->m_RemoveOutsideMaskButton->setEnabled(true); + m_Controls->m_RemoveInsideMaskButton->setEnabled(true); } } // are planar figures selected? if ( m_SelectedPF.empty() ) { m_Controls->doExtractFibersButton->setEnabled(false); m_Controls->PFCompoANDButton->setEnabled(false); m_Controls->PFCompoORButton->setEnabled(false); m_Controls->PFCompoNOTButton->setEnabled(false); m_Controls->m_GenerateRoiImage->setEnabled(false); } else { if ( !m_SelectedFB.empty() ) m_Controls->m_GenerateRoiImage->setEnabled(true); else m_Controls->m_GenerateRoiImage->setEnabled(false); if (m_SelectedPF.size() > 1) { m_Controls->PFCompoANDButton->setEnabled(true); m_Controls->PFCompoORButton->setEnabled(true); m_Controls->PFCompoNOTButton->setEnabled(false); } else { m_Controls->PFCompoANDButton->setEnabled(false); m_Controls->PFCompoORButton->setEnabled(false); m_Controls->PFCompoNOTButton->setEnabled(true); } } } void QmitkFiberExtractionView::OnSelectionChanged( std::vector nodes ) { //reset existing Vectors containing FiberBundles and PlanarFigures from a previous selection m_SelectedFB.clear(); m_SelectedPF.clear(); m_SelectedSurfaces.clear(); m_SelectedImage = NULL; m_MaskImageNode = NULL; m_Controls->m_FibLabel->setText("mandatory"); m_Controls->m_PfLabel->setText("needed for extraction"); for( std::vector::iterator it = nodes.begin(); it != nodes.end(); ++it ) { mitk::DataNode::Pointer node = *it; if ( dynamic_cast(node->GetData()) ) { m_Controls->m_FibLabel->setText(node->GetName().c_str()); m_SelectedFB.push_back(node); } else if (dynamic_cast(node->GetData())) { m_Controls->m_PfLabel->setText(node->GetName().c_str()); m_SelectedPF.push_back(node); } else if (dynamic_cast(node->GetData())) { m_SelectedImage = dynamic_cast(node->GetData()); bool isBinary = false; node->GetPropertyValue("binary", isBinary); if (isBinary) { m_MaskImageNode = node; m_Controls->m_PfLabel->setText(node->GetName().c_str()); } } else if (dynamic_cast(node->GetData())) { m_Controls->m_PfLabel->setText(node->GetName().c_str()); m_SelectedSurfaces.push_back(dynamic_cast(node->GetData())); } } UpdateGui(); GenerateStats(); } void QmitkFiberExtractionView::OnDrawPolygon() { // bool checked = m_Controls->m_PolygonButton->isChecked(); // if(!this->AssertDrawingIsPossible(checked)) // return; mitk::PlanarPolygon::Pointer figure = mitk::PlanarPolygon::New(); figure->ClosedOn(); this->AddFigureToDataStorage(figure, QString("Polygon%1").arg(++m_PolygonCounter)); MITK_DEBUG << "PlanarPolygon created ..."; mitk::DataStorage::SetOfObjects::ConstPointer _NodeSet = this->GetDefaultDataStorage()->GetAll(); mitk::DataNode* node = 0; mitk::PlanarFigureInteractor::Pointer figureInteractor = 0; mitk::PlanarFigure* figureP = 0; for(mitk::DataStorage::SetOfObjects::ConstIterator it=_NodeSet->Begin(); it!=_NodeSet->End() ; it++) { node = const_cast(it->Value().GetPointer()); figureP = dynamic_cast(node->GetData()); if(figureP) { figureInteractor = dynamic_cast(node->GetInteractor()); if(figureInteractor.IsNull()) figureInteractor = mitk::PlanarFigureInteractor::New("PlanarFigureInteractor", node); mitk::GlobalInteraction::GetInstance()->AddInteractor(figureInteractor); } } } void QmitkFiberExtractionView::OnDrawCircle() { mitk::PlanarCircle::Pointer figure = mitk::PlanarCircle::New(); this->AddFigureToDataStorage(figure, QString("Circle%1").arg(++m_CircleCounter)); this->GetDataStorage()->Modified(); mitk::DataStorage::SetOfObjects::ConstPointer _NodeSet = this->GetDefaultDataStorage()->GetAll(); mitk::DataNode* node = 0; mitk::PlanarFigureInteractor::Pointer figureInteractor = 0; mitk::PlanarFigure* figureP = 0; for(mitk::DataStorage::SetOfObjects::ConstIterator it=_NodeSet->Begin(); it!=_NodeSet->End(); it++) { node = const_cast(it->Value().GetPointer()); figureP = dynamic_cast(node->GetData()); if(figureP) { figureInteractor = dynamic_cast(node->GetInteractor()); if(figureInteractor.IsNull()) figureInteractor = mitk::PlanarFigureInteractor::New("PlanarFigureInteractor", node); mitk::GlobalInteraction::GetInstance()->AddInteractor(figureInteractor); } } } void QmitkFiberExtractionView::Activated() { } void QmitkFiberExtractionView::AddFigureToDataStorage(mitk::PlanarFigure* figure, const QString& name, const char *propertyKey, mitk::BaseProperty *property ) { // initialize figure's geometry with empty geometry mitk::PlaneGeometry::Pointer emptygeometry = mitk::PlaneGeometry::New(); figure->SetGeometry2D( emptygeometry ); //set desired data to DataNode where Planarfigure is stored mitk::DataNode::Pointer newNode = mitk::DataNode::New(); newNode->SetName(name.toStdString()); newNode->SetData(figure); newNode->AddProperty( "planarfigure.default.line.color", mitk::ColorProperty::New(1.0,0.0,0.0)); newNode->AddProperty( "planarfigure.line.width", mitk::FloatProperty::New(2.0)); newNode->AddProperty( "planarfigure.drawshadow", mitk::BoolProperty::New(true)); newNode->AddProperty( "selected", mitk::BoolProperty::New(true) ); newNode->AddProperty( "planarfigure.ishovering", mitk::BoolProperty::New(true) ); newNode->AddProperty( "planarfigure.drawoutline", mitk::BoolProperty::New(true) ); newNode->AddProperty( "planarfigure.drawquantities", mitk::BoolProperty::New(false) ); newNode->AddProperty( "planarfigure.drawshadow", mitk::BoolProperty::New(true) ); newNode->AddProperty( "planarfigure.line.width", mitk::FloatProperty::New(3.0) ); newNode->AddProperty( "planarfigure.shadow.widthmodifier", mitk::FloatProperty::New(2.0) ); newNode->AddProperty( "planarfigure.outline.width", mitk::FloatProperty::New(2.0) ); newNode->AddProperty( "planarfigure.helperline.width", mitk::FloatProperty::New(2.0) ); newNode->AddProperty( "planarfigure.default.line.color", mitk::ColorProperty::New(1.0,1.0,1.0) ); newNode->AddProperty( "planarfigure.default.line.opacity", mitk::FloatProperty::New(2.0) ); newNode->AddProperty( "planarfigure.default.outline.color", mitk::ColorProperty::New(1.0,0.0,0.0) ); newNode->AddProperty( "planarfigure.default.outline.opacity", mitk::FloatProperty::New(2.0) ); newNode->AddProperty( "planarfigure.default.helperline.color", mitk::ColorProperty::New(1.0,0.0,0.0) ); newNode->AddProperty( "planarfigure.default.helperline.opacity", mitk::FloatProperty::New(2.0) ); newNode->AddProperty( "planarfigure.default.markerline.color", mitk::ColorProperty::New(0.0,0.0,0.0) ); newNode->AddProperty( "planarfigure.default.markerline.opacity", mitk::FloatProperty::New(2.0) ); newNode->AddProperty( "planarfigure.default.marker.color", mitk::ColorProperty::New(1.0,1.0,1.0) ); newNode->AddProperty( "planarfigure.default.marker.opacity",mitk::FloatProperty::New(2.0) ); newNode->AddProperty( "planarfigure.hover.line.color", mitk::ColorProperty::New(1.0,0.0,0.0) ); newNode->AddProperty( "planarfigure.hover.line.opacity", mitk::FloatProperty::New(2.0) ); newNode->AddProperty( "planarfigure.hover.outline.color", mitk::ColorProperty::New(1.0,0.0,0.0) ); newNode->AddProperty( "planarfigure.hover.outline.opacity", mitk::FloatProperty::New(2.0) ); newNode->AddProperty( "planarfigure.hover.helperline.color", mitk::ColorProperty::New(1.0,0.0,0.0) ); newNode->AddProperty( "planarfigure.hover.helperline.opacity", mitk::FloatProperty::New(2.0) ); newNode->AddProperty( "planarfigure.hover.markerline.color", mitk::ColorProperty::New(1.0,0.0,0.0) ); newNode->AddProperty( "planarfigure.hover.markerline.opacity", mitk::FloatProperty::New(2.0) ); newNode->AddProperty( "planarfigure.hover.marker.color", mitk::ColorProperty::New(1.0,0.0,0.0) ); newNode->AddProperty( "planarfigure.hover.marker.opacity", mitk::FloatProperty::New(2.0) ); newNode->AddProperty( "planarfigure.selected.line.color", mitk::ColorProperty::New(1.0,0.0,0.0) ); newNode->AddProperty( "planarfigure.selected.line.opacity",mitk::FloatProperty::New(2.0) ); newNode->AddProperty( "planarfigure.selected.outline.color", mitk::ColorProperty::New(1.0,0.0,0.0) ); newNode->AddProperty( "planarfigure.selected.outline.opacity", mitk::FloatProperty::New(2.0)); newNode->AddProperty( "planarfigure.selected.helperline.color", mitk::ColorProperty::New(1.0,0.0,0.0) ); newNode->AddProperty( "planarfigure.selected.helperline.opacity",mitk::FloatProperty::New(2.0) ); newNode->AddProperty( "planarfigure.selected.markerline.color", mitk::ColorProperty::New(1.0,0.0,0.0) ); newNode->AddProperty( "planarfigure.selected.markerline.opacity", mitk::FloatProperty::New(2.0) ); newNode->AddProperty( "planarfigure.selected.marker.color", mitk::ColorProperty::New(1.0,0.0,0.0) ); newNode->AddProperty( "planarfigure.selected.marker.opacity",mitk::FloatProperty::New(2.0)); // figure drawn on the topmost layer / image newNode->SetColor(1.0,1.0,1.0); newNode->SetOpacity(0.8); GetDataStorage()->Add(newNode ); std::vector selectedNodes = GetDataManagerSelection(); for(unsigned int i = 0; i < selectedNodes.size(); i++) { selectedNodes[i]->SetSelected(false); } newNode->SetSelected(true); } void QmitkFiberExtractionView::DoFiberExtraction() { if ( m_SelectedFB.empty() ){ QMessageBox::information( NULL, "Warning", "No fibe bundle selected!"); MITK_WARN("QmitkFiberExtractionView") << "no fibe bundle selected"; return; } for (int i=0; i(m_SelectedFB.at(i)->GetData()); mitk::PlanarFigure::Pointer roi = dynamic_cast (m_SelectedPF.at(0)->GetData()); mitk::FiberBundleX::Pointer extFB = fib->ExtractFiberSubset(roi); if (extFB->GetNumFibers()<=0) { QMessageBox::information(NULL, "No output generated:", "The resulting fiber bundle contains no fibers."); continue; } mitk::DataNode::Pointer node; node = mitk::DataNode::New(); node->SetData(extFB); QString name(m_SelectedFB.at(i)->GetName().c_str()); name += "_"; name += m_SelectedPF.at(0)->GetName().c_str(); node->SetName(name.toStdString()); GetDataStorage()->Add(node); m_SelectedFB.at(i)->SetVisibility(false); } } void QmitkFiberExtractionView::GenerateAndComposite() { mitk::PlanarFigureComposite::Pointer PFCAnd = mitk::PlanarFigureComposite::New(); mitk::PlaneGeometry* currentGeometry2D = dynamic_cast( const_cast(GetActiveStdMultiWidget()->GetRenderWindow1()->GetRenderer()->GetCurrentWorldGeometry2D())); PFCAnd->SetGeometry2D(currentGeometry2D); PFCAnd->setOperationType(mitk::PFCOMPOSITION_AND_OPERATION); for( std::vector::iterator it = m_SelectedPF.begin(); it != m_SelectedPF.end(); ++it ) { mitk::DataNode::Pointer nodePF = *it; mitk::PlanarFigure::Pointer tmpPF = dynamic_cast( nodePF->GetData() ); PFCAnd->addPlanarFigure( tmpPF ); PFCAnd->addDataNode( nodePF ); PFCAnd->setDisplayName("AND_COMPO"); } AddCompositeToDatastorage(PFCAnd, NULL); } void QmitkFiberExtractionView::GenerateOrComposite() { mitk::PlanarFigureComposite::Pointer PFCOr = mitk::PlanarFigureComposite::New(); mitk::PlaneGeometry* currentGeometry2D = dynamic_cast( const_cast(GetActiveStdMultiWidget()->GetRenderWindow1()->GetRenderer()->GetCurrentWorldGeometry2D())); PFCOr->SetGeometry2D(currentGeometry2D); PFCOr->setOperationType(mitk::PFCOMPOSITION_OR_OPERATION); for( std::vector::iterator it = m_SelectedPF.begin(); it != m_SelectedPF.end(); ++it ) { mitk::DataNode::Pointer nodePF = *it; mitk::PlanarFigure::Pointer tmpPF = dynamic_cast( nodePF->GetData() ); PFCOr->addPlanarFigure( tmpPF ); PFCOr->addDataNode( nodePF ); PFCOr->setDisplayName("OR_COMPO"); } AddCompositeToDatastorage(PFCOr, NULL); } void QmitkFiberExtractionView::GenerateNotComposite() { mitk::PlanarFigureComposite::Pointer PFCNot = mitk::PlanarFigureComposite::New(); mitk::PlaneGeometry* currentGeometry2D = dynamic_cast( const_cast(GetActiveStdMultiWidget()->GetRenderWindow1()->GetRenderer()->GetCurrentWorldGeometry2D())); PFCNot->SetGeometry2D(currentGeometry2D); PFCNot->setOperationType(mitk::PFCOMPOSITION_NOT_OPERATION); for( std::vector::iterator it = m_SelectedPF.begin(); it != m_SelectedPF.end(); ++it ) { mitk::DataNode::Pointer nodePF = *it; mitk::PlanarFigure::Pointer tmpPF = dynamic_cast( nodePF->GetData() ); PFCNot->addPlanarFigure( tmpPF ); PFCNot->addDataNode( nodePF ); PFCNot->setDisplayName("NOT_COMPO"); } AddCompositeToDatastorage(PFCNot, NULL); } /* CLEANUP NEEDED */ void QmitkFiberExtractionView::AddCompositeToDatastorage(mitk::PlanarFigureComposite::Pointer pfcomp, mitk::DataNode::Pointer parentDataNode ) { mitk::DataNode::Pointer newPFCNode; newPFCNode = mitk::DataNode::New(); newPFCNode->SetName( pfcomp->getDisplayName() ); newPFCNode->SetData(pfcomp); newPFCNode->SetVisibility(true); switch (pfcomp->getOperationType()) { case 0: { if (!parentDataNode.IsNull()) { GetDataStorage()->Add(newPFCNode, parentDataNode); } else { GetDataStorage()->Add(newPFCNode); } //iterate through its childs for(int i=0; igetNumberOfChildren(); ++i) { mitk::PlanarFigure::Pointer tmpPFchild = pfcomp->getChildAt(i); mitk::DataNode::Pointer savedPFchildNode = pfcomp->getDataNodeAt(i); mitk::PlanarFigureComposite::Pointer pfcompcast= dynamic_cast(tmpPFchild.GetPointer()); if ( !pfcompcast.IsNull() ) { // child is of type planar Figure composite // make new node of the child, cuz later the child has to be removed of its old position in datamanager // feed new dataNode with information of the savedDataNode, which is gonna be removed soon mitk::DataNode::Pointer newChildPFCNode; newChildPFCNode = mitk::DataNode::New(); newChildPFCNode->SetData(tmpPFchild); newChildPFCNode->SetName( savedPFchildNode->GetName() ); pfcompcast->setDisplayName( savedPFchildNode->GetName() ); //name might be changed in DataManager by user //update inside vector the dataNodePointer pfcomp->replaceDataNodeAt(i, newChildPFCNode); AddCompositeToDatastorage(pfcompcast, newPFCNode); //the current PFCNode becomes the childs parent // remove savedNode here, cuz otherwise its children will change their position in the dataNodeManager // without having its parent anymore //GetDataStorage()->Remove(savedPFchildNode); if ( GetDataStorage()->Exists(savedPFchildNode)) { MITK_DEBUG << savedPFchildNode->GetName() << " exists in DS...trying to remove it"; }else{ MITK_DEBUG << "[ERROR] does NOT exist, but can I read its Name? " << savedPFchildNode->GetName(); } // remove old child position in dataStorage GetDataStorage()->Remove(savedPFchildNode); if ( GetDataStorage()->Exists(savedPFchildNode)) { MITK_DEBUG << savedPFchildNode->GetName() << " still exists"; } } else { // child is not of type PlanarFigureComposite, so its one of the planarFigures // create new dataNode containing the data of the old dataNode, but position in dataManager will be // modified cuz we re setting a (new) parent. mitk::DataNode::Pointer newPFchildNode = mitk::DataNode::New(); newPFchildNode->SetName(savedPFchildNode->GetName() ); newPFchildNode->SetData(tmpPFchild); newPFchildNode->SetVisibility(true); // replace the dataNode in PFComp DataNodeVector pfcomp->replaceDataNodeAt(i, newPFchildNode); if ( GetDataStorage()->Exists(savedPFchildNode)) { MITK_DEBUG << savedPFchildNode->GetName() << " exists in DS...trying to remove it"; } else { MITK_DEBUG << "[ERROR] does NOT exist, but can I read its Name? " << savedPFchildNode->GetName(); } // remove old child position in dataStorage GetDataStorage()->Remove(savedPFchildNode); if ( GetDataStorage()->Exists(savedPFchildNode)) { MITK_DEBUG << savedPFchildNode->GetName() << " still exists"; } MITK_DEBUG << "adding " << newPFchildNode->GetName() << " to " << newPFCNode->GetName(); //add new child to datamanager with its new position as child of newPFCNode parent GetDataStorage()->Add(newPFchildNode, newPFCNode); } } GetDataStorage()->Modified(); break; } case 1: { if (!parentDataNode.IsNull()) { MITK_DEBUG << "adding " << newPFCNode->GetName() << " to " << parentDataNode->GetName() ; GetDataStorage()->Add(newPFCNode, parentDataNode); } else { MITK_DEBUG << "adding " << newPFCNode->GetName(); GetDataStorage()->Add(newPFCNode); } for(int i=0; igetNumberOfChildren(); ++i) { mitk::PlanarFigure::Pointer tmpPFchild = pfcomp->getChildAt(i); mitk::DataNode::Pointer savedPFchildNode = pfcomp->getDataNodeAt(i); mitk::PlanarFigureComposite::Pointer pfcompcast= dynamic_cast(tmpPFchild.GetPointer()); if ( !pfcompcast.IsNull() ) { // child is of type planar Figure composite // make new node of the child, cuz later the child has to be removed of its old position in datamanager // feed new dataNode with information of the savedDataNode, which is gonna be removed soon mitk::DataNode::Pointer newChildPFCNode; newChildPFCNode = mitk::DataNode::New(); newChildPFCNode->SetData(tmpPFchild); newChildPFCNode->SetName( savedPFchildNode->GetName() ); pfcompcast->setDisplayName( savedPFchildNode->GetName() ); //name might be changed in DataManager by user //update inside vector the dataNodePointer pfcomp->replaceDataNodeAt(i, newChildPFCNode); AddCompositeToDatastorage(pfcompcast, newPFCNode); //the current PFCNode becomes the childs parent // remove savedNode here, cuz otherwise its children will change their position in the dataNodeManager // without having its parent anymore //GetDataStorage()->Remove(savedPFchildNode); if ( GetDataStorage()->Exists(savedPFchildNode)) { MITK_DEBUG << savedPFchildNode->GetName() << " exists in DS...trying to remove it"; }else{ MITK_DEBUG << "[ERROR] does NOT exist, but can I read its Name? " << savedPFchildNode->GetName(); } // remove old child position in dataStorage GetDataStorage()->Remove(savedPFchildNode); if ( GetDataStorage()->Exists(savedPFchildNode)) { MITK_DEBUG << savedPFchildNode->GetName() << " still exists"; } } else { // child is not of type PlanarFigureComposite, so its one of the planarFigures // create new dataNode containing the data of the old dataNode, but position in dataManager will be // modified cuz we re setting a (new) parent. mitk::DataNode::Pointer newPFchildNode = mitk::DataNode::New(); newPFchildNode->SetName(savedPFchildNode->GetName() ); newPFchildNode->SetData(tmpPFchild); newPFchildNode->SetVisibility(true); // replace the dataNode in PFComp DataNodeVector pfcomp->replaceDataNodeAt(i, newPFchildNode); if ( GetDataStorage()->Exists(savedPFchildNode)) { MITK_DEBUG << savedPFchildNode->GetName() << " exists in DS...trying to remove it"; }else{ MITK_DEBUG << "[ERROR] does NOT exist, but can I read its Name? " << savedPFchildNode->GetName(); } // remove old child position in dataStorage GetDataStorage()->Remove(savedPFchildNode); if ( GetDataStorage()->Exists(savedPFchildNode)) { MITK_DEBUG << savedPFchildNode->GetName() << " still exists"; } MITK_DEBUG << "adding " << newPFchildNode->GetName() << " to " << newPFCNode->GetName(); //add new child to datamanager with its new position as child of newPFCNode parent GetDataStorage()->Add(newPFchildNode, newPFCNode); } } GetDataStorage()->Modified(); break; } case 2: { if (!parentDataNode.IsNull()) { MITK_DEBUG << "adding " << newPFCNode->GetName() << " to " << parentDataNode->GetName() ; GetDataStorage()->Add(newPFCNode, parentDataNode); } else { MITK_DEBUG << "adding " << newPFCNode->GetName(); GetDataStorage()->Add(newPFCNode); } //iterate through its childs for(int i=0; igetNumberOfChildren(); ++i) { mitk::PlanarFigure::Pointer tmpPFchild = pfcomp->getChildAt(i); mitk::DataNode::Pointer savedPFchildNode = pfcomp->getDataNodeAt(i); mitk::PlanarFigureComposite::Pointer pfcompcast= dynamic_cast(tmpPFchild.GetPointer()); if ( !pfcompcast.IsNull() ) { // child is of type planar Figure composite // makeRemoveBundle new node of the child, cuz later the child has to be removed of its old position in datamanager // feed new dataNode with information of the savedDataNode, which is gonna be removed soon mitk::DataNode::Pointer newChildPFCNode; newChildPFCNode = mitk::DataNode::New(); newChildPFCNode->SetData(tmpPFchild); newChildPFCNode->SetName( savedPFchildNode->GetName() ); pfcompcast->setDisplayName( savedPFchildNode->GetName() ); //name might be changed in DataManager by user //update inside vector the dataNodePointer pfcomp->replaceDataNodeAt(i, newChildPFCNode); AddCompositeToDatastorage(pfcompcast, newPFCNode); //the current PFCNode becomes the childs parent // remove savedNode here, cuz otherwise its children will change their position in the dataNodeManager // without having its parent anymore //GetDataStorage()->Remove(savedPFchildNode); if ( GetDataStorage()->Exists(savedPFchildNode)) { MITK_DEBUG << savedPFchildNode->GetName() << " exists in DS...trying to remove it"; }else{ MITK_DEBUG << "[ERROR] does NOT exist, but can I read its Name? " << savedPFchildNode->GetName(); } // remove old child position in dataStorage GetDataStorage()->Remove(savedPFchildNode); if ( GetDataStorage()->Exists(savedPFchildNode)) { MITK_DEBUG << savedPFchildNode->GetName() << " still exists"; } } else { // child is not of type PlanarFigureComposite, so its one of the planarFigures // create new dataNode containing the data of the old dataNode, but position in dataManager will be // modified cuz we re setting a (new) parent. mitk::DataNode::Pointer newPFchildNode = mitk::DataNode::New(); newPFchildNode->SetName(savedPFchildNode->GetName() ); newPFchildNode->SetData(tmpPFchild); newPFchildNode->SetVisibility(true); // replace the dataNode in PFComp DataNodeVector pfcomp->replaceDataNodeAt(i, newPFchildNode); if ( GetDataStorage()->Exists(savedPFchildNode)) { MITK_DEBUG << savedPFchildNode->GetName() << " exists in DS...trying to remove it"; }else{ MITK_DEBUG << "[ERROR] does NOT exist, but can I read its Name? " << savedPFchildNode->GetName(); } // remove old child position in dataStorage GetDataStorage()->Remove(savedPFchildNode); if ( GetDataStorage()->Exists(savedPFchildNode)) { MITK_DEBUG << savedPFchildNode->GetName() << " still exists"; } MITK_DEBUG << "adding " << newPFchildNode->GetName() << " to " << newPFCNode->GetName(); //add new child to datamanager with its new position as child of newPFCNode parent GetDataStorage()->Add(newPFchildNode, newPFCNode); } } GetDataStorage()->Modified(); break; } default: MITK_DEBUG << "we have an UNDEFINED composition... ERROR" ; break; } } void QmitkFiberExtractionView::JoinBundles() { if ( m_SelectedFB.size()<2 ){ QMessageBox::information( NULL, "Warning", "Select at least two fiber bundles!"); MITK_WARN("QmitkFiberExtractionView") << "Select at least two fiber bundles!"; return; } mitk::FiberBundleX::Pointer newBundle = dynamic_cast(m_SelectedFB.at(0)->GetData()); m_SelectedFB.at(0)->SetVisibility(false); QString name(""); name += QString(m_SelectedFB.at(0)->GetName().c_str()); for (int i=1; iAddBundle(dynamic_cast(m_SelectedFB.at(i)->GetData())); name += "+"+QString(m_SelectedFB.at(i)->GetName().c_str()); m_SelectedFB.at(i)->SetVisibility(false); } mitk::DataNode::Pointer fbNode = mitk::DataNode::New(); fbNode->SetData(newBundle); fbNode->SetName(name.toStdString()); fbNode->SetVisibility(true); GetDataStorage()->Add(fbNode); } void QmitkFiberExtractionView::SubstractBundles() { if ( m_SelectedFB.size()<2 ){ QMessageBox::information( NULL, "Warning", "Select at least two fiber bundles!"); MITK_WARN("QmitkFiberExtractionView") << "Select at least two fiber bundles!"; return; } mitk::FiberBundleX::Pointer newBundle = dynamic_cast(m_SelectedFB.at(0)->GetData()); m_SelectedFB.at(0)->SetVisibility(false); QString name(""); name += QString(m_SelectedFB.at(0)->GetName().c_str()); for (int i=1; iSubtractBundle(dynamic_cast(m_SelectedFB.at(i)->GetData())); if (newBundle.IsNull()) break; name += "-"+QString(m_SelectedFB.at(i)->GetName().c_str()); m_SelectedFB.at(i)->SetVisibility(false); } if (newBundle.IsNull()) { QMessageBox::information(NULL, "No output generated:", "The resulting fiber bundle contains no fibers. Did you select the fiber bundles in the correct order? X-Y is not equal to Y-X!"); return; } mitk::DataNode::Pointer fbNode = mitk::DataNode::New(); fbNode->SetData(newBundle); fbNode->SetName(name.toStdString()); fbNode->SetVisibility(true); GetDataStorage()->Add(fbNode); } void QmitkFiberExtractionView::GenerateStats() { if ( m_SelectedFB.empty() ) return; QString stats(""); for( int i=0; i(node->GetData())) { if (i>0) stats += "\n-----------------------------\n"; stats += QString(node->GetName().c_str()) + "\n"; mitk::FiberBundleX::Pointer fib = dynamic_cast(node->GetData()); stats += "Number of fibers: "+ QString::number(fib->GetNumFibers()) + "\n"; stats += "Min. length: "+ QString::number(fib->GetMinFiberLength(),'f',1) + " mm\n"; stats += "Max. length: "+ QString::number(fib->GetMaxFiberLength(),'f',1) + " mm\n"; stats += "Mean length: "+ QString::number(fib->GetMeanFiberLength(),'f',1) + " mm\n"; stats += "Median length: "+ QString::number(fib->GetMedianFiberLength(),'f',1) + " mm\n"; stats += "Standard deviation: "+ QString::number(fib->GetLengthStDev(),'f',1) + " mm\n"; } } this->m_Controls->m_StatsTextEdit->setText(stats); } diff --git a/Plugins/org.mitk.gui.qt.diffusionimaging/src/internal/QmitkFiberExtractionView.h b/Plugins/org.mitk.gui.qt.diffusionimaging/src/internal/QmitkFiberExtractionView.h index cc411a0a94..d1f7913143 100644 --- a/Plugins/org.mitk.gui.qt.diffusionimaging/src/internal/QmitkFiberExtractionView.h +++ b/Plugins/org.mitk.gui.qt.diffusionimaging/src/internal/QmitkFiberExtractionView.h @@ -1,172 +1,174 @@ /*=================================================================== 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. ===================================================================*/ #ifndef QmitkFiberExtractionView_h #define QmitkFiberExtractionView_h #include #include "ui_QmitkFiberExtractionViewControls.h" #include #include #include #include #include #include #include #include #include #include #include #include #include #include #include #include #include #include /*! \brief View to process fiber bundles. Supplies methods to extract fibers from the bundle, join and subtract bundles, generate images from the selected bundle and much more. \sa QmitkFunctionality \ingroup Functionalities */ class QmitkFiberExtractionView : public QmitkFunctionality { // this is needed for all Qt objects that should have a Qt meta-object // (everything that derives from QObject and wants to have signal/slots) Q_OBJECT public: typedef itk::Image< unsigned char, 3 > itkUCharImageType; static const std::string VIEW_ID; QmitkFiberExtractionView(); virtual ~QmitkFiberExtractionView(); virtual void CreateQtPartControl(QWidget *parent); virtual void StdMultiWidgetAvailable (QmitkStdMultiWidget &stdMultiWidget); virtual void StdMultiWidgetNotAvailable(); virtual void Activated(); protected slots: void OnDrawCircle(); ///< add circle interactors etc. void OnDrawPolygon(); ///< add circle interactors etc. void DoFiberExtraction(); ///< Extract fibers from selected bundle void GenerateAndComposite(); void GenerateOrComposite(); void GenerateNotComposite(); + void DoRemoveOutsideMask(); + void DoRemoveInsideMask(); void JoinBundles(); ///< merge selected fiber bundles void SubstractBundles(); ///< subtract bundle A from bundle B. Not commutative! Defined by order of selection. void GenerateRoiImage(); ///< generate binary image of selected planar figures. void ExtractPassingMask(); ///< extract all fibers passing the selected surface mesh void ExtractEndingInMask(); ///< extract all fibers passing the selected surface mesh virtual void AddFigureToDataStorage(mitk::PlanarFigure* figure, const QString& name, const char *propertyKey = NULL, mitk::BaseProperty *property = NULL ); protected: /// \brief called by QmitkFunctionality when DataManager's selection has changed virtual void OnSelectionChanged( std::vector nodes ); Ui::QmitkFiberExtractionViewControls* m_Controls; QmitkStdMultiWidget* m_MultiWidget; /** Connection from VTK to ITK */ template void ConnectPipelines(VTK_Exporter* exporter, ITK_Importer importer) { importer->SetUpdateInformationCallback(exporter->GetUpdateInformationCallback()); importer->SetPipelineModifiedCallback(exporter->GetPipelineModifiedCallback()); importer->SetWholeExtentCallback(exporter->GetWholeExtentCallback()); importer->SetSpacingCallback(exporter->GetSpacingCallback()); importer->SetOriginCallback(exporter->GetOriginCallback()); importer->SetScalarTypeCallback(exporter->GetScalarTypeCallback()); importer->SetNumberOfComponentsCallback(exporter->GetNumberOfComponentsCallback()); importer->SetPropagateUpdateExtentCallback(exporter->GetPropagateUpdateExtentCallback()); importer->SetUpdateDataCallback(exporter->GetUpdateDataCallback()); importer->SetDataExtentCallback(exporter->GetDataExtentCallback()); importer->SetBufferPointerCallback(exporter->GetBufferPointerCallback()); importer->SetCallbackUserData(exporter->GetCallbackUserData()); } template void ConnectPipelines(ITK_Exporter exporter, VTK_Importer* importer) { importer->SetUpdateInformationCallback(exporter->GetUpdateInformationCallback()); importer->SetPipelineModifiedCallback(exporter->GetPipelineModifiedCallback()); importer->SetWholeExtentCallback(exporter->GetWholeExtentCallback()); importer->SetSpacingCallback(exporter->GetSpacingCallback()); importer->SetOriginCallback(exporter->GetOriginCallback()); importer->SetScalarTypeCallback(exporter->GetScalarTypeCallback()); importer->SetNumberOfComponentsCallback(exporter->GetNumberOfComponentsCallback()); importer->SetPropagateUpdateExtentCallback(exporter->GetPropagateUpdateExtentCallback()); importer->SetUpdateDataCallback(exporter->GetUpdateDataCallback()); importer->SetDataExtentCallback(exporter->GetDataExtentCallback()); importer->SetBufferPointerCallback(exporter->GetBufferPointerCallback()); importer->SetCallbackUserData(exporter->GetCallbackUserData()); } template < typename TPixel, unsigned int VImageDimension > void InternalCalculateMaskFromPlanarFigure( itk::Image< TPixel, VImageDimension > *image, unsigned int axis, std::string nodeName ); template < typename TPixel, unsigned int VImageDimension > void InternalReorientImagePlane( const itk::Image< TPixel, VImageDimension > *image, mitk::Geometry3D* planegeo3D, int additionalIndex ); void GenerateStats(); ///< generate statistics of selected fiber bundles void UpdateGui(); ///< update button activity etc. dpending on current datamanager selection int m_CircleCounter; ///< used for data node naming int m_PolygonCounter; ///< used for data node naming std::vector m_SelectedFB; ///< selected fiber bundle nodes std::vector m_SelectedPF; ///< selected planar figure nodes std::vector m_SelectedSurfaces; mitk::Image::Pointer m_SelectedImage; mitk::Image::Pointer m_InternalImage; mitk::PlanarFigure::Pointer m_PlanarFigure; itkUCharImageType::Pointer m_InternalImageMask3D; itkUCharImageType::Pointer m_PlanarFigureImage; float m_UpsamplingFactor; ///< upsampling factor for all image generations mitk::DataNode::Pointer m_MaskImageNode; void AddCompositeToDatastorage(mitk::PlanarFigureComposite::Pointer, mitk::DataNode::Pointer); void debugPFComposition(mitk::PlanarFigureComposite::Pointer , int ); void CompositeExtraction(mitk::DataNode::Pointer node, mitk::Image* image); mitk::DataNode::Pointer GenerateTractDensityImage(mitk::FiberBundleX::Pointer fib, bool binary, bool absolute); mitk::DataNode::Pointer GenerateColorHeatmap(mitk::FiberBundleX::Pointer fib); mitk::DataNode::Pointer GenerateFiberEndingsImage(mitk::FiberBundleX::Pointer fib); mitk::DataNode::Pointer GenerateFiberEndingsPointSet(mitk::FiberBundleX::Pointer fib); }; #endif // _QMITKFIBERTRACKINGVIEW_H_INCLUDED diff --git a/Plugins/org.mitk.gui.qt.diffusionimaging/src/internal/QmitkFiberExtractionViewControls.ui b/Plugins/org.mitk.gui.qt.diffusionimaging/src/internal/QmitkFiberExtractionViewControls.ui index 3d376dae84..ec17207875 100644 --- a/Plugins/org.mitk.gui.qt.diffusionimaging/src/internal/QmitkFiberExtractionViewControls.ui +++ b/Plugins/org.mitk.gui.qt.diffusionimaging/src/internal/QmitkFiberExtractionViewControls.ui @@ -1,565 +1,612 @@ QmitkFiberExtractionViewControls 0 0 492 866 Form Please Select Input Data <html><head/><body><p><span style=" color:#ff0000;">mandatory</span></p></body></html> <html><head/><body><p><span style=" color:#969696;">needed for extraction</span></p></body></html> Input DTI Fiber Bundle: Binary seed ROI. If not specified, the whole image area is seeded. ROI: Qt::Vertical 20 40 Fiber Extraction 0 0 200 0 16777215 60 QFrame::NoFrame QFrame::Raised 0 30 30 Draw circular ROI. Select reference fiber bundle to execute. :/QmitkDiffusionImaging/circle.png:/QmitkDiffusionImaging/circle.png 32 32 false true 30 30 Draw rectangular ROI. Select reference fiber bundle to execute. :/QmitkDiffusionImaging/rectangle.png:/QmitkDiffusionImaging/rectangle.png 32 32 true true 30 30 Draw polygonal ROI. Select reference fiber bundle to execute. :/QmitkDiffusionImaging/polygon.png:/QmitkDiffusionImaging/polygon.png 32 32 true true Qt::Horizontal 40 20 QFrame::NoFrame QFrame::Raised 0 + + + + false + + + + 0 + 0 + + + + + 16777215 + 16777215 + + + + + 11 + + + + Generate a binary image containing all selected ROIs. Select at least one ROI (planar figure) and a reference fiber bundle or image. + + + ROI Image + + + false 0 0 200 16777215 11 Returns all fibers contained in bundle X that are not contained in bundle Y (not commutative!). Select at least two fiber bundles to execute. Substract - - + + false 0 0 200 16777215 11 - Extract fibers starting/ending inside of the selected binary mask. + Merge selected fiber bundles. Select at least two fiber bundles to execute. - Ending in Mask + Join - - - - Qt::Horizontal + + + + false - + + + 0 + 0 + + + - 40 - 20 + 200 + 16777215 - + + + 11 + + + + Extract fibers starting/ending inside of the selected binary mask. + + + Ending in Mask + + - - + + false 0 0 200 16777215 11 - Merge selected fiber bundles. Select at least two fiber bundles to execute. + Extract fibers passing through the selected binary mask. - Join + Passing Mask false 0 0 200 16777215 11 Extract fibers passing through selected ROI or composite ROI. Select ROI and fiber bundle to execute. Extract - - + + false 0 0 - 16777215 + 200 16777215 11 - Generate a binary image containing all selected ROIs. Select at least one ROI (planar figure) and a reference fiber bundle or image. + Remove all fiber parts outside of the mask. - ROI Image + Remove Outside Mask - - + + false 0 0 200 16777215 11 - Extract fibers passing through the selected binary mask. + Remove all fiber parts inside of the mask. - Passing Mask + Remove Inside Mask 0 0 200 0 16777215 60 QFrame::NoFrame QFrame::Raised 0 Qt::Horizontal 40 20 false 60 16777215 Create AND composition with selected ROIs. AND false 60 16777215 Create OR composition with selected ROIs. OR false 60 16777215 Create NOT composition from selected ROI. NOT Fiber Statistics Courier 10 Pitch false true diff --git a/Plugins/org.mitk.gui.qt.diffusionimaging/src/internal/QmitkFiberProcessingView.cpp b/Plugins/org.mitk.gui.qt.diffusionimaging/src/internal/QmitkFiberProcessingView.cpp index a52818d6df..fae4bfdc7e 100644 --- a/Plugins/org.mitk.gui.qt.diffusionimaging/src/internal/QmitkFiberProcessingView.cpp +++ b/Plugins/org.mitk.gui.qt.diffusionimaging/src/internal/QmitkFiberProcessingView.cpp @@ -1,470 +1,470 @@ /*=================================================================== 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. ===================================================================*/ // Blueberry #include #include // Qmitk #include "QmitkFiberProcessingView.h" #include // Qt #include // MITK #include #include #include #include #include #include #include #include #include #include #include #include // ITK #include #include #include #include #include #include #include #include const std::string QmitkFiberProcessingView::VIEW_ID = "org.mitk.views.fiberprocessing"; const std::string id_DataManager = "org.mitk.views.datamanager"; using namespace mitk; QmitkFiberProcessingView::QmitkFiberProcessingView() : QmitkFunctionality() , m_Controls( 0 ) , m_MultiWidget( NULL ) , m_UpsamplingFactor(5) { } // Destructor QmitkFiberProcessingView::~QmitkFiberProcessingView() { } void QmitkFiberProcessingView::CreateQtPartControl( QWidget *parent ) { // build up qt view, unless already done if ( !m_Controls ) { // create GUI widgets from the Qt Designer's .ui file m_Controls = new Ui::QmitkFiberProcessingViewControls; m_Controls->setupUi( parent ); connect( m_Controls->m_ProcessFiberBundleButton, SIGNAL(clicked()), this, SLOT(ProcessSelectedBundles()) ); connect( m_Controls->m_ResampleFibersButton, SIGNAL(clicked()), this, SLOT(ResampleSelectedBundles()) ); connect(m_Controls->m_FaColorFibersButton, SIGNAL(clicked()), this, SLOT(DoImageColorCoding())); connect( m_Controls->m_PruneFibersButton, SIGNAL(clicked()), this, SLOT(PruneBundle()) ); connect( m_Controls->m_CurvatureThresholdButton, SIGNAL(clicked()), this, SLOT(ApplyCurvatureThreshold()) ); connect( m_Controls->m_MirrorFibersButton, SIGNAL(clicked()), this, SLOT(MirrorFibers()) ); } } void QmitkFiberProcessingView::StdMultiWidgetAvailable (QmitkStdMultiWidget &stdMultiWidget) { m_MultiWidget = &stdMultiWidget; } void QmitkFiberProcessingView::StdMultiWidgetNotAvailable() { m_MultiWidget = NULL; } void QmitkFiberProcessingView::UpdateGui() { // are fiber bundles selected? if ( m_SelectedFB.empty() ) { m_Controls->m_ProcessFiberBundleButton->setEnabled(false); m_Controls->m_ResampleFibersButton->setEnabled(false); m_Controls->m_FaColorFibersButton->setEnabled(false); m_Controls->m_PruneFibersButton->setEnabled(false); m_Controls->m_CurvatureThresholdButton->setEnabled(false); if (m_SelectedSurfaces.size()>0) m_Controls->m_MirrorFibersButton->setEnabled(true); else m_Controls->m_MirrorFibersButton->setEnabled(false); } else { m_Controls->m_ProcessFiberBundleButton->setEnabled(true); m_Controls->m_ResampleFibersButton->setEnabled(true); m_Controls->m_PruneFibersButton->setEnabled(true); m_Controls->m_CurvatureThresholdButton->setEnabled(true); m_Controls->m_MirrorFibersButton->setEnabled(true); if (m_SelectedImage.IsNotNull()) m_Controls->m_FaColorFibersButton->setEnabled(true); } } void QmitkFiberProcessingView::OnSelectionChanged( std::vector nodes ) { //reset existing Vectors containing FiberBundles and PlanarFigures from a previous selection m_SelectedFB.clear(); m_SelectedSurfaces.clear(); m_SelectedImage = NULL; for( std::vector::iterator it = nodes.begin(); it != nodes.end(); ++it ) { mitk::DataNode::Pointer node = *it; if ( dynamic_cast(node->GetData()) ) { m_SelectedFB.push_back(node); } else if (dynamic_cast(node->GetData())) m_SelectedImage = dynamic_cast(node->GetData()); else if (dynamic_cast(node->GetData())) { m_SelectedSurfaces.push_back(dynamic_cast(node->GetData())); } } UpdateGui(); GenerateStats(); } void QmitkFiberProcessingView::Activated() { } void QmitkFiberProcessingView::PruneBundle() { int minLength = this->m_Controls->m_PruneFibersSpinBox->value(); int maxLength = this->m_Controls->m_MaxPruneFibersSpinBox->value(); for (int i=0; i(m_SelectedFB.at(i)->GetData()); if (!fib->RemoveShortFibers(minLength)) QMessageBox::information(NULL, "No output generated:", "The resulting fiber bundle contains no fibers."); else if (!fib->RemoveLongFibers(maxLength)) QMessageBox::information(NULL, "No output generated:", "The resulting fiber bundle contains no fibers."); } GenerateStats(); RenderingManager::GetInstance()->RequestUpdateAll(); } void QmitkFiberProcessingView::ApplyCurvatureThreshold() { int mm = this->m_Controls->m_MinCurvatureRadiusBox->value(); for (int i=0; i(m_SelectedFB.at(i)->GetData()); if (!fib->ApplyCurvatureThreshold(mm, this->m_Controls->m_RemoveFiberDueToCurvatureCheckbox->isChecked())) QMessageBox::information(NULL, "No output generated:", "The resulting fiber bundle contains no fibers."); } GenerateStats(); RenderingManager::GetInstance()->RequestUpdateAll(); } void QmitkFiberProcessingView::GenerateStats() { if ( m_SelectedFB.empty() ) return; QString stats(""); for( int i=0; i(node->GetData())) { if (i>0) stats += "\n-----------------------------\n"; stats += QString(node->GetName().c_str()) + "\n"; mitk::FiberBundleX::Pointer fib = dynamic_cast(node->GetData()); stats += "Number of fibers: "+ QString::number(fib->GetNumFibers()) + "\n"; stats += "Min. length: "+ QString::number(fib->GetMinFiberLength(),'f',1) + " mm\n"; stats += "Max. length: "+ QString::number(fib->GetMaxFiberLength(),'f',1) + " mm\n"; stats += "Mean length: "+ QString::number(fib->GetMeanFiberLength(),'f',1) + " mm\n"; stats += "Median length: "+ QString::number(fib->GetMedianFiberLength(),'f',1) + " mm\n"; stats += "Standard deviation: "+ QString::number(fib->GetLengthStDev(),'f',1) + " mm\n"; } } this->m_Controls->m_StatsTextEdit->setText(stats); } void QmitkFiberProcessingView::ProcessSelectedBundles() { if ( m_SelectedFB.empty() ){ QMessageBox::information( NULL, "Warning", "No fibe bundle selected!"); MITK_WARN("QmitkFiberProcessingView") << "no fibe bundle selected"; return; } int generationMethod = m_Controls->m_GenerationBox->currentIndex(); for( int i=0; i(node->GetData())) { mitk::FiberBundleX::Pointer fib = dynamic_cast(node->GetData()); QString name(node->GetName().c_str()); DataNode::Pointer newNode = NULL; switch(generationMethod){ case 0: newNode = GenerateTractDensityImage(fib, false, true); name += "_TDI"; break; case 1: newNode = GenerateTractDensityImage(fib, false, false); name += "_TDI"; break; case 2: newNode = GenerateTractDensityImage(fib, true, false); name += "_envelope"; break; case 3: newNode = GenerateColorHeatmap(fib); break; case 4: newNode = GenerateFiberEndingsImage(fib); name += "_fiber_endings"; break; case 5: newNode = GenerateFiberEndingsPointSet(fib); name += "_fiber_endings"; break; } if (newNode.IsNotNull()) { newNode->SetName(name.toStdString()); GetDataStorage()->Add(newNode); } } } } // generate pointset displaying the fiber endings mitk::DataNode::Pointer QmitkFiberProcessingView::GenerateFiberEndingsPointSet(mitk::FiberBundleX::Pointer fib) { mitk::PointSet::Pointer pointSet = mitk::PointSet::New(); vtkSmartPointer fiberPolyData = fib->GetFiberPolyData(); vtkSmartPointer vLines = fiberPolyData->GetLines(); vLines->InitTraversal(); int count = 0; int numFibers = fib->GetNumFibers(); for( int i=0; iGetNextCell ( numPoints, points ); if (numPoints>0) { double* point = fiberPolyData->GetPoint(points[0]); itk::Point itkPoint; itkPoint[0] = point[0]; itkPoint[1] = point[1]; itkPoint[2] = point[2]; pointSet->InsertPoint(count, itkPoint); count++; } if (numPoints>2) { double* point = fiberPolyData->GetPoint(points[numPoints-1]); itk::Point itkPoint; itkPoint[0] = point[0]; itkPoint[1] = point[1]; itkPoint[2] = point[2]; pointSet->InsertPoint(count, itkPoint); count++; } } mitk::DataNode::Pointer node = mitk::DataNode::New(); node->SetData( pointSet ); return node; } // generate image displaying the fiber endings mitk::DataNode::Pointer QmitkFiberProcessingView::GenerateFiberEndingsImage(mitk::FiberBundleX::Pointer fib) { typedef unsigned char OutPixType; typedef itk::Image OutImageType; typedef itk::TractsToFiberEndingsImageFilter< OutImageType > ImageGeneratorType; ImageGeneratorType::Pointer generator = ImageGeneratorType::New(); generator->SetFiberBundle(fib); generator->SetUpsamplingFactor(m_Controls->m_UpsamplingSpinBox->value()); if (m_SelectedImage.IsNotNull()) { OutImageType::Pointer itkImage = OutImageType::New(); CastToItkImage(m_SelectedImage, itkImage); generator->SetInputImage(itkImage); generator->SetUseImageGeometry(true); } generator->Update(); // get output image OutImageType::Pointer outImg = generator->GetOutput(); mitk::Image::Pointer img = mitk::Image::New(); img->InitializeByItk(outImg.GetPointer()); img->SetVolume(outImg->GetBufferPointer()); // init data node mitk::DataNode::Pointer node = mitk::DataNode::New(); node->SetData(img); return node; } // generate rgba heatmap from fiber bundle mitk::DataNode::Pointer QmitkFiberProcessingView::GenerateColorHeatmap(mitk::FiberBundleX::Pointer fib) { typedef itk::RGBAPixel OutPixType; typedef itk::Image OutImageType; typedef itk::TractsToRgbaImageFilter< OutImageType > ImageGeneratorType; ImageGeneratorType::Pointer generator = ImageGeneratorType::New(); generator->SetFiberBundle(fib); generator->SetUpsamplingFactor(m_Controls->m_UpsamplingSpinBox->value()); if (m_SelectedImage.IsNotNull()) { itk::Image::Pointer itkImage = itk::Image::New(); CastToItkImage(m_SelectedImage, itkImage); generator->SetInputImage(itkImage); generator->SetUseImageGeometry(true); } generator->Update(); // get output image typedef itk::Image OutType; OutType::Pointer outImg = generator->GetOutput(); mitk::Image::Pointer img = mitk::Image::New(); img->InitializeByItk(outImg.GetPointer()); img->SetVolume(outImg->GetBufferPointer()); // init data node mitk::DataNode::Pointer node = mitk::DataNode::New(); node->SetData(img); return node; } // generate tract density image from fiber bundle mitk::DataNode::Pointer QmitkFiberProcessingView::GenerateTractDensityImage(mitk::FiberBundleX::Pointer fib, bool binary, bool absolute) { typedef float OutPixType; typedef itk::Image OutImageType; itk::TractDensityImageFilter< OutImageType >::Pointer generator = itk::TractDensityImageFilter< OutImageType >::New(); generator->SetFiberBundle(fib); generator->SetBinaryOutput(binary); generator->SetOutputAbsoluteValues(absolute); generator->SetUpsamplingFactor(m_Controls->m_UpsamplingSpinBox->value()); if (m_SelectedImage.IsNotNull()) { OutImageType::Pointer itkImage = OutImageType::New(); CastToItkImage(m_SelectedImage, itkImage); generator->SetInputImage(itkImage); generator->SetUseImageGeometry(true); } generator->Update(); // get output image typedef itk::Image OutType; OutType::Pointer outImg = generator->GetOutput(); mitk::Image::Pointer img = mitk::Image::New(); img->InitializeByItk(outImg.GetPointer()); img->SetVolume(outImg->GetBufferPointer()); // init data node mitk::DataNode::Pointer node = mitk::DataNode::New(); node->SetData(img); return node; } void QmitkFiberProcessingView::ResampleSelectedBundles() { - int factor = this->m_Controls->m_ResampleFibersSpinBox->value(); + double factor = this->m_Controls->m_ResampleFibersSpinBox->value(); for (int i=0; i(m_SelectedFB.at(i)->GetData()); fib->DoFiberSmoothing(factor); } GenerateStats(); RenderingManager::GetInstance()->RequestUpdateAll(); } void QmitkFiberProcessingView::MirrorFibers() { unsigned int axis = this->m_Controls->m_AxisSelectionBox->currentIndex(); for (int i=0; i(m_SelectedFB.at(i)->GetData()); fib->MirrorFibers(axis); } if (m_SelectedFB.size()>0) GenerateStats(); if (m_SelectedSurfaces.size()>0) { for (int i=0; i poly = surf->GetVtkPolyData(); vtkSmartPointer vtkNewPoints = vtkSmartPointer::New(); for (int i=0; iGetNumberOfPoints(); i++) { double* point = poly->GetPoint(i); point[axis] *= -1; vtkNewPoints->InsertNextPoint(point); } poly->SetPoints(vtkNewPoints); surf->CalculateBoundingBox(); } } RenderingManager::GetInstance()->RequestUpdateAll(); } void QmitkFiberProcessingView::DoImageColorCoding() { if (m_SelectedImage.IsNull()) return; for( int i=0; i(m_SelectedFB.at(i)->GetData()); fib->SetFAMap(m_SelectedImage); fib->SetColorCoding(mitk::FiberBundleX::COLORCODING_FA_BASED); fib->DoColorCodingFaBased(); } if(m_MultiWidget) m_MultiWidget->RequestUpdate(); } diff --git a/Plugins/org.mitk.gui.qt.diffusionimaging/src/internal/QmitkFiberProcessingViewControls.ui b/Plugins/org.mitk.gui.qt.diffusionimaging/src/internal/QmitkFiberProcessingViewControls.ui index ed85cb7d95..d5ef063f7d 100644 --- a/Plugins/org.mitk.gui.qt.diffusionimaging/src/internal/QmitkFiberProcessingViewControls.ui +++ b/Plugins/org.mitk.gui.qt.diffusionimaging/src/internal/QmitkFiberProcessingViewControls.ui @@ -1,477 +1,480 @@ QmitkFiberProcessingViewControls 0 0 492 866 Form Fiber Statistics Courier 10 Pitch false true Qt::Vertical 20 40 Fiber Processing QFormLayout::AllNonFixedFieldsGrow false 0 0 200 16777215 11 Perform selected operation on all selected fiber bundles. Generate Image QFrame::NoFrame QFrame::Raised 0 0 0 0 0 Tract Density Image (TDI) Normalized TDI Binary Envelope Fiber Bundle Image Fiber Endings Image Fiber Endings Pointset Upsampling factor 1 0.100000000000000 10.000000000000000 0.100000000000000 1.000000000000000 false 0 0 200 16777215 11 Resample fibers using a Kochanek spline interpolation. Smooth Fibers - - - - Points per cm - - - 1 - - - 50 - - - 5 - - - false 0 0 200 16777215 11 Remove fibers shorter/longer than the specified length (in mm). Length Threshold QFrame::NoFrame QFrame::Raised 0 0 Minimum fiber length in mm 0 1000 20 Maximum fiber length in mm 0 10000 500 false 0 0 200 16777215 11 Remove fibers with a too high curvature Curvature Threshold QFrame::NoFrame QFrame::Raised 6 0 0 Minimum radius of circle created by three consecutive points of a fiber 100.000000000000000 0.100000000000000 2.000000000000000 Remove whole fiber if it is exceeding the curvature threshold, otherwise remove only high curvature part. Remove Fiber true false 0 0 200 16777215 11 Mirror fibers around specified axis. Mirror Fibers 0 3 3 Sagittal Coronal Axial false 0 0 200 16777215 11 Apply float image values (0-1) as color coding to the selected fiber bundle. Color By Scalar Map + + + + Fiber point distance in mm + + + 1 + + + 0.100000000000000 + + + 0.100000000000000 + + + 1.000000000000000 + + + diff --git a/Plugins/org.mitk.gui.qt.diffusionimaging/src/internal/QmitkFiberfoxView.cpp b/Plugins/org.mitk.gui.qt.diffusionimaging/src/internal/QmitkFiberfoxView.cpp index ff0bd67487..2da9116c31 100755 --- a/Plugins/org.mitk.gui.qt.diffusionimaging/src/internal/QmitkFiberfoxView.cpp +++ b/Plugins/org.mitk.gui.qt.diffusionimaging/src/internal/QmitkFiberfoxView.cpp @@ -1,1789 +1,1789 @@ /*=================================================================== 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. ===================================================================*/ //misc #define _USE_MATH_DEFINES #include // Blueberry #include #include // Qmitk #include "QmitkFiberfoxView.h" // MITK #include #include #include #include #include #include #include #include #include #include #include #include #include #include #include #include #include #include #include #include #include #include #include #include #include #include #include #include #include #include #define _USE_MATH_DEFINES #include const std::string QmitkFiberfoxView::VIEW_ID = "org.mitk.views.fiberfoxview"; QmitkFiberfoxView::QmitkFiberfoxView() : QmitkAbstractView() , m_Controls( 0 ) , m_SelectedImage( NULL ) { } // Destructor QmitkFiberfoxView::~QmitkFiberfoxView() { } void QmitkFiberfoxView::CreateQtPartControl( QWidget *parent ) { // build up qt view, unless already done if ( !m_Controls ) { // create GUI widgets from the Qt Designer's .ui file m_Controls = new Ui::QmitkFiberfoxViewControls; m_Controls->setupUi( parent ); m_Controls->m_StickWidget1->setVisible(true); m_Controls->m_StickWidget2->setVisible(false); m_Controls->m_ZeppelinWidget1->setVisible(false); m_Controls->m_ZeppelinWidget2->setVisible(false); m_Controls->m_TensorWidget1->setVisible(false); m_Controls->m_TensorWidget2->setVisible(false); m_Controls->m_BallWidget1->setVisible(true); m_Controls->m_BallWidget2->setVisible(false); m_Controls->m_AstrosticksWidget1->setVisible(false); m_Controls->m_AstrosticksWidget2->setVisible(false); m_Controls->m_DotWidget1->setVisible(false); m_Controls->m_DotWidget2->setVisible(false); m_Controls->m_Comp4FractionFrame->setVisible(false); m_Controls->m_DiffusionPropsMessage->setVisible(false); m_Controls->m_GeometryMessage->setVisible(false); m_Controls->m_AdvancedSignalOptionsFrame->setVisible(false); m_Controls->m_AdvancedFiberOptionsFrame->setVisible(false); m_Controls->m_VarianceBox->setVisible(false); m_Controls->m_GibbsRingingFrame->setVisible(false); m_Controls->m_NoiseFrame->setVisible(false); m_Controls->m_GhostFrame->setVisible(false); m_Controls->m_DistortionsFrame->setVisible(false); m_Controls->m_EddyFrame->setVisible(false); m_Controls->m_FrequencyMapBox->SetDataStorage(this->GetDataStorage()); mitk::TNodePredicateDataType::Pointer isMitkImage = mitk::TNodePredicateDataType::New(); mitk::NodePredicateDataType::Pointer isDwi = mitk::NodePredicateDataType::New("DiffusionImage"); mitk::NodePredicateDataType::Pointer isDti = mitk::NodePredicateDataType::New("TensorImage"); mitk::NodePredicateDataType::Pointer isQbi = mitk::NodePredicateDataType::New("QBallImage"); mitk::NodePredicateOr::Pointer isDiffusionImage = mitk::NodePredicateOr::New(isDwi, isDti); isDiffusionImage = mitk::NodePredicateOr::New(isDiffusionImage, isQbi); mitk::NodePredicateNot::Pointer noDiffusionImage = mitk::NodePredicateNot::New(isDiffusionImage); mitk::NodePredicateAnd::Pointer finalPredicate = mitk::NodePredicateAnd::New(isMitkImage, noDiffusionImage); m_Controls->m_FrequencyMapBox->SetPredicate(finalPredicate); connect((QObject*) m_Controls->m_GenerateImageButton, SIGNAL(clicked()), (QObject*) this, SLOT(GenerateImage())); connect((QObject*) m_Controls->m_GenerateFibersButton, SIGNAL(clicked()), (QObject*) this, SLOT(GenerateFibers())); connect((QObject*) m_Controls->m_CircleButton, SIGNAL(clicked()), (QObject*) this, SLOT(OnDrawROI())); connect((QObject*) m_Controls->m_FlipButton, SIGNAL(clicked()), (QObject*) this, SLOT(OnFlipButton())); connect((QObject*) m_Controls->m_JoinBundlesButton, SIGNAL(clicked()), (QObject*) this, SLOT(JoinBundles())); connect((QObject*) m_Controls->m_VarianceBox, SIGNAL(valueChanged(double)), (QObject*) this, SLOT(OnVarianceChanged(double))); connect((QObject*) m_Controls->m_DistributionBox, SIGNAL(currentIndexChanged(int)), (QObject*) this, SLOT(OnDistributionChanged(int))); connect((QObject*) m_Controls->m_FiberDensityBox, SIGNAL(valueChanged(int)), (QObject*) this, SLOT(OnFiberDensityChanged(int))); - connect((QObject*) m_Controls->m_FiberSamplingBox, SIGNAL(valueChanged(int)), (QObject*) this, SLOT(OnFiberSamplingChanged(int))); + connect((QObject*) m_Controls->m_FiberSamplingBox, SIGNAL(valueChanged(double)), (QObject*) this, SLOT(OnFiberSamplingChanged(double))); connect((QObject*) m_Controls->m_TensionBox, SIGNAL(valueChanged(double)), (QObject*) this, SLOT(OnTensionChanged(double))); connect((QObject*) m_Controls->m_ContinuityBox, SIGNAL(valueChanged(double)), (QObject*) this, SLOT(OnContinuityChanged(double))); connect((QObject*) m_Controls->m_BiasBox, SIGNAL(valueChanged(double)), (QObject*) this, SLOT(OnBiasChanged(double))); connect((QObject*) m_Controls->m_AddGibbsRinging, SIGNAL(stateChanged(int)), (QObject*) this, SLOT(OnAddGibbsRinging(int))); connect((QObject*) m_Controls->m_AddNoise, SIGNAL(stateChanged(int)), (QObject*) this, SLOT(OnAddNoise(int))); connect((QObject*) m_Controls->m_AddGhosts, SIGNAL(stateChanged(int)), (QObject*) this, SLOT(OnAddGhosts(int))); connect((QObject*) m_Controls->m_AddDistortions, SIGNAL(stateChanged(int)), (QObject*) this, SLOT(OnAddDistortions(int))); connect((QObject*) m_Controls->m_AddEddy, SIGNAL(stateChanged(int)), (QObject*) this, SLOT(OnAddEddy(int))); connect((QObject*) m_Controls->m_ConstantRadiusBox, SIGNAL(stateChanged(int)), (QObject*) this, SLOT(OnConstantRadius(int))); connect((QObject*) m_Controls->m_CopyBundlesButton, SIGNAL(clicked()), (QObject*) this, SLOT(CopyBundles())); connect((QObject*) m_Controls->m_TransformBundlesButton, SIGNAL(clicked()), (QObject*) this, SLOT(ApplyTransform())); connect((QObject*) m_Controls->m_AlignOnGrid, SIGNAL(clicked()), (QObject*) this, SLOT(AlignOnGrid())); connect((QObject*) m_Controls->m_Compartment1Box, SIGNAL(currentIndexChanged(int)), (QObject*) this, SLOT(Comp1ModelFrameVisibility(int))); connect((QObject*) m_Controls->m_Compartment2Box, SIGNAL(currentIndexChanged(int)), (QObject*) this, SLOT(Comp2ModelFrameVisibility(int))); connect((QObject*) m_Controls->m_Compartment3Box, SIGNAL(currentIndexChanged(int)), (QObject*) this, SLOT(Comp3ModelFrameVisibility(int))); connect((QObject*) m_Controls->m_Compartment4Box, SIGNAL(currentIndexChanged(int)), (QObject*) this, SLOT(Comp4ModelFrameVisibility(int))); connect((QObject*) m_Controls->m_AdvancedOptionsBox, SIGNAL( stateChanged(int)), (QObject*) this, SLOT(ShowAdvancedOptions(int))); connect((QObject*) m_Controls->m_AdvancedOptionsBox_2, SIGNAL( stateChanged(int)), (QObject*) this, SLOT(ShowAdvancedOptions(int))); } } void QmitkFiberfoxView::ShowAdvancedOptions(int state) { if (state) { m_Controls->m_AdvancedFiberOptionsFrame->setVisible(true); m_Controls->m_AdvancedSignalOptionsFrame->setVisible(true); m_Controls->m_AdvancedOptionsBox->setChecked(true); m_Controls->m_AdvancedOptionsBox_2->setChecked(true); } else { m_Controls->m_AdvancedFiberOptionsFrame->setVisible(false); m_Controls->m_AdvancedSignalOptionsFrame->setVisible(false); m_Controls->m_AdvancedOptionsBox->setChecked(false); m_Controls->m_AdvancedOptionsBox_2->setChecked(false); } } void QmitkFiberfoxView::Comp1ModelFrameVisibility(int index) { m_Controls->m_StickWidget1->setVisible(false); m_Controls->m_ZeppelinWidget1->setVisible(false); m_Controls->m_TensorWidget1->setVisible(false); switch (index) { case 0: m_Controls->m_StickWidget1->setVisible(true); break; case 1: m_Controls->m_ZeppelinWidget1->setVisible(true); break; case 2: m_Controls->m_TensorWidget1->setVisible(true); break; } } void QmitkFiberfoxView::Comp2ModelFrameVisibility(int index) { m_Controls->m_StickWidget2->setVisible(false); m_Controls->m_ZeppelinWidget2->setVisible(false); m_Controls->m_TensorWidget2->setVisible(false); switch (index) { case 0: break; case 1: m_Controls->m_StickWidget2->setVisible(true); break; case 2: m_Controls->m_ZeppelinWidget2->setVisible(true); break; case 3: m_Controls->m_TensorWidget2->setVisible(true); break; } } void QmitkFiberfoxView::Comp3ModelFrameVisibility(int index) { m_Controls->m_BallWidget1->setVisible(false); m_Controls->m_AstrosticksWidget1->setVisible(false); m_Controls->m_DotWidget1->setVisible(false); switch (index) { case 0: m_Controls->m_BallWidget1->setVisible(true); break; case 1: m_Controls->m_AstrosticksWidget1->setVisible(true); break; case 2: m_Controls->m_DotWidget1->setVisible(true); break; } } void QmitkFiberfoxView::Comp4ModelFrameVisibility(int index) { m_Controls->m_BallWidget2->setVisible(false); m_Controls->m_AstrosticksWidget2->setVisible(false); m_Controls->m_DotWidget2->setVisible(false); m_Controls->m_Comp4FractionFrame->setVisible(false); switch (index) { case 0: break; case 1: m_Controls->m_BallWidget2->setVisible(true); m_Controls->m_Comp4FractionFrame->setVisible(true); break; case 2: m_Controls->m_AstrosticksWidget2->setVisible(true); m_Controls->m_Comp4FractionFrame->setVisible(true); break; case 3: m_Controls->m_DotWidget2->setVisible(true); m_Controls->m_Comp4FractionFrame->setVisible(true); break; } } void QmitkFiberfoxView::OnConstantRadius(int value) { if (value>0 && m_Controls->m_RealTimeFibers->isChecked()) GenerateFibers(); } void QmitkFiberfoxView::OnAddEddy(int value) { if (value>0) m_Controls->m_EddyFrame->setVisible(true); else m_Controls->m_EddyFrame->setVisible(false); } void QmitkFiberfoxView::OnAddDistortions(int value) { if (value>0) m_Controls->m_DistortionsFrame->setVisible(true); else m_Controls->m_DistortionsFrame->setVisible(false); } void QmitkFiberfoxView::OnAddGhosts(int value) { if (value>0) m_Controls->m_GhostFrame->setVisible(true); else m_Controls->m_GhostFrame->setVisible(false); } void QmitkFiberfoxView::OnAddNoise(int value) { if (value>0) m_Controls->m_NoiseFrame->setVisible(true); else m_Controls->m_NoiseFrame->setVisible(false); } void QmitkFiberfoxView::OnAddGibbsRinging(int value) { if (value>0) m_Controls->m_GibbsRingingFrame->setVisible(true); else m_Controls->m_GibbsRingingFrame->setVisible(false); } void QmitkFiberfoxView::OnDistributionChanged(int value) { if (value==1) m_Controls->m_VarianceBox->setVisible(true); else m_Controls->m_VarianceBox->setVisible(false); if (m_Controls->m_RealTimeFibers->isChecked()) GenerateFibers(); } void QmitkFiberfoxView::OnVarianceChanged(double value) { if (m_Controls->m_RealTimeFibers->isChecked()) GenerateFibers(); } void QmitkFiberfoxView::OnFiberDensityChanged(int value) { if (m_Controls->m_RealTimeFibers->isChecked()) GenerateFibers(); } -void QmitkFiberfoxView::OnFiberSamplingChanged(int value) +void QmitkFiberfoxView::OnFiberSamplingChanged(double value) { if (m_Controls->m_RealTimeFibers->isChecked()) GenerateFibers(); } void QmitkFiberfoxView::OnTensionChanged(double value) { if (m_Controls->m_RealTimeFibers->isChecked()) GenerateFibers(); } void QmitkFiberfoxView::OnContinuityChanged(double value) { if (m_Controls->m_RealTimeFibers->isChecked()) GenerateFibers(); } void QmitkFiberfoxView::OnBiasChanged(double value) { if (m_Controls->m_RealTimeFibers->isChecked()) GenerateFibers(); } void QmitkFiberfoxView::AlignOnGrid() { for (int i=0; i(m_SelectedFiducials.at(i)->GetData()); mitk::Point3D wc0 = pe->GetWorldControlPoint(0); mitk::DataStorage::SetOfObjects::ConstPointer parentFibs = GetDataStorage()->GetSources(m_SelectedFiducials.at(i)); for( mitk::DataStorage::SetOfObjects::const_iterator it = parentFibs->begin(); it != parentFibs->end(); ++it ) { mitk::DataNode::Pointer pFibNode = *it; if ( pFibNode.IsNotNull() && dynamic_cast(pFibNode->GetData()) ) { mitk::DataStorage::SetOfObjects::ConstPointer parentImgs = GetDataStorage()->GetSources(pFibNode); for( mitk::DataStorage::SetOfObjects::const_iterator it2 = parentImgs->begin(); it2 != parentImgs->end(); ++it2 ) { mitk::DataNode::Pointer pImgNode = *it2; if ( pImgNode.IsNotNull() && dynamic_cast(pImgNode->GetData()) ) { mitk::Image::Pointer img = dynamic_cast(pImgNode->GetData()); mitk::Geometry3D::Pointer geom = img->GetGeometry(); itk::Index<3> idx; geom->WorldToIndex(wc0, idx); mitk::Point3D cIdx; cIdx[0]=idx[0]; cIdx[1]=idx[1]; cIdx[2]=idx[2]; mitk::Point3D world; geom->IndexToWorld(cIdx,world); mitk::Vector3D trans = world - wc0; pe->GetGeometry()->Translate(trans); break; } } break; } } } for( int i=0; iGetSources(fibNode); for( mitk::DataStorage::SetOfObjects::const_iterator it = sources->begin(); it != sources->end(); ++it ) { mitk::DataNode::Pointer imgNode = *it; if ( imgNode.IsNotNull() && dynamic_cast(imgNode->GetData()) ) { mitk::DataStorage::SetOfObjects::ConstPointer derivations = GetDataStorage()->GetDerivations(fibNode); for( mitk::DataStorage::SetOfObjects::const_iterator it2 = derivations->begin(); it2 != derivations->end(); ++it2 ) { mitk::DataNode::Pointer fiducialNode = *it2; if ( fiducialNode.IsNotNull() && dynamic_cast(fiducialNode->GetData()) ) { mitk::PlanarEllipse::Pointer pe = dynamic_cast(fiducialNode->GetData()); mitk::Point3D wc0 = pe->GetWorldControlPoint(0); mitk::Image::Pointer img = dynamic_cast(imgNode->GetData()); mitk::Geometry3D::Pointer geom = img->GetGeometry(); itk::Index<3> idx; geom->WorldToIndex(wc0, idx); mitk::Point3D cIdx; cIdx[0]=idx[0]; cIdx[1]=idx[1]; cIdx[2]=idx[2]; mitk::Point3D world; geom->IndexToWorld(cIdx,world); mitk::Vector3D trans = world - wc0; pe->GetGeometry()->Translate(trans); } } break; } } } for( int i=0; i(m_SelectedImages.at(i)->GetData()); mitk::DataStorage::SetOfObjects::ConstPointer derivations = GetDataStorage()->GetDerivations(m_SelectedImages.at(i)); for( mitk::DataStorage::SetOfObjects::const_iterator it = derivations->begin(); it != derivations->end(); ++it ) { mitk::DataNode::Pointer fibNode = *it; if ( fibNode.IsNotNull() && dynamic_cast(fibNode->GetData()) ) { mitk::DataStorage::SetOfObjects::ConstPointer derivations2 = GetDataStorage()->GetDerivations(fibNode); for( mitk::DataStorage::SetOfObjects::const_iterator it2 = derivations2->begin(); it2 != derivations2->end(); ++it2 ) { mitk::DataNode::Pointer fiducialNode = *it2; if ( fiducialNode.IsNotNull() && dynamic_cast(fiducialNode->GetData()) ) { mitk::PlanarEllipse::Pointer pe = dynamic_cast(fiducialNode->GetData()); mitk::Point3D wc0 = pe->GetWorldControlPoint(0); mitk::Geometry3D::Pointer geom = img->GetGeometry(); itk::Index<3> idx; geom->WorldToIndex(wc0, idx); mitk::Point3D cIdx; cIdx[0]=idx[0]; cIdx[1]=idx[1]; cIdx[2]=idx[2]; mitk::Point3D world; geom->IndexToWorld(cIdx,world); mitk::Vector3D trans = world - wc0; pe->GetGeometry()->Translate(trans); } } } } } mitk::RenderingManager::GetInstance()->RequestUpdateAll(); if (m_Controls->m_RealTimeFibers->isChecked()) GenerateFibers(); } void QmitkFiberfoxView::OnFlipButton() { if (m_SelectedFiducial.IsNull()) return; std::map::iterator it = m_DataNodeToPlanarFigureData.find(m_SelectedFiducial.GetPointer()); if( it != m_DataNodeToPlanarFigureData.end() ) { QmitkPlanarFigureData& data = it->second; data.m_Flipped += 1; data.m_Flipped %= 2; } if (m_Controls->m_RealTimeFibers->isChecked()) GenerateFibers(); } QmitkFiberfoxView::GradientListType QmitkFiberfoxView::GenerateHalfShell(int NPoints) { NPoints *= 2; GradientListType pointshell; int numB0 = NPoints/20; if (numB0==0) numB0=1; GradientType g; g.Fill(0.0); for (int i=0; i theta; theta.set_size(NPoints); vnl_vector phi; phi.set_size(NPoints); double C = sqrt(4*M_PI); phi(0) = 0.0; phi(NPoints-1) = 0.0; for(int i=0; i0 && i std::vector > QmitkFiberfoxView::MakeGradientList() { std::vector > retval; vnl_matrix_fixed* U = itk::PointShell >::DistributePointShell(); // Add 0 vector for B0 int numB0 = ndirs/10; if (numB0==0) numB0=1; itk::Vector v; v.Fill(0.0); for (int i=0; i v; v[0] = U->get(0,i); v[1] = U->get(1,i); v[2] = U->get(2,i); retval.push_back(v); } return retval; } void QmitkFiberfoxView::OnAddBundle() { if (m_SelectedImage.IsNull()) return; mitk::DataStorage::SetOfObjects::ConstPointer children = GetDataStorage()->GetDerivations(m_SelectedImage); mitk::FiberBundleX::Pointer bundle = mitk::FiberBundleX::New(); mitk::DataNode::Pointer node = mitk::DataNode::New(); node->SetData( bundle ); QString name = QString("Bundle_%1").arg(children->size()); node->SetName(name.toStdString()); m_SelectedBundles.push_back(node); UpdateGui(); GetDataStorage()->Add(node, m_SelectedImage); } void QmitkFiberfoxView::OnDrawROI() { if (m_SelectedBundles.empty()) OnAddBundle(); if (m_SelectedBundles.empty()) return; mitk::DataStorage::SetOfObjects::ConstPointer children = GetDataStorage()->GetDerivations(m_SelectedBundles.at(0)); mitk::PlanarEllipse::Pointer figure = mitk::PlanarEllipse::New(); mitk::DataNode::Pointer node = mitk::DataNode::New(); node->SetData( figure ); QList nodes = this->GetDataManagerSelection(); for( int i=0; iSetSelected(false); m_SelectedFiducial = node; QString name = QString("Fiducial_%1").arg(children->size()); node->SetName(name.toStdString()); node->SetSelected(true); GetDataStorage()->Add(node, m_SelectedBundles.at(0)); this->DisableCrosshairNavigation(); mitk::PlanarFigureInteractor::Pointer figureInteractor = dynamic_cast(node->GetInteractor()); if(figureInteractor.IsNull()) figureInteractor = mitk::PlanarFigureInteractor::New("PlanarFigureInteractor", node); mitk::GlobalInteraction::GetInstance()->AddInteractor(figureInteractor); UpdateGui(); } bool CompareLayer(mitk::DataNode::Pointer i,mitk::DataNode::Pointer j) { int li = -1; i->GetPropertyValue("layer", li); int lj = -1; j->GetPropertyValue("layer", lj); return liGetSources(m_SelectedFiducial); for( mitk::DataStorage::SetOfObjects::const_iterator it = parents->begin(); it != parents->end(); ++it ) if(dynamic_cast((*it)->GetData())) m_SelectedBundles.push_back(*it); if (m_SelectedBundles.empty()) return; } vector< vector< mitk::PlanarEllipse::Pointer > > fiducials; vector< vector< unsigned int > > fliplist; for (int i=0; iGetDerivations(m_SelectedBundles.at(i)); std::vector< mitk::DataNode::Pointer > childVector; for( mitk::DataStorage::SetOfObjects::const_iterator it = children->begin(); it != children->end(); ++it ) childVector.push_back(*it); sort(childVector.begin(), childVector.end(), CompareLayer); vector< mitk::PlanarEllipse::Pointer > fib; vector< unsigned int > flip; float radius = 1; int count = 0; for( std::vector< mitk::DataNode::Pointer >::const_iterator it = childVector.begin(); it != childVector.end(); ++it ) { mitk::DataNode::Pointer node = *it; if ( node.IsNotNull() && dynamic_cast(node->GetData()) ) { mitk::PlanarEllipse* ellipse = dynamic_cast(node->GetData()); if (m_Controls->m_ConstantRadiusBox->isChecked()) { ellipse->SetTreatAsCircle(true); mitk::Point2D c = ellipse->GetControlPoint(0); mitk::Point2D p = ellipse->GetControlPoint(1); mitk::Vector2D v = p-c; if (count==0) { radius = v.GetVnlVector().magnitude(); ellipse->SetControlPoint(1, p); } else { v.Normalize(); v *= radius; ellipse->SetControlPoint(1, c+v); } } fib.push_back(ellipse); std::map::iterator it = m_DataNodeToPlanarFigureData.find(node.GetPointer()); if( it != m_DataNodeToPlanarFigureData.end() ) { QmitkPlanarFigureData& data = it->second; flip.push_back(data.m_Flipped); } else flip.push_back(0); } count++; } if (fib.size()>1) { fiducials.push_back(fib); fliplist.push_back(flip); } else if (fib.size()>0) m_SelectedBundles.at(i)->SetData( mitk::FiberBundleX::New() ); mitk::RenderingManager::GetInstance()->RequestUpdateAll(); } itk::FibersFromPlanarFiguresFilter::Pointer filter = itk::FibersFromPlanarFiguresFilter::New(); filter->SetFiducials(fiducials); filter->SetFlipList(fliplist); switch(m_Controls->m_DistributionBox->currentIndex()){ case 0: filter->SetFiberDistribution(itk::FibersFromPlanarFiguresFilter::DISTRIBUTE_UNIFORM); break; case 1: filter->SetFiberDistribution(itk::FibersFromPlanarFiguresFilter::DISTRIBUTE_GAUSSIAN); filter->SetVariance(m_Controls->m_VarianceBox->value()); break; } filter->SetDensity(m_Controls->m_FiberDensityBox->value()); filter->SetTension(m_Controls->m_TensionBox->value()); filter->SetContinuity(m_Controls->m_ContinuityBox->value()); filter->SetBias(m_Controls->m_BiasBox->value()); filter->SetFiberSampling(m_Controls->m_FiberSamplingBox->value()); filter->Update(); vector< mitk::FiberBundleX::Pointer > fiberBundles = filter->GetFiberBundles(); for (int i=0; iSetData( fiberBundles.at(i) ); if (fiberBundles.at(i)->GetNumFibers()>50000) m_SelectedBundles.at(i)->SetVisibility(false); } mitk::RenderingManager::GetInstance()->RequestUpdateAll(); } void QmitkFiberfoxView::GenerateImage() { itk::ImageRegion<3> imageRegion; imageRegion.SetSize(0, m_Controls->m_SizeX->value()); imageRegion.SetSize(1, m_Controls->m_SizeY->value()); imageRegion.SetSize(2, m_Controls->m_SizeZ->value()); mitk::Vector3D spacing; spacing[0] = m_Controls->m_SpacingX->value(); spacing[1] = m_Controls->m_SpacingY->value(); spacing[2] = m_Controls->m_SpacingZ->value(); mitk::Point3D origin; origin[0] = spacing[0]/2; origin[1] = spacing[1]/2; origin[2] = spacing[2]/2; itk::Matrix directionMatrix; directionMatrix.SetIdentity(); if (m_SelectedImage.IsNotNull()) { mitk::Image* img = dynamic_cast(m_SelectedImage->GetData()); itk::Image< float, 3 >::Pointer itkImg = itk::Image< float, 3 >::New(); CastToItkImage< itk::Image< float, 3 > >(img, itkImg); imageRegion = itkImg->GetLargestPossibleRegion(); spacing = itkImg->GetSpacing(); origin = itkImg->GetOrigin(); directionMatrix = itkImg->GetDirection(); } DiffusionSignalModel::GradientListType gradientList; double bVal = 1000; if (m_SelectedDWI.IsNull()) { gradientList = GenerateHalfShell(m_Controls->m_NumGradientsBox->value());; bVal = m_Controls->m_BvalueBox->value(); } else { mitk::DiffusionImage::Pointer dwi = dynamic_cast*>(m_SelectedDWI->GetData()); imageRegion = dwi->GetVectorImage()->GetLargestPossibleRegion(); spacing = dwi->GetVectorImage()->GetSpacing(); origin = dwi->GetVectorImage()->GetOrigin(); directionMatrix = dwi->GetVectorImage()->GetDirection(); bVal = dwi->GetB_Value(); mitk::DiffusionImage::GradientDirectionContainerType::Pointer dirs = dwi->GetDirections(); for (int i=0; iSize(); i++) { DiffusionSignalModel::GradientType g; g[0] = dirs->at(i)[0]; g[1] = dirs->at(i)[1]; g[2] = dirs->at(i)[2]; gradientList.push_back(g); } } if (m_SelectedBundles.empty()) { if (m_SelectedDWI.IsNotNull()) // add artifacts to existing diffusion weighted image { for (int i=0; i*>(m_SelectedImages.at(i)->GetData())) continue; mitk::DiffusionImage::Pointer diffImg = dynamic_cast*>(m_SelectedImages.at(i)->GetData()); double noiseVariance = 0; if (m_Controls->m_AddNoise->isChecked()) { noiseVariance = m_Controls->m_NoiseLevel->value(); artifactModelString += "_NOISE"; artifactModelString += QString::number(noiseVariance); } mitk::RicianNoiseModel noiseModel; noiseModel.SetNoiseVariance(noiseVariance); if ( this->m_Controls->m_TEbox->value() < imageRegion.GetSize(1)*m_Controls->m_LineReadoutTimeBox->value() ) { this->m_Controls->m_TEbox->setValue( imageRegion.GetSize(1)*m_Controls->m_LineReadoutTimeBox->value() ); QMessageBox::information( NULL, "Warning", "Echo time is too short! Time not sufficient to read slice. Automaticall adjusted to "+QString::number(this->m_Controls->m_TEbox->value())+" ms"); } double lineReadoutTime = m_Controls->m_LineReadoutTimeBox->value(); // add N/2 ghosting double kOffset = 0; if (m_Controls->m_AddGhosts->isChecked()) { artifactModelString += "_GHOST"; kOffset = m_Controls->m_kOffsetBox->value(); } if ( this->m_Controls->m_TEbox->value() < imageRegion.GetSize(1)*m_Controls->m_LineReadoutTimeBox->value() ) { this->m_Controls->m_TEbox->setValue( imageRegion.GetSize(1)*m_Controls->m_LineReadoutTimeBox->value() ); QMessageBox::information( NULL, "Warning", "Echo time is too short! Time not sufficient to read slice. Automaticall adjusted to "+QString::number(this->m_Controls->m_TEbox->value())+" ms"); } itk::AddArtifactsToDwiImageFilter< short >::Pointer filter = itk::AddArtifactsToDwiImageFilter< short >::New(); filter->SetInput(diffImg->GetVectorImage()); filter->SettLine(lineReadoutTime); filter->SetkOffset(kOffset); filter->SetNoiseModel(&noiseModel); filter->SetGradientList(gradientList); filter->SetTE(this->m_Controls->m_TEbox->value()); if (m_Controls->m_AddEddy->isChecked()) { filter->SetSimulateEddyCurrents(true); filter->SetEddyGradientStrength(m_Controls->m_EddyGradientStrength->value()); artifactModelString += "_EDDY"; } if (m_Controls->m_AddGibbsRinging->isChecked()) { resultNode->AddProperty("Fiberfox.kRinging-Upsampling", DoubleProperty::New(m_Controls->m_ImageUpsamplingBox->value())); filter->SetUpsampling(m_Controls->m_ImageUpsamplingBox->value()); } if (m_Controls->m_AddDistortions->isChecked() && m_Controls->m_FrequencyMapBox->GetSelectedNode().IsNotNull()) { mitk::DataNode::Pointer fMapNode = m_Controls->m_FrequencyMapBox->GetSelectedNode(); mitk::Image* img = dynamic_cast(fMapNode->GetData()); ItkDoubleImgType::Pointer itkImg = ItkDoubleImgType::New(); CastToItkImage< ItkDoubleImgType >(img, itkImg); if (imageRegion.GetSize(0)==itkImg->GetLargestPossibleRegion().GetSize(0) && imageRegion.GetSize(1)==itkImg->GetLargestPossibleRegion().GetSize(1) && imageRegion.GetSize(2)==itkImg->GetLargestPossibleRegion().GetSize(2)) { filter->SetFrequencyMap(itkImg); artifactModelString += "_DISTORTED"; } } filter->Update(); resultNode->AddProperty("Fiberfox.Line-Offset", DoubleProperty::New(kOffset)); resultNode->AddProperty("Fiberfox.Noise-Variance", DoubleProperty::New(noiseVariance)); resultNode->AddProperty("Fiberfox.Tinhom", IntProperty::New(m_Controls->m_T2starBox->value())); resultNode->AddProperty("binary", BoolProperty::New(false)); mitk::DiffusionImage::Pointer image = mitk::DiffusionImage::New(); image->SetVectorImage( filter->GetOutput() ); image->SetB_Value(diffImg->GetB_Value()); image->SetDirections(diffImg->GetDirections()); image->InitializeFromVectorImage(); resultNode->SetData( image ); resultNode->SetName(m_SelectedImages.at(i)->GetName()+artifactModelString.toStdString()); GetDataStorage()->Add(resultNode); } return; } mitk::Image::Pointer image = mitk::ImageGenerator::GenerateGradientImage( m_Controls->m_SizeX->value(), m_Controls->m_SizeY->value(), m_Controls->m_SizeZ->value(), m_Controls->m_SpacingX->value(), m_Controls->m_SpacingY->value(), m_Controls->m_SpacingZ->value()); mitk::Geometry3D* geom = image->GetGeometry(); geom->SetOrigin(origin); mitk::DataNode::Pointer node = mitk::DataNode::New(); node->SetData( image ); node->SetName("Dummy"); unsigned int window = m_Controls->m_SizeX->value()*m_Controls->m_SizeY->value()*m_Controls->m_SizeZ->value(); unsigned int level = window/2; mitk::LevelWindow lw; lw.SetLevelWindow(level, window); node->SetProperty( "levelwindow", mitk::LevelWindowProperty::New( lw ) ); GetDataStorage()->Add(node); m_SelectedImage = node; mitk::BaseData::Pointer basedata = node->GetData(); if (basedata.IsNotNull()) { mitk::RenderingManager::GetInstance()->InitializeViews( basedata->GetTimeSlicedGeometry(), mitk::RenderingManager::REQUEST_UPDATE_ALL, true ); mitk::RenderingManager::GetInstance()->RequestUpdateAll(); } UpdateGui(); return; } for (int i=0; im_Compartment4Box->currentIndex()>0) { comp4Weight = m_Controls->m_Comp4FractionBox->value(); comp3Weight -= comp4Weight; } mitk::StickModel stickModel1; mitk::StickModel stickModel2; mitk::TensorModel zeppelinModel1; mitk::TensorModel zeppelinModel2; mitk::TensorModel tensorModel1; mitk::TensorModel tensorModel2; mitk::BallModel ballModel1; mitk::BallModel ballModel2; mitk::AstroStickModel astrosticksModel1; mitk::AstroStickModel astrosticksModel2; mitk::DotModel dotModel1; mitk::DotModel dotModel2; // compartment 1 switch (m_Controls->m_Compartment1Box->currentIndex()) { case 0: MITK_INFO << "Using stick model"; stickModel1.SetGradientList(gradientList); stickModel1.SetDiffusivity(m_Controls->m_StickWidget1->GetD()); stickModel1.SetT2(m_Controls->m_StickWidget1->GetT2()); fiberModelList.push_back(&stickModel1); signalModelString += "Stick"; resultNode->AddProperty("Fiberfox.Compartment1.Description", StringProperty::New("Intra-axonal compartment") ); resultNode->AddProperty("Fiberfox.Compartment1.Model", StringProperty::New("Stick") ); resultNode->AddProperty("Fiberfox.Compartment1.D", DoubleProperty::New(m_Controls->m_StickWidget1->GetD()) ); resultNode->AddProperty("Fiberfox.Compartment1.T2", DoubleProperty::New(stickModel1.GetT2()) ); break; case 1: MITK_INFO << "Using zeppelin model"; zeppelinModel1.SetGradientList(gradientList); zeppelinModel1.SetBvalue(bVal); zeppelinModel1.SetDiffusivity1(m_Controls->m_ZeppelinWidget1->GetD1()); zeppelinModel1.SetDiffusivity2(m_Controls->m_ZeppelinWidget1->GetD2()); zeppelinModel1.SetDiffusivity3(m_Controls->m_ZeppelinWidget1->GetD2()); zeppelinModel1.SetT2(m_Controls->m_ZeppelinWidget1->GetT2()); fiberModelList.push_back(&zeppelinModel1); signalModelString += "Zeppelin"; resultNode->AddProperty("Fiberfox.Compartment1.Description", StringProperty::New("Intra-axonal compartment") ); resultNode->AddProperty("Fiberfox.Compartment1.Model", StringProperty::New("Zeppelin") ); resultNode->AddProperty("Fiberfox.Compartment1.D1", DoubleProperty::New(m_Controls->m_ZeppelinWidget1->GetD1()) ); resultNode->AddProperty("Fiberfox.Compartment1.D2", DoubleProperty::New(m_Controls->m_ZeppelinWidget1->GetD2()) ); resultNode->AddProperty("Fiberfox.Compartment1.T2", DoubleProperty::New(zeppelinModel1.GetT2()) ); break; case 2: MITK_INFO << "Using tensor model"; tensorModel1.SetGradientList(gradientList); tensorModel1.SetBvalue(bVal); tensorModel1.SetDiffusivity1(m_Controls->m_TensorWidget1->GetD1()); tensorModel1.SetDiffusivity2(m_Controls->m_TensorWidget1->GetD2()); tensorModel1.SetDiffusivity3(m_Controls->m_TensorWidget1->GetD3()); tensorModel1.SetT2(m_Controls->m_TensorWidget1->GetT2()); fiberModelList.push_back(&tensorModel1); signalModelString += "Tensor"; resultNode->AddProperty("Fiberfox.Compartment1.Description", StringProperty::New("Intra-axonal compartment") ); resultNode->AddProperty("Fiberfox.Compartment1.Model", StringProperty::New("Tensor") ); resultNode->AddProperty("Fiberfox.Compartment1.D1", DoubleProperty::New(m_Controls->m_TensorWidget1->GetD1()) ); resultNode->AddProperty("Fiberfox.Compartment1.D2", DoubleProperty::New(m_Controls->m_TensorWidget1->GetD2()) ); resultNode->AddProperty("Fiberfox.Compartment1.D3", DoubleProperty::New(m_Controls->m_TensorWidget1->GetD3()) ); resultNode->AddProperty("Fiberfox.Compartment1.T2", DoubleProperty::New(zeppelinModel1.GetT2()) ); break; } // compartment 2 switch (m_Controls->m_Compartment2Box->currentIndex()) { case 0: break; case 1: stickModel2.SetGradientList(gradientList); stickModel2.SetDiffusivity(m_Controls->m_StickWidget2->GetD()); stickModel2.SetT2(m_Controls->m_StickWidget2->GetT2()); fiberModelList.push_back(&stickModel2); signalModelString += "Stick"; resultNode->AddProperty("Fiberfox.Compartment2.Description", StringProperty::New("Inter-axonal compartment") ); resultNode->AddProperty("Fiberfox.Compartment2.Model", StringProperty::New("Stick") ); resultNode->AddProperty("Fiberfox.Compartment2.D", DoubleProperty::New(m_Controls->m_StickWidget2->GetD()) ); resultNode->AddProperty("Fiberfox.Compartment2.T2", DoubleProperty::New(stickModel2.GetT2()) ); break; case 2: zeppelinModel2.SetGradientList(gradientList); zeppelinModel2.SetBvalue(bVal); zeppelinModel2.SetDiffusivity1(m_Controls->m_ZeppelinWidget2->GetD1()); zeppelinModel2.SetDiffusivity2(m_Controls->m_ZeppelinWidget2->GetD2()); zeppelinModel2.SetDiffusivity3(m_Controls->m_ZeppelinWidget2->GetD2()); zeppelinModel2.SetT2(m_Controls->m_ZeppelinWidget2->GetT2()); fiberModelList.push_back(&zeppelinModel2); signalModelString += "Zeppelin"; resultNode->AddProperty("Fiberfox.Compartment2.Description", StringProperty::New("Inter-axonal compartment") ); resultNode->AddProperty("Fiberfox.Compartment2.Model", StringProperty::New("Zeppelin") ); resultNode->AddProperty("Fiberfox.Compartment2.D1", DoubleProperty::New(m_Controls->m_ZeppelinWidget2->GetD1()) ); resultNode->AddProperty("Fiberfox.Compartment2.D2", DoubleProperty::New(m_Controls->m_ZeppelinWidget2->GetD2()) ); resultNode->AddProperty("Fiberfox.Compartment2.T2", DoubleProperty::New(zeppelinModel2.GetT2()) ); break; case 3: tensorModel2.SetGradientList(gradientList); tensorModel2.SetBvalue(bVal); tensorModel2.SetDiffusivity1(m_Controls->m_TensorWidget2->GetD1()); tensorModel2.SetDiffusivity2(m_Controls->m_TensorWidget2->GetD2()); tensorModel2.SetDiffusivity3(m_Controls->m_TensorWidget2->GetD3()); tensorModel2.SetT2(m_Controls->m_TensorWidget2->GetT2()); fiberModelList.push_back(&tensorModel2); signalModelString += "Tensor"; resultNode->AddProperty("Fiberfox.Compartment2.Description", StringProperty::New("Inter-axonal compartment") ); resultNode->AddProperty("Fiberfox.Compartment2.Model", StringProperty::New("Tensor") ); resultNode->AddProperty("Fiberfox.Compartment2.D1", DoubleProperty::New(m_Controls->m_TensorWidget2->GetD1()) ); resultNode->AddProperty("Fiberfox.Compartment2.D2", DoubleProperty::New(m_Controls->m_TensorWidget2->GetD2()) ); resultNode->AddProperty("Fiberfox.Compartment2.D3", DoubleProperty::New(m_Controls->m_TensorWidget2->GetD3()) ); resultNode->AddProperty("Fiberfox.Compartment2.T2", DoubleProperty::New(zeppelinModel2.GetT2()) ); break; } // compartment 3 switch (m_Controls->m_Compartment3Box->currentIndex()) { case 0: ballModel1.SetGradientList(gradientList); ballModel1.SetBvalue(bVal); ballModel1.SetDiffusivity(m_Controls->m_BallWidget1->GetD()); ballModel1.SetT2(m_Controls->m_BallWidget1->GetT2()); ballModel1.SetWeight(comp3Weight); nonFiberModelList.push_back(&ballModel1); signalModelString += "Ball"; resultNode->AddProperty("Fiberfox.Compartment3.Description", StringProperty::New("Extra-axonal compartment 1") ); resultNode->AddProperty("Fiberfox.Compartment3.Model", StringProperty::New("Ball") ); resultNode->AddProperty("Fiberfox.Compartment3.D", DoubleProperty::New(m_Controls->m_BallWidget1->GetD()) ); resultNode->AddProperty("Fiberfox.Compartment3.T2", DoubleProperty::New(ballModel1.GetT2()) ); break; case 1: astrosticksModel1.SetGradientList(gradientList); astrosticksModel1.SetBvalue(bVal); astrosticksModel1.SetDiffusivity(m_Controls->m_AstrosticksWidget1->GetD()); astrosticksModel1.SetT2(m_Controls->m_AstrosticksWidget1->GetT2()); astrosticksModel1.SetRandomizeSticks(m_Controls->m_AstrosticksWidget1->GetRandomizeSticks()); astrosticksModel1.SetWeight(comp3Weight); nonFiberModelList.push_back(&astrosticksModel1); signalModelString += "Astrosticks"; resultNode->AddProperty("Fiberfox.Compartment3.Description", StringProperty::New("Extra-axonal compartment 1") ); resultNode->AddProperty("Fiberfox.Compartment3.Model", StringProperty::New("Astrosticks") ); resultNode->AddProperty("Fiberfox.Compartment3.D", DoubleProperty::New(m_Controls->m_AstrosticksWidget1->GetD()) ); resultNode->AddProperty("Fiberfox.Compartment3.T2", DoubleProperty::New(astrosticksModel1.GetT2()) ); resultNode->AddProperty("Fiberfox.Compartment3.RandomSticks", BoolProperty::New(m_Controls->m_AstrosticksWidget1->GetRandomizeSticks()) ); break; case 2: dotModel1.SetGradientList(gradientList); dotModel1.SetT2(m_Controls->m_DotWidget1->GetT2()); dotModel1.SetWeight(comp3Weight); nonFiberModelList.push_back(&dotModel1); signalModelString += "Dot"; resultNode->AddProperty("Fiberfox.Compartment3.Description", StringProperty::New("Extra-axonal compartment 1") ); resultNode->AddProperty("Fiberfox.Compartment3.Model", StringProperty::New("Dot") ); resultNode->AddProperty("Fiberfox.Compartment3.T2", DoubleProperty::New(dotModel1.GetT2()) ); break; } // compartment 4 switch (m_Controls->m_Compartment4Box->currentIndex()) { case 0: break; case 1: ballModel2.SetGradientList(gradientList); ballModel2.SetBvalue(bVal); ballModel2.SetDiffusivity(m_Controls->m_BallWidget2->GetD()); ballModel2.SetT2(m_Controls->m_BallWidget2->GetT2()); ballModel2.SetWeight(comp4Weight); nonFiberModelList.push_back(&ballModel2); signalModelString += "Ball"; resultNode->AddProperty("Fiberfox.Compartment4.Description", StringProperty::New("Extra-axonal compartment 2") ); resultNode->AddProperty("Fiberfox.Compartment4.Model", StringProperty::New("Ball") ); resultNode->AddProperty("Fiberfox.Compartment4.D", DoubleProperty::New(m_Controls->m_BallWidget2->GetD()) ); resultNode->AddProperty("Fiberfox.Compartment4.T2", DoubleProperty::New(ballModel2.GetT2()) ); break; case 2: astrosticksModel2.SetGradientList(gradientList); astrosticksModel2.SetBvalue(bVal); astrosticksModel2.SetDiffusivity(m_Controls->m_AstrosticksWidget2->GetD()); astrosticksModel2.SetT2(m_Controls->m_AstrosticksWidget2->GetT2()); astrosticksModel2.SetRandomizeSticks(m_Controls->m_AstrosticksWidget2->GetRandomizeSticks()); astrosticksModel2.SetWeight(comp4Weight); nonFiberModelList.push_back(&astrosticksModel2); signalModelString += "Astrosticks"; resultNode->AddProperty("Fiberfox.Compartment4.Description", StringProperty::New("Extra-axonal compartment 2") ); resultNode->AddProperty("Fiberfox.Compartment4.Model", StringProperty::New("Astrosticks") ); resultNode->AddProperty("Fiberfox.Compartment4.D", DoubleProperty::New(m_Controls->m_AstrosticksWidget2->GetD()) ); resultNode->AddProperty("Fiberfox.Compartment4.T2", DoubleProperty::New(astrosticksModel2.GetT2()) ); resultNode->AddProperty("Fiberfox.Compartment4.RandomSticks", BoolProperty::New(m_Controls->m_AstrosticksWidget2->GetRandomizeSticks()) ); break; case 3: dotModel2.SetGradientList(gradientList); dotModel2.SetT2(m_Controls->m_DotWidget2->GetT2()); dotModel2.SetWeight(comp4Weight); nonFiberModelList.push_back(&dotModel2); signalModelString += "Dot"; resultNode->AddProperty("Fiberfox.Compartment4.Description", StringProperty::New("Extra-axonal compartment 2") ); resultNode->AddProperty("Fiberfox.Compartment4.Model", StringProperty::New("Dot") ); resultNode->AddProperty("Fiberfox.Compartment4.T2", DoubleProperty::New(dotModel2.GetT2()) ); break; } itk::TractsToDWIImageFilter::KspaceArtifactList artifactList; // artifact models QString artifactModelString(""); double noiseVariance = 0; if (m_Controls->m_AddNoise->isChecked()) { noiseVariance = m_Controls->m_NoiseLevel->value(); artifactModelString += "_NOISE"; artifactModelString += QString::number(noiseVariance); resultNode->AddProperty("Fiberfox.Noise-Variance", DoubleProperty::New(noiseVariance)); } mitk::RicianNoiseModel noiseModel; noiseModel.SetNoiseVariance(noiseVariance); if (m_Controls->m_AddGibbsRinging->isChecked()) { artifactModelString += "_RINGING"; resultNode->AddProperty("Fiberfox.Ringing-Upsampling", DoubleProperty::New(m_Controls->m_ImageUpsamplingBox->value())); tractsToDwiFilter->SetUpsampling(m_Controls->m_ImageUpsamplingBox->value()); } if ( this->m_Controls->m_TEbox->value() < imageRegion.GetSize(1)*m_Controls->m_LineReadoutTimeBox->value() ) { this->m_Controls->m_TEbox->setValue( imageRegion.GetSize(1)*m_Controls->m_LineReadoutTimeBox->value() ); QMessageBox::information( NULL, "Warning", "Echo time is too short! Time not sufficient to read slice. Automaticall adjusted to "+QString::number(this->m_Controls->m_TEbox->value())+" ms"); } double lineReadoutTime = m_Controls->m_LineReadoutTimeBox->value(); // adjusting line readout time to the adapted image size needed for the DFT int y = imageRegion.GetSize(1); if ( y%2 == 1 ) y += 1; if ( y>imageRegion.GetSize(1) ) lineReadoutTime *= (double)imageRegion.GetSize(1)/y; // add N/2 ghosting double kOffset = 0; if (m_Controls->m_AddGhosts->isChecked()) { artifactModelString += "_GHOST"; kOffset = m_Controls->m_kOffsetBox->value(); resultNode->AddProperty("Fiberfox.Line-Offset", DoubleProperty::New(kOffset)); } // add distortions if (m_Controls->m_AddDistortions->isChecked() && m_Controls->m_FrequencyMapBox->GetSelectedNode().IsNotNull()) { mitk::DataNode::Pointer fMapNode = m_Controls->m_FrequencyMapBox->GetSelectedNode(); mitk::Image* img = dynamic_cast(fMapNode->GetData()); ItkDoubleImgType::Pointer itkImg = ItkDoubleImgType::New(); CastToItkImage< ItkDoubleImgType >(img, itkImg); if (imageRegion.GetSize(0)==itkImg->GetLargestPossibleRegion().GetSize(0) && imageRegion.GetSize(1)==itkImg->GetLargestPossibleRegion().GetSize(1) && imageRegion.GetSize(2)==itkImg->GetLargestPossibleRegion().GetSize(2)) { tractsToDwiFilter->SetFrequencyMap(itkImg); artifactModelString += "_DISTORTED"; } } if (m_Controls->m_AddEddy->isChecked()) { tractsToDwiFilter->SetSimulateEddyCurrents(true); tractsToDwiFilter->SetEddyGradientStrength(m_Controls->m_EddyGradientStrength->value()); artifactModelString += "_EDDY"; } mitk::FiberBundleX::Pointer fiberBundle = dynamic_cast(m_SelectedBundles.at(i)->GetData()); if (fiberBundle->GetNumFibers()<=0) continue; if (m_Controls->m_RelaxationBox->isChecked()) artifactModelString += "_RELAX"; tractsToDwiFilter->SetSimulateRelaxation(m_Controls->m_RelaxationBox->isChecked()); tractsToDwiFilter->SetImageRegion(imageRegion); tractsToDwiFilter->SetSpacing(spacing); tractsToDwiFilter->SetOrigin(origin); tractsToDwiFilter->SetDirectionMatrix(directionMatrix); tractsToDwiFilter->SetFiberBundle(fiberBundle); tractsToDwiFilter->SetFiberModels(fiberModelList); tractsToDwiFilter->SetNonFiberModels(nonFiberModelList); tractsToDwiFilter->SetNoiseModel(&noiseModel); tractsToDwiFilter->SetKspaceArtifacts(artifactList); tractsToDwiFilter->SetkOffset(kOffset); tractsToDwiFilter->SettLine(m_Controls->m_LineReadoutTimeBox->value()); tractsToDwiFilter->SettInhom(this->m_Controls->m_T2starBox->value()); tractsToDwiFilter->SetTE(this->m_Controls->m_TEbox->value()); tractsToDwiFilter->SetNumberOfRepetitions(m_Controls->m_RepetitionsBox->value()); tractsToDwiFilter->SetEnforcePureFiberVoxels(m_Controls->m_EnforcePureFiberVoxelsBox->isChecked()); tractsToDwiFilter->SetInterpolationShrink(m_Controls->m_InterpolationShrink->value()); tractsToDwiFilter->SetFiberRadius(m_Controls->m_FiberRadius->value()); tractsToDwiFilter->SetSignalScale(m_Controls->m_SignalScaleBox->value()); if (m_Controls->m_InterpolationShrink->value()<1000) tractsToDwiFilter->SetUseInterpolation(true); if (m_TissueMask.IsNotNull()) { ItkUcharImgType::Pointer mask = ItkUcharImgType::New(); mitk::CastToItkImage(m_TissueMask, mask); tractsToDwiFilter->SetTissueMask(mask); } tractsToDwiFilter->Update(); mitk::DiffusionImage::Pointer image = mitk::DiffusionImage::New(); image->SetVectorImage( tractsToDwiFilter->GetOutput() ); image->SetB_Value(bVal); image->SetDirections(gradientList); image->InitializeFromVectorImage(); resultNode->SetData( image ); resultNode->SetName(m_SelectedBundles.at(i)->GetName() +"_D"+QString::number(imageRegion.GetSize(0)).toStdString() +"-"+QString::number(imageRegion.GetSize(1)).toStdString() +"-"+QString::number(imageRegion.GetSize(2)).toStdString() +"_S"+QString::number(spacing[0]).toStdString() +"-"+QString::number(spacing[1]).toStdString() +"-"+QString::number(spacing[2]).toStdString() +"_b"+QString::number(bVal).toStdString() +"_"+signalModelString.toStdString() +artifactModelString.toStdString()); GetDataStorage()->Add(resultNode, m_SelectedBundles.at(i)); resultNode->AddProperty("Fiberfox.InterpolationShrink", IntProperty::New(m_Controls->m_InterpolationShrink->value())); resultNode->AddProperty("Fiberfox.SignalScale", IntProperty::New(m_Controls->m_SignalScaleBox->value())); resultNode->AddProperty("Fiberfox.FiberRadius", IntProperty::New(m_Controls->m_FiberRadius->value())); resultNode->AddProperty("Fiberfox.Tinhom", IntProperty::New(m_Controls->m_T2starBox->value())); resultNode->AddProperty("Fiberfox.Repetitions", IntProperty::New(m_Controls->m_RepetitionsBox->value())); resultNode->AddProperty("Fiberfox.b-value", DoubleProperty::New(bVal)); resultNode->AddProperty("Fiberfox.Model", StringProperty::New(signalModelString.toStdString())); resultNode->AddProperty("Fiberfox.PureFiberVoxels", BoolProperty::New(m_Controls->m_EnforcePureFiberVoxelsBox->isChecked())); resultNode->AddProperty("binary", BoolProperty::New(false)); resultNode->SetProperty( "levelwindow", mitk::LevelWindowProperty::New(tractsToDwiFilter->GetLevelWindow()) ); if (m_Controls->m_VolumeFractionsBox->isChecked()) { std::vector< itk::TractsToDWIImageFilter::ItkDoubleImgType::Pointer > volumeFractions = tractsToDwiFilter->GetVolumeFractions(); for (int k=0; kInitializeByItk(volumeFractions.at(k).GetPointer()); image->SetVolume(volumeFractions.at(k)->GetBufferPointer()); mitk::DataNode::Pointer node = mitk::DataNode::New(); node->SetData( image ); node->SetName(m_SelectedBundles.at(i)->GetName()+"_CompartmentVolume-"+QString::number(k).toStdString()); GetDataStorage()->Add(node, m_SelectedBundles.at(i)); } } mitk::BaseData::Pointer basedata = resultNode->GetData(); if (basedata.IsNotNull()) { mitk::RenderingManager::GetInstance()->InitializeViews( basedata->GetTimeSlicedGeometry(), mitk::RenderingManager::REQUEST_UPDATE_ALL, true ); mitk::RenderingManager::GetInstance()->RequestUpdateAll(); } } } void QmitkFiberfoxView::ApplyTransform() { vector< mitk::DataNode::Pointer > selectedBundles; for( int i=0; iGetDerivations(m_SelectedImages.at(i)); for( mitk::DataStorage::SetOfObjects::const_iterator it = derivations->begin(); it != derivations->end(); ++it ) { mitk::DataNode::Pointer fibNode = *it; if ( fibNode.IsNotNull() && dynamic_cast(fibNode->GetData()) ) selectedBundles.push_back(fibNode); } } if (selectedBundles.empty()) selectedBundles = m_SelectedBundles2; if (!selectedBundles.empty()) { std::vector::const_iterator it = selectedBundles.begin(); for (it; it!=selectedBundles.end(); ++it) { mitk::FiberBundleX::Pointer fib = dynamic_cast((*it)->GetData()); fib->RotateAroundAxis(m_Controls->m_XrotBox->value(), m_Controls->m_YrotBox->value(), m_Controls->m_ZrotBox->value()); fib->TranslateFibers(m_Controls->m_XtransBox->value(), m_Controls->m_YtransBox->value(), m_Controls->m_ZtransBox->value()); fib->ScaleFibers(m_Controls->m_XscaleBox->value(), m_Controls->m_YscaleBox->value(), m_Controls->m_ZscaleBox->value()); // handle child fiducials if (m_Controls->m_IncludeFiducials->isChecked()) { mitk::DataStorage::SetOfObjects::ConstPointer derivations = GetDataStorage()->GetDerivations(*it); for( mitk::DataStorage::SetOfObjects::const_iterator it2 = derivations->begin(); it2 != derivations->end(); ++it2 ) { mitk::DataNode::Pointer fiducialNode = *it2; if ( fiducialNode.IsNotNull() && dynamic_cast(fiducialNode->GetData()) ) { mitk::PlanarEllipse* pe = dynamic_cast(fiducialNode->GetData()); mitk::Geometry3D* geom = pe->GetGeometry(); // translate mitk::Vector3D world; world[0] = m_Controls->m_XtransBox->value(); world[1] = m_Controls->m_YtransBox->value(); world[2] = m_Controls->m_ZtransBox->value(); geom->Translate(world); // calculate rotation matrix double x = m_Controls->m_XrotBox->value()*M_PI/180; double y = m_Controls->m_YrotBox->value()*M_PI/180; double z = m_Controls->m_ZrotBox->value()*M_PI/180; itk::Matrix< float, 3, 3 > rotX; rotX.SetIdentity(); rotX[1][1] = cos(x); rotX[2][2] = rotX[1][1]; rotX[1][2] = -sin(x); rotX[2][1] = -rotX[1][2]; itk::Matrix< float, 3, 3 > rotY; rotY.SetIdentity(); rotY[0][0] = cos(y); rotY[2][2] = rotY[0][0]; rotY[0][2] = sin(y); rotY[2][0] = -rotY[0][2]; itk::Matrix< float, 3, 3 > rotZ; rotZ.SetIdentity(); rotZ[0][0] = cos(z); rotZ[1][1] = rotZ[0][0]; rotZ[0][1] = -sin(z); rotZ[1][0] = -rotZ[0][1]; itk::Matrix< float, 3, 3 > rot = rotZ*rotY*rotX; // transform control point coordinate into geometry translation geom->SetOrigin(pe->GetWorldControlPoint(0)); mitk::Point2D cp; cp.Fill(0.0); pe->SetControlPoint(0, cp); // rotate fiducial geom->GetIndexToWorldTransform()->SetMatrix(rot*geom->GetIndexToWorldTransform()->GetMatrix()); // implicit translation mitk::Vector3D trans; trans[0] = geom->GetOrigin()[0]-fib->GetGeometry()->GetCenter()[0]; trans[1] = geom->GetOrigin()[1]-fib->GetGeometry()->GetCenter()[1]; trans[2] = geom->GetOrigin()[2]-fib->GetGeometry()->GetCenter()[2]; mitk::Vector3D newWc = rot*trans; newWc = newWc-trans; geom->Translate(newWc); } } } } } else { for (int i=0; i(m_SelectedFiducials.at(i)->GetData()); mitk::Geometry3D* geom = pe->GetGeometry(); // translate mitk::Vector3D world; world[0] = m_Controls->m_XtransBox->value(); world[1] = m_Controls->m_YtransBox->value(); world[2] = m_Controls->m_ZtransBox->value(); geom->Translate(world); // calculate rotation matrix double x = m_Controls->m_XrotBox->value()*M_PI/180; double y = m_Controls->m_YrotBox->value()*M_PI/180; double z = m_Controls->m_ZrotBox->value()*M_PI/180; itk::Matrix< float, 3, 3 > rotX; rotX.SetIdentity(); rotX[1][1] = cos(x); rotX[2][2] = rotX[1][1]; rotX[1][2] = -sin(x); rotX[2][1] = -rotX[1][2]; itk::Matrix< float, 3, 3 > rotY; rotY.SetIdentity(); rotY[0][0] = cos(y); rotY[2][2] = rotY[0][0]; rotY[0][2] = sin(y); rotY[2][0] = -rotY[0][2]; itk::Matrix< float, 3, 3 > rotZ; rotZ.SetIdentity(); rotZ[0][0] = cos(z); rotZ[1][1] = rotZ[0][0]; rotZ[0][1] = -sin(z); rotZ[1][0] = -rotZ[0][1]; itk::Matrix< float, 3, 3 > rot = rotZ*rotY*rotX; // transform control point coordinate into geometry translation geom->SetOrigin(pe->GetWorldControlPoint(0)); mitk::Point2D cp; cp.Fill(0.0); pe->SetControlPoint(0, cp); // rotate fiducial geom->GetIndexToWorldTransform()->SetMatrix(rot*geom->GetIndexToWorldTransform()->GetMatrix()); } if (m_Controls->m_RealTimeFibers->isChecked()) GenerateFibers(); } mitk::RenderingManager::GetInstance()->RequestUpdateAll(); } void QmitkFiberfoxView::CopyBundles() { if ( m_SelectedBundles.size()<1 ){ QMessageBox::information( NULL, "Warning", "Select at least one fiber bundle!"); MITK_WARN("QmitkFiberProcessingView") << "Select at least one fiber bundle!"; return; } std::vector::const_iterator it = m_SelectedBundles.begin(); for (it; it!=m_SelectedBundles.end(); ++it) { // find parent image mitk::DataNode::Pointer parentNode; mitk::DataStorage::SetOfObjects::ConstPointer parentImgs = GetDataStorage()->GetSources(*it); for( mitk::DataStorage::SetOfObjects::const_iterator it2 = parentImgs->begin(); it2 != parentImgs->end(); ++it2 ) { mitk::DataNode::Pointer pImgNode = *it2; if ( pImgNode.IsNotNull() && dynamic_cast(pImgNode->GetData()) ) { parentNode = pImgNode; break; } } mitk::FiberBundleX::Pointer fib = dynamic_cast((*it)->GetData()); mitk::FiberBundleX::Pointer newBundle = fib->GetDeepCopy(); QString name((*it)->GetName().c_str()); name += "_copy"; mitk::DataNode::Pointer fbNode = mitk::DataNode::New(); fbNode->SetData(newBundle); fbNode->SetName(name.toStdString()); fbNode->SetVisibility(true); if (parentNode.IsNotNull()) GetDataStorage()->Add(fbNode, parentNode); else GetDataStorage()->Add(fbNode); // copy child fiducials if (m_Controls->m_IncludeFiducials->isChecked()) { mitk::DataStorage::SetOfObjects::ConstPointer derivations = GetDataStorage()->GetDerivations(*it); for( mitk::DataStorage::SetOfObjects::const_iterator it2 = derivations->begin(); it2 != derivations->end(); ++it2 ) { mitk::DataNode::Pointer fiducialNode = *it2; if ( fiducialNode.IsNotNull() && dynamic_cast(fiducialNode->GetData()) ) { mitk::PlanarEllipse::Pointer pe = mitk::PlanarEllipse::New(); pe->DeepCopy(dynamic_cast(fiducialNode->GetData())); mitk::DataNode::Pointer newNode = mitk::DataNode::New(); newNode->SetData(pe); newNode->SetName(fiducialNode->GetName()); GetDataStorage()->Add(newNode, fbNode); } } } } mitk::RenderingManager::GetInstance()->RequestUpdateAll(); } void QmitkFiberfoxView::JoinBundles() { if ( m_SelectedBundles.size()<2 ){ QMessageBox::information( NULL, "Warning", "Select at least two fiber bundles!"); MITK_WARN("QmitkFiberProcessingView") << "Select at least two fiber bundles!"; return; } std::vector::const_iterator it = m_SelectedBundles.begin(); mitk::FiberBundleX::Pointer newBundle = dynamic_cast((*it)->GetData()); QString name(""); name += QString((*it)->GetName().c_str()); ++it; for (it; it!=m_SelectedBundles.end(); ++it) { newBundle = newBundle->AddBundle(dynamic_cast((*it)->GetData())); name += "+"+QString((*it)->GetName().c_str()); } mitk::DataNode::Pointer fbNode = mitk::DataNode::New(); fbNode->SetData(newBundle); fbNode->SetName(name.toStdString()); fbNode->SetVisibility(true); GetDataStorage()->Add(fbNode); mitk::RenderingManager::GetInstance()->RequestUpdateAll(); } void QmitkFiberfoxView::UpdateGui() { m_Controls->m_FiberBundleLabel->setText("mandatory"); m_Controls->m_GeometryFrame->setEnabled(true); m_Controls->m_GeometryMessage->setVisible(false); m_Controls->m_DiffusionPropsMessage->setVisible(false); m_Controls->m_FiberGenMessage->setVisible(true); m_Controls->m_TransformBundlesButton->setEnabled(false); m_Controls->m_CopyBundlesButton->setEnabled(false); m_Controls->m_GenerateFibersButton->setEnabled(false); m_Controls->m_FlipButton->setEnabled(false); m_Controls->m_CircleButton->setEnabled(false); m_Controls->m_BvalueBox->setEnabled(true); m_Controls->m_NumGradientsBox->setEnabled(true); m_Controls->m_JoinBundlesButton->setEnabled(false); m_Controls->m_AlignOnGrid->setEnabled(false); if (m_SelectedFiducial.IsNotNull()) { m_Controls->m_TransformBundlesButton->setEnabled(true); m_Controls->m_FlipButton->setEnabled(true); m_Controls->m_AlignOnGrid->setEnabled(true); } if (m_SelectedImage.IsNotNull() || !m_SelectedBundles.empty()) { m_Controls->m_TransformBundlesButton->setEnabled(true); m_Controls->m_CircleButton->setEnabled(true); m_Controls->m_FiberGenMessage->setVisible(false); m_Controls->m_AlignOnGrid->setEnabled(true); } if (m_TissueMask.IsNotNull() || m_SelectedImage.IsNotNull()) { m_Controls->m_GeometryMessage->setVisible(true); m_Controls->m_GeometryFrame->setEnabled(false); } if (m_SelectedDWI.IsNotNull()) { m_Controls->m_DiffusionPropsMessage->setVisible(true); m_Controls->m_BvalueBox->setEnabled(false); m_Controls->m_NumGradientsBox->setEnabled(false); m_Controls->m_GeometryMessage->setVisible(true); m_Controls->m_GeometryFrame->setEnabled(false); } if (!m_SelectedBundles.empty()) { m_Controls->m_CopyBundlesButton->setEnabled(true); m_Controls->m_GenerateFibersButton->setEnabled(true); m_Controls->m_FiberBundleLabel->setText(m_SelectedBundles.at(0)->GetName().c_str()); if (m_SelectedBundles.size()>1) m_Controls->m_JoinBundlesButton->setEnabled(true); } } void QmitkFiberfoxView::OnSelectionChanged( berry::IWorkbenchPart::Pointer, const QList& nodes ) { m_SelectedBundles2.clear(); m_SelectedImages.clear(); m_SelectedFiducials.clear(); m_SelectedFiducial = NULL; m_TissueMask = NULL; m_SelectedBundles.clear(); m_SelectedImage = NULL; m_SelectedDWI = NULL; m_Controls->m_TissueMaskLabel->setText("optional"); // iterate all selected objects, adjust warning visibility for( int i=0; i*>(node->GetData()) ) { m_SelectedDWI = node; m_SelectedImage = node; m_SelectedImages.push_back(node); } else if( node.IsNotNull() && dynamic_cast(node->GetData()) ) { m_SelectedImages.push_back(node); m_SelectedImage = node; bool isBinary = false; node->GetPropertyValue("binary", isBinary); if (isBinary) { m_TissueMask = dynamic_cast(node->GetData()); m_Controls->m_TissueMaskLabel->setText(node->GetName().c_str()); } } else if ( node.IsNotNull() && dynamic_cast(node->GetData()) ) { m_SelectedBundles2.push_back(node); if (m_Controls->m_RealTimeFibers->isChecked()) { m_SelectedBundles.push_back(node); mitk::FiberBundleX::Pointer newFib = dynamic_cast(node->GetData()); if (newFib->GetNumFibers()!=m_Controls->m_FiberDensityBox->value()) GenerateFibers(); } else m_SelectedBundles.push_back(node); } else if ( node.IsNotNull() && dynamic_cast(node->GetData()) ) { m_SelectedFiducials.push_back(node); m_SelectedFiducial = node; m_SelectedBundles.clear(); mitk::DataStorage::SetOfObjects::ConstPointer parents = GetDataStorage()->GetSources(node); for( mitk::DataStorage::SetOfObjects::const_iterator it = parents->begin(); it != parents->end(); ++it ) { mitk::DataNode::Pointer pNode = *it; if ( pNode.IsNotNull() && dynamic_cast(pNode->GetData()) ) m_SelectedBundles.push_back(pNode); } } } UpdateGui(); } void QmitkFiberfoxView::EnableCrosshairNavigation() { MITK_DEBUG << "EnableCrosshairNavigation"; // enable the crosshair navigation if (mitk::ILinkedRenderWindowPart* linkedRenderWindow = dynamic_cast(this->GetRenderWindowPart())) { MITK_DEBUG << "enabling linked navigation"; linkedRenderWindow->EnableLinkedNavigation(true); // linkedRenderWindow->EnableSlicingPlanes(true); } if (m_Controls->m_RealTimeFibers->isChecked()) GenerateFibers(); } void QmitkFiberfoxView::DisableCrosshairNavigation() { MITK_DEBUG << "DisableCrosshairNavigation"; // disable the crosshair navigation during the drawing if (mitk::ILinkedRenderWindowPart* linkedRenderWindow = dynamic_cast(this->GetRenderWindowPart())) { MITK_DEBUG << "disabling linked navigation"; linkedRenderWindow->EnableLinkedNavigation(false); // linkedRenderWindow->EnableSlicingPlanes(false); } } void QmitkFiberfoxView::NodeRemoved(const mitk::DataNode* node) { mitk::DataNode* nonConstNode = const_cast(node); std::map::iterator it = m_DataNodeToPlanarFigureData.find(nonConstNode); if( it != m_DataNodeToPlanarFigureData.end() ) { QmitkPlanarFigureData& data = it->second; // remove observers data.m_Figure->RemoveObserver( data.m_EndPlacementObserverTag ); data.m_Figure->RemoveObserver( data.m_SelectObserverTag ); data.m_Figure->RemoveObserver( data.m_StartInteractionObserverTag ); data.m_Figure->RemoveObserver( data.m_EndInteractionObserverTag ); m_DataNodeToPlanarFigureData.erase( it ); } } void QmitkFiberfoxView::NodeAdded( const mitk::DataNode* node ) { // add observer for selection in renderwindow mitk::PlanarFigure* figure = dynamic_cast(node->GetData()); bool isPositionMarker (false); node->GetBoolProperty("isContourMarker", isPositionMarker); if( figure && !isPositionMarker ) { MITK_DEBUG << "figure added. will add interactor if needed."; mitk::PlanarFigureInteractor::Pointer figureInteractor = dynamic_cast(node->GetInteractor()); mitk::DataNode* nonConstNode = const_cast( node ); if(figureInteractor.IsNull()) { figureInteractor = mitk::PlanarFigureInteractor::New("PlanarFigureInteractor", nonConstNode); } else { // just to be sure that the interactor is not added twice mitk::GlobalInteraction::GetInstance()->RemoveInteractor(figureInteractor); } MITK_DEBUG << "adding interactor to globalinteraction"; mitk::GlobalInteraction::GetInstance()->AddInteractor(figureInteractor); MITK_DEBUG << "will now add observers for planarfigure"; QmitkPlanarFigureData data; data.m_Figure = figure; // // add observer for event when figure has been placed typedef itk::SimpleMemberCommand< QmitkFiberfoxView > SimpleCommandType; // SimpleCommandType::Pointer initializationCommand = SimpleCommandType::New(); // initializationCommand->SetCallbackFunction( this, &QmitkFiberfoxView::PlanarFigureInitialized ); // data.m_EndPlacementObserverTag = figure->AddObserver( mitk::EndPlacementPlanarFigureEvent(), initializationCommand ); // add observer for event when figure is picked (selected) typedef itk::MemberCommand< QmitkFiberfoxView > MemberCommandType; MemberCommandType::Pointer selectCommand = MemberCommandType::New(); selectCommand->SetCallbackFunction( this, &QmitkFiberfoxView::PlanarFigureSelected ); data.m_SelectObserverTag = figure->AddObserver( mitk::SelectPlanarFigureEvent(), selectCommand ); // add observer for event when interaction with figure starts SimpleCommandType::Pointer startInteractionCommand = SimpleCommandType::New(); startInteractionCommand->SetCallbackFunction( this, &QmitkFiberfoxView::DisableCrosshairNavigation); data.m_StartInteractionObserverTag = figure->AddObserver( mitk::StartInteractionPlanarFigureEvent(), startInteractionCommand ); // add observer for event when interaction with figure starts SimpleCommandType::Pointer endInteractionCommand = SimpleCommandType::New(); endInteractionCommand->SetCallbackFunction( this, &QmitkFiberfoxView::EnableCrosshairNavigation); data.m_EndInteractionObserverTag = figure->AddObserver( mitk::EndInteractionPlanarFigureEvent(), endInteractionCommand ); m_DataNodeToPlanarFigureData[nonConstNode] = data; } } void QmitkFiberfoxView::PlanarFigureSelected( itk::Object* object, const itk::EventObject& ) { mitk::TNodePredicateDataType::Pointer isPf = mitk::TNodePredicateDataType::New(); mitk::DataStorage::SetOfObjects::ConstPointer allPfs = this->GetDataStorage()->GetSubset( isPf ); for ( mitk::DataStorage::SetOfObjects::const_iterator it = allPfs->begin(); it!=allPfs->end(); ++it) { mitk::DataNode* node = *it; if( node->GetData() == object ) { node->SetSelected(true); m_SelectedFiducial = node; } else node->SetSelected(false); } UpdateGui(); this->RequestRenderWindowUpdate(); } void QmitkFiberfoxView::SetFocus() { m_Controls->m_CircleButton->setFocus(); } diff --git a/Plugins/org.mitk.gui.qt.diffusionimaging/src/internal/QmitkFiberfoxView.h b/Plugins/org.mitk.gui.qt.diffusionimaging/src/internal/QmitkFiberfoxView.h index 159f196062..95cb15ff89 100755 --- a/Plugins/org.mitk.gui.qt.diffusionimaging/src/internal/QmitkFiberfoxView.h +++ b/Plugins/org.mitk.gui.qt.diffusionimaging/src/internal/QmitkFiberfoxView.h @@ -1,142 +1,142 @@ /*=================================================================== 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 #include #include #include "ui_QmitkFiberfoxViewControls.h" #include #include #include #include #include /*! \brief View for fiber based diffusion software phantoms (Fiberfox). \sa QmitkFunctionality \ingroup Functionalities */ // Forward Qt class declarations using namespace std; class QmitkFiberfoxView : public QmitkAbstractView { // this is needed for all Qt objects that should have a Qt meta-object // (everything that derives from QObject and wants to have signal/slots) Q_OBJECT public: static const string VIEW_ID; QmitkFiberfoxView(); virtual ~QmitkFiberfoxView(); virtual void CreateQtPartControl(QWidget *parent); void SetFocus(); typedef itk::Image ItkDoubleImgType; typedef itk::Image ItkUcharImgType; typedef itk::Vector GradientType; typedef vector GradientListType; template vector > MakeGradientList() ; protected slots: void OnDrawROI(); ///< adds new ROI, handles interactors etc. void OnAddBundle(); ///< adds new fiber bundle to datastorage void OnFlipButton(); ///< negate one coordinate of the fiber waypoints in the selcted planar figure. needed in case of unresolvable twists void GenerateFibers(); ///< generate fibers from the selected ROIs void GenerateImage(); ///< generate artificial image from the selected fiber bundle void JoinBundles(); ///< merges selcted fiber bundles into one void CopyBundles(); ///< add copy of the selected bundle to the datamanager void ApplyTransform(); ///< rotate and shift selected bundles void AlignOnGrid(); ///< shift selected fiducials to nearest voxel center void Comp1ModelFrameVisibility(int index);///< only show parameters of selected fiber model type void Comp2ModelFrameVisibility(int index);///< only show parameters of selected non-fiber model type void Comp3ModelFrameVisibility(int index);///< only show parameters of selected non-fiber model type void Comp4ModelFrameVisibility(int index);///< only show parameters of selected non-fiber model type void ShowAdvancedOptions(int state); /** update fibers if any parameter changes */ void OnFiberDensityChanged(int value); - void OnFiberSamplingChanged(int value); + void OnFiberSamplingChanged(double value); void OnTensionChanged(double value); void OnContinuityChanged(double value); void OnBiasChanged(double value); void OnVarianceChanged(double value); void OnDistributionChanged(int value); void OnAddGibbsRinging(int value); void OnAddNoise(int value); void OnAddGhosts(int value); void OnAddDistortions(int value); void OnAddEddy(int value); void OnConstantRadius(int value); protected: /// \brief called by QmitkFunctionality when DataManager's selection has changed virtual void OnSelectionChanged(berry::IWorkbenchPart::Pointer, const QList&); GradientListType GenerateHalfShell(int NPoints); ///< generate vectors distributed over the halfsphere Ui::QmitkFiberfoxViewControls* m_Controls; void UpdateGui(); ///< enable/disbale buttons etc. according to current datamanager selection void PlanarFigureSelected( itk::Object* object, const itk::EventObject& ); void EnableCrosshairNavigation(); ///< enable crosshair navigation if planar figure interaction ends void DisableCrosshairNavigation(); ///< disable crosshair navigation if planar figure interaction starts void NodeAdded( const mitk::DataNode* node ); ///< add observers void NodeRemoved(const mitk::DataNode* node); ///< remove observers /** structure to keep track of planar figures and observers */ struct QmitkPlanarFigureData { QmitkPlanarFigureData() : m_Figure(0) , m_EndPlacementObserverTag(0) , m_SelectObserverTag(0) , m_StartInteractionObserverTag(0) , m_EndInteractionObserverTag(0) , m_Flipped(0) { } mitk::PlanarFigure* m_Figure; unsigned int m_EndPlacementObserverTag; unsigned int m_SelectObserverTag; unsigned int m_StartInteractionObserverTag; unsigned int m_EndInteractionObserverTag; unsigned int m_Flipped; }; std::map m_DataNodeToPlanarFigureData; ///< map each planar figure uniquely to a QmitkPlanarFigureData mitk::Image::Pointer m_TissueMask; ///< mask defining which regions of the image should contain signal and which are containing only noise mitk::DataNode::Pointer m_SelectedFiducial; ///< selected planar ellipse mitk::DataNode::Pointer m_SelectedImage; mitk::DataNode::Pointer m_SelectedDWI; vector< mitk::DataNode::Pointer > m_SelectedBundles; vector< mitk::DataNode::Pointer > m_SelectedBundles2; vector< mitk::DataNode::Pointer > m_SelectedFiducials; vector< mitk::DataNode::Pointer > m_SelectedImages; }; diff --git a/Plugins/org.mitk.gui.qt.diffusionimaging/src/internal/QmitkFiberfoxViewControls.ui b/Plugins/org.mitk.gui.qt.diffusionimaging/src/internal/QmitkFiberfoxViewControls.ui index 63972bd20f..59ea9db940 100755 --- a/Plugins/org.mitk.gui.qt.diffusionimaging/src/internal/QmitkFiberfoxViewControls.ui +++ b/Plugins/org.mitk.gui.qt.diffusionimaging/src/internal/QmitkFiberfoxViewControls.ui @@ -1,2204 +1,2214 @@ QmitkFiberfoxViewControls 0 0 493 - 1565 + 1588 Form 0 Fiber Definition Qt::Vertical 20 40 color: rgb(255, 0, 0); Please select an image or an existing fiber bundle to draw the fiber fiducials. If you can't provide a suitable image, generate one using the "Signal Generation" tab. Qt::AutoText Qt::AlignJustify|Qt::AlignVCenter true Fiducial Options All fiducials are treated as circles with the same radius as the first fiducial. Use Constant Fiducial Radius false false Align selected fiducials with voxel grid. Shifts selected fiducials to nearest voxel center. Align With Grid Operations false Copy Bundles false Transform Selection QFrame::NoFrame QFrame::Raised 0 Y false Rotation angle (in degree) around x-axis. -360.000000000000000 360.000000000000000 0.100000000000000 Axis: false Rotation angle (in degree) around y-axis. -360.000000000000000 360.000000000000000 0.100000000000000 Translation: false Translation (in mm) in direction of the z-axis. -1000.000000000000000 1000.000000000000000 0.100000000000000 Translation (in mm) in direction of the y-axis. -1000.000000000000000 1000.000000000000000 0.100000000000000 X false Rotation: false Z false Rotation angle (in degree) around z-axis. -360.000000000000000 360.000000000000000 0.100000000000000 Translation (in mm) in direction of the x-axis. -1000.000000000000000 1000.000000000000000 0.100000000000000 Scaling: false Scaling factor for selected fiber bundle along the x-axis. 0.010000000000000 10.000000000000000 0.010000000000000 1.000000000000000 Scaling factor for selected fiber bundle along the y-axis. 0.010000000000000 10.000000000000000 0.010000000000000 1.000000000000000 Scaling factor for selected fiber bundle along the z-axis. 0.010000000000000 10.000000000000000 0.010000000000000 1.000000000000000 false Join Bundles If checked, the fiducials belonging to the modified bundle are also modified. Include Fiducials true Fiber Options QFrame::NoFrame QFrame::Raised 0 QFrame::NoFrame QFrame::Raised 0 Tension: false Fiber Sampling: false 3 -1.000000000000000 1.000000000000000 0.100000000000000 0.000000000000000 - - - - Fiber sampling points (per cm) - - - 1 - - - 100 - - - 1 - - - 10 - - - 3 -1.000000000000000 1.000000000000000 0.100000000000000 0.000000000000000 Bias: false Continuity: false 3 -1.000000000000000 1.000000000000000 0.100000000000000 0.000000000000000 + + + + Distance of fiber sampling points (in mm) + + + 1 + + + 0.100000000000000 + + + 0.100000000000000 + + + 1.000000000000000 + + + QFrame::NoFrame QFrame::Raised 0 6 #Fibers: false Specify number of fibers to generate for the selected bundle. 1 1000000 100 100 false Generate Fibers QFrame::NoFrame QFrame::Raised 0 Select fiber distribution inside of the fiducials. Uniform Gaussian Fiber Distribution: false Variance of the gaussian 3 0.001000000000000 10.000000000000000 0.010000000000000 0.100000000000000 QFrame::NoFrame QFrame::Raised 0 Disable to only generate fibers if "Generate Fibers" button is pressed. Real Time Fibers true Disable to only generate fibers if "Generate Fibers" button is pressed. Advanced Options false QFrame::NoFrame QFrame::Raised 0 false 30 30 Draw elliptical fiducial. :/QmitkDiffusionImaging/circle.png:/QmitkDiffusionImaging/circle.png 32 32 false true false 30 30 Flip fiber waypoints of selcted fiducial around one axis. :/QmitkDiffusionImaging/refresh.xpm:/QmitkDiffusionImaging/refresh.xpm 32 32 false true Qt::Horizontal 40 20 Signal Generation - - - - Intra-axonal Compartment - - - - - - Select signal model for intra-axonal compartment. - - - - Stick Model - - - - - Zeppelin Model - - - - - Tensor Model - - - - - - - - - - - - - - - - Data Fiber Bundle: false <html><head/><body><p><span style=" color:#ff0000;">mandatory</span></p></body></html> true Tissue Mask: false <html><head/><body><p><span style=" color:#969696;">optional</span></p></body></html> true - - - - Extra-axonal Compartments - - - - - - Select signal model for extra-axonal compartment. - - - - Ball Model - - - - - Astrosticks Model - - - - - Dot Model - - - - - - - - - - - - - - - - - - - - Select signal model for extra-axonal compartment. - - - - -- - - - - - Ball Model - - - - - Astrosticks Model - - - - - Dot Model - - - - - - - - Qt::Horizontal - - - - - - - - - - QFrame::NoFrame - - - QFrame::Raised - - - - 0 - - - - - Weighting factor between the two extra-axonal compartments. - - - 1.000000000000000 - - - 0.100000000000000 - - - 0.300000000000000 - - - - - - - Compartment Fraction: - - - - - - - - - - - - - - - - true - - - Start DWI generation from selected fiebr bundle. If no fiber bundle is selected, a grayscale image containing a simple gradient is generated. - - - Generate Image - - - Image Settings QFrame::NoFrame QFrame::Raised 0 6 <html><head/><body><p><span style=" font-style:italic;">TE</span>, <span style=" font-style:italic;">T</span><span style=" font-style:italic; vertical-align:sub;">inhom</span> and <span style=" font-style:italic;">T2</span> will have no effect if unchecked.</p></body></html> Simulate Signal Relaxation true Repetitions: T2* relaxation time (in milliseconds). 100.000000000000000 0.100000000000000 1.000000000000000 Fiber Radius: Fiber radius used to calculate volume fractions (in µm). Set to 0 for automatic radius estimation. 0 1000 0 TE in milliseconds 1 10000 1 100 Interpolation Shrink: Line Readout Time: false <html><head/><body><p>Echo Time <span style=" font-style:italic;">TE</span>: </p></body></html> false Disable partial volume. Treat voxel content as fiber-only if at least one fiber is present. Disable Partial Volume Effects false Output one image per compartment containing the corresponding volume fractions per voxel. Output Volume Fractions false <html><head/><body><p><span style=" font-style:italic;">T</span><span style=" font-style:italic; vertical-align:sub;">inhom</span> Relaxation: </p></body></html> false Number of signal averages. Increase to reduce noise. 1 100 1 1 Relaxation time due to magnetic field inhomogeneities (T2', in milliseconds). 1 10000 1 50 TE in milliseconds 1 10000 1 100 <html><head/><body><p>Large values shrink (towards nearest neighbour interpolation), small values strech interpolation function (towards linear interpolation). 1000 equals nearest neighbour interpolation.</p></body></html> 1 1000 1000 Signal Scale: color: rgb(255, 0, 0); Using geometry of selected image! color: rgb(255, 0, 0); Using gradients of selected DWI! QFrame::NoFrame QFrame::Raised 0 3 0.100000000000000 50.000000000000000 0.100000000000000 2.000000000000000 Image Spacing: 3 0.100000000000000 50.000000000000000 0.100000000000000 2.000000000000000 3 0.100000000000000 50.000000000000000 0.100000000000000 2.000000000000000 Image Dimensions: Fiber sampling factor which determines the accuracy of the calculated fiber and non-fiber volume fractions. 1 1000 1 11 Fiber sampling factor which determines the accuracy of the calculated fiber and non-fiber volume fractions. 1 1000 1 11 Fiber sampling factor which determines the accuracy of the calculated fiber and non-fiber volume fractions. 1 1000 1 3 QFrame::NoFrame QFrame::Raised 0 6 Gradient Directions: Number of gradient directions distributed over the half sphere. 0 10000 1 30 b-Value: false b-value in mm/s² 0 10000 100 1000 Advanced Options - + Qt::Vertical 20 40 - + Noise and other Artifacts Add N/2 Ghosts false true QFrame::NoFrame QFrame::Raised 6 0 K-Space Line Offset: false A larger offset increases the inensity of the ghost image. 3 1.000000000000000 0.010000000000000 0.100000000000000 QFrame::NoFrame QFrame::Raised 0 Variance: Variance of Rician noise model. 4 0.000000000000000 100000.000000000000000 0.001000000000000 25.000000000000000 Add ringing artifacts occuring at strong edges in the image. Add Gibbs Ringing false Add Rician Noise false true QFrame::NoFrame QFrame::Raised 6 0 Upsampling: false Larger values increase the ringing range. Beware of performance issues! 2 1.000000000000000 10.000000000000000 0.100000000000000 2.000000000000000 Add Distortions false true QFrame::NoFrame QFrame::Raised QFormLayout::AllNonFixedFieldsGrow 6 0 - + - Gradient Strength: + Magnitude: false - + - A larger offset increases the inensity of the ghost image. + Maximum magnitude of eddy current induced magnetic field inhomogeneities (in mT). 5 1000.000000000000000 0.001000000000000 0.001000000000000 + + + + color: rgb(255, 0, 0); + + + Experimental! + + + true QFrame::NoFrame QFrame::Raised 6 0 Frequency Map: false Select image specifying the frequency inhomogeneities (in Hz). !!!EXPERIMENTAL!!! Add Eddy Current Effects false - + Inter-axonal Compartment Select signal model for intra-axonal compartment. -- Stick Model Zeppelin Model Tensor Model + + + + Extra-axonal Compartments + + + + + + Select signal model for extra-axonal compartment. + + + + Ball Model + + + + + Astrosticks Model + + + + + Dot Model + + + + + + + + + + + + + + + + + + + + Select signal model for extra-axonal compartment. + + + + -- + + + + + Ball Model + + + + + Astrosticks Model + + + + + Dot Model + + + + + + + + Qt::Horizontal + + + + + + + + + + QFrame::NoFrame + + + QFrame::Raised + + + + 0 + + + + + Weighting factor between the two extra-axonal compartments. + + + 1.000000000000000 + + + 0.100000000000000 + + + 0.300000000000000 + + + + + + + Compartment Fraction: + + + + + + + + + + + + + + + + true + + + Start DWI generation from selected fiebr bundle. If no fiber bundle is selected, a grayscale image containing a simple gradient is generated. + + + Generate Image + + + + + + + Intra-axonal Compartment + + + + + + Select signal model for intra-axonal compartment. + + + + Stick Model + + + + + Zeppelin Model + + + + + Tensor Model + + + + + + + + + + + + + + + + QmitkDataStorageComboBox QComboBox
QmitkDataStorageComboBox.h
 QmitkTensorModelParametersWidget QWidget
QmitkTensorModelParametersWidget.h
1 QmitkStickModelParametersWidget QWidget
QmitkStickModelParametersWidget.h
1 QmitkZeppelinModelParametersWidget QWidget
QmitkZeppelinModelParametersWidget.h
1 QmitkBallModelParametersWidget QWidget
QmitkBallModelParametersWidget.h
1 QmitkAstrosticksModelParametersWidget QWidget
QmitkAstrosticksModelParametersWidget.h
1 QmitkDotModelParametersWidget QWidget
QmitkDotModelParametersWidget.h
1 m_CircleButton m_FlipButton m_RealTimeFibers m_AdvancedOptionsBox m_DistributionBox m_VarianceBox m_FiberDensityBox m_FiberSamplingBox m_TensionBox m_ContinuityBox m_BiasBox m_GenerateFibersButton m_ConstantRadiusBox m_AlignOnGrid m_XrotBox m_YrotBox m_ZrotBox m_XtransBox m_YtransBox m_ZtransBox m_XscaleBox m_YscaleBox m_ZscaleBox m_TransformBundlesButton m_CopyBundlesButton m_JoinBundlesButton m_IncludeFiducials m_GenerateImageButton m_SizeX m_SizeY m_SizeZ m_SpacingX m_SpacingY m_SpacingZ m_NumGradientsBox m_BvalueBox m_AdvancedOptionsBox_2 m_RepetitionsBox m_SignalScaleBox m_TEbox m_LineReadoutTimeBox m_T2starBox m_FiberRadius m_InterpolationShrink m_EnforcePureFiberVoxelsBox m_Compartment1Box m_Compartment2Box m_Compartment3Box m_Compartment4Box m_Comp4FractionBox m_AddNoise m_NoiseLevel m_AddGhosts m_kOffsetBox m_AddDistortions m_FrequencyMapBox m_AddGibbsRinging tabWidget diff --git a/Plugins/org.mitk.gui.qt.diffusionimaging/src/internal/mitkPluginActivator.cpp b/Plugins/org.mitk.gui.qt.diffusionimaging/src/internal/mitkPluginActivator.cpp index 2fbf11dd7c..df007f0f3d 100644 --- a/Plugins/org.mitk.gui.qt.diffusionimaging/src/internal/mitkPluginActivator.cpp +++ b/Plugins/org.mitk.gui.qt.diffusionimaging/src/internal/mitkPluginActivator.cpp @@ -1,85 +1,85 @@ /*=================================================================== 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 "mitkPluginActivator.h" #include #include "src/internal/QmitkDiffusionImagingPublicPerspective.h" #include "src/internal/QmitkQBallReconstructionView.h" #include "src/internal/QmitkPreprocessingView.h" #include "src/internal/QmitkDiffusionDicomImportView.h" #include "src/internal/QmitkDiffusionQuantificationView.h" #include "src/internal/QmitkTensorReconstructionView.h" #include "src/internal/QmitkControlVisualizationPropertiesView.h" #include "src/internal/QmitkODFDetailsView.h" #include "src/internal/QmitkGibbsTrackingView.h" #include "src/internal/QmitkStochasticFiberTrackingView.h" #include "src/internal/QmitkFiberProcessingView.h" -#include "src/internal/QmitkFiberBundleDeveloperView.h" +//#include "src/internal/QmitkFiberBundleDeveloperView.h" #include "src/internal/QmitkPartialVolumeAnalysisView.h" #include "src/internal/QmitkIVIMView.h" #include "src/internal/QmitkTractbasedSpatialStatisticsView.h" #include "src/internal/QmitkTbssSkeletonizationView.h" #include "src/internal/QmitkStreamlineTrackingView.h" #include "src/internal/Connectomics/QmitkConnectomicsDataView.h" #include "src/internal/Connectomics/QmitkConnectomicsNetworkOperationsView.h" #include "src/internal/Connectomics/QmitkConnectomicsStatisticsView.h" #include "src/internal/QmitkOdfMaximaExtractionView.h" #include "src/internal/QmitkFiberfoxView.h" #include "src/internal/QmitkFiberExtractionView.h" #include "src/internal/QmitkFieldmapGeneratorView.h" namespace mitk { void PluginActivator::start(ctkPluginContext* context) { BERRY_REGISTER_EXTENSION_CLASS(QmitkDiffusionImagingPublicPerspective, context) BERRY_REGISTER_EXTENSION_CLASS(QmitkQBallReconstructionView, context) BERRY_REGISTER_EXTENSION_CLASS(QmitkPreprocessingView, context) BERRY_REGISTER_EXTENSION_CLASS(QmitkDiffusionDicomImport, context) BERRY_REGISTER_EXTENSION_CLASS(QmitkDiffusionQuantificationView, context) BERRY_REGISTER_EXTENSION_CLASS(QmitkTensorReconstructionView, context) BERRY_REGISTER_EXTENSION_CLASS(QmitkControlVisualizationPropertiesView, context) BERRY_REGISTER_EXTENSION_CLASS(QmitkODFDetailsView, context) BERRY_REGISTER_EXTENSION_CLASS(QmitkGibbsTrackingView, context) BERRY_REGISTER_EXTENSION_CLASS(QmitkStochasticFiberTrackingView, context) BERRY_REGISTER_EXTENSION_CLASS(QmitkFiberProcessingView, context) - BERRY_REGISTER_EXTENSION_CLASS(QmitkFiberBundleDeveloperView, context) +// BERRY_REGISTER_EXTENSION_CLASS(QmitkFiberBundleDeveloperView, context) BERRY_REGISTER_EXTENSION_CLASS(QmitkPartialVolumeAnalysisView, context) BERRY_REGISTER_EXTENSION_CLASS(QmitkIVIMView, context) BERRY_REGISTER_EXTENSION_CLASS(QmitkTractbasedSpatialStatisticsView, context) BERRY_REGISTER_EXTENSION_CLASS(QmitkTbssSkeletonizationView, context) BERRY_REGISTER_EXTENSION_CLASS(QmitkConnectomicsDataView, context) BERRY_REGISTER_EXTENSION_CLASS(QmitkConnectomicsNetworkOperationsView, context) BERRY_REGISTER_EXTENSION_CLASS(QmitkConnectomicsStatisticsView, context) BERRY_REGISTER_EXTENSION_CLASS(QmitkStreamlineTrackingView, context) BERRY_REGISTER_EXTENSION_CLASS(QmitkOdfMaximaExtractionView, context) BERRY_REGISTER_EXTENSION_CLASS(QmitkFiberfoxView, context) BERRY_REGISTER_EXTENSION_CLASS(QmitkFiberExtractionView, context) BERRY_REGISTER_EXTENSION_CLASS(QmitkFieldmapGeneratorView, context) } void PluginActivator::stop(ctkPluginContext* context) { Q_UNUSED(context) } } Q_EXPORT_PLUGIN2(org_mitk_gui_qt_diffusionimaging, mitk::PluginActivator)