diff --git a/Modules/FiberDissection/Interactor/mitkSphereInteractor.cpp b/Modules/FiberDissection/Interactor/mitkSphereInteractor.cpp new file mode 100644 index 0000000..cf7d4ee --- /dev/null +++ b/Modules/FiberDissection/Interactor/mitkSphereInteractor.cpp @@ -0,0 +1,142 @@ +/*============================================================================ + +The Medical Imaging Interaction Toolkit (MITK) + +Copyright (c) German Cancer Research Center (DKFZ) +All rights reserved. + +Use of this source code is governed by a 3-clause BSD license that can be +found in the LICENSE file. + +============================================================================*/ + +#include "mitkSphereZonesInteractor.h" +#include "mitkDataStorage.h" +#include "mitkDataNode.h" +#include "mitkSurface.h" +#include "mitkInteractionPositionEvent.h" + +#include + +const char* mitk::SphereInteractor::DATANODE_PROPERTY_SIZE = "zone.size"; +const char* mitk::SphereInteractor::DATANODE_PROPERTY_CREATED = "zone.created"; + +void mitk::SphereInteractor::UpdateSurface(mitk::DataNode::Pointer dataNode) +{ + if (!dataNode->GetData()) + { + MITK_WARN("SphereInteractor")("DataInteractor") + << "Cannot update surface for node as no data is set to the node."; + return; + } + + mitk::Point3D origin = dataNode->GetData()->GetGeometry()->GetOrigin(); + + float radius; + if (!dataNode->GetFloatProperty(DATANODE_PROPERTY_SIZE, radius)) + { + MITK_WARN("SphereInteractor")("DataInteractor") + << "Cannut update surface for node as no radius is specified in the node properties."; + return; + } + + mitk::Surface::Pointer zone = mitk::Surface::New(); + + // create a vtk sphere with given radius + vtkSmartPointer vtkSphere = vtkSmartPointer::New(); + vtkSphere->SetRadius(radius); + vtkSphere->SetCenter(0, 0, 0); + vtkSphere->SetPhiResolution(20); + vtkSphere->SetThetaResolution(20); + vtkSphere->Update(); + zone->SetVtkPolyData(vtkSphere->GetOutput()); + + // set vtk sphere and origin to data node (origin must be set + // again, because of the new sphere set as data) + dataNode->SetData(zone); + dataNode->GetData()->GetGeometry()->SetOrigin(origin); + + // update the RenderWindow to show the changed surface + mitk::RenderingManager::GetInstance()->RequestUpdateAll(); +} + +mitk::SphereInteractor::SphereInteractor() +{ +} + +mitk::SphereInteractor::~SphereInteractor() +{ +} + +void mitk::SphereInteractor::ConnectActionsAndFunctions() +{ + CONNECT_FUNCTION("addCenter", AddCenter); + CONNECT_FUNCTION("changeRadius", ChangeRadius); + CONNECT_FUNCTION("endCreation", EndCreation); + CONNECT_FUNCTION("abortCreation", AbortCreation); +} + +void mitk::SphereInteractor::DataNodeChanged() +{ + mitk::DataNode::Pointer dataNode = this->GetDataNode(); + if (dataNode.IsNotNull() && dataNode->GetData() == nullptr) + { + dataNode->SetData(mitk::Surface::New()); + } +} + +void mitk::SphereInteractor::AddCenter(mitk::StateMachineAction*, mitk::InteractionEvent* interactionEvent) +{ + // cast InteractionEvent to a position event in order to read out the mouse position + mitk::InteractionPositionEvent* positionEvent = dynamic_cast(interactionEvent); + mitk::DataNode::Pointer dataNode = this->GetDataNode(); + dataNode->SetBoolProperty(DATANODE_PROPERTY_CREATED, false); + + // make sure that data node contains data + mitk::BaseData::Pointer dataNodeData = this->GetDataNode()->GetData(); + if (dataNodeData.IsNull()) + { + dataNodeData = mitk::Surface::New(); + this->GetDataNode()->SetData(dataNodeData); + } + + // set origin of the data node to the mouse click position + dataNodeData->GetGeometry()->SetOrigin(positionEvent->GetPositionInWorld()); + MITK_INFO("USNavigationLogging") << "Critical Structure added on position " << positionEvent->GetPointerPositionOnScreen() << " (Image Coordinates); " + << positionEvent->GetPositionInWorld() << " (World Coordinates)"; + + dataNode->SetFloatProperty("opacity", 0.60f); + + //return true; +} + +void mitk::SphereInteractor::ChangeRadius(mitk::StateMachineAction*, mitk::InteractionEvent* interactionEvent) +{ + // cast InteractionEvent to a position event in order to read out the mouse position + mitk::InteractionPositionEvent* positionEvent = dynamic_cast(interactionEvent); + mitk::DataNode::Pointer curNode = this->GetDataNode(); + mitk::Point3D mousePosition = positionEvent->GetPositionInWorld(); + + mitk::ScalarType radius = mousePosition.EuclideanDistanceTo(curNode->GetData()->GetGeometry()->GetOrigin()); + curNode->SetFloatProperty(DATANODE_PROPERTY_SIZE, radius); + + mitk::SphereInteractor::UpdateSurface(curNode); + + //return true; +} + +void mitk::SphereInteractor::EndCreation(mitk::StateMachineAction*, mitk::InteractionEvent* /*interactionEvent*/) +{ + this->GetDataNode()->SetBoolProperty(DATANODE_PROPERTY_CREATED, true); + //return true; +} + +void mitk::SphereInteractor::AbortCreation(mitk::StateMachineAction*, mitk::InteractionEvent*) +{ + this->GetDataNode()->SetData(mitk::Surface::New()); + + // update the RenderWindow to remove the surface + mitk::RenderingManager::GetInstance()->RequestUpdateAll(); + + //return true; +} diff --git a/Modules/FiberDissection/Interactor/mitkSphereInteractor.h b/Modules/FiberDissection/Interactor/mitkSphereInteractor.h new file mode 100644 index 0000000..146fb87 --- /dev/null +++ b/Modules/FiberDissection/Interactor/mitkSphereInteractor.h @@ -0,0 +1,106 @@ +/*============================================================================ + +The Medical Imaging Interaction Toolkit (MITK) + +Copyright (c) German Cancer Research Center (DKFZ) +All rights reserved. + +Use of this source code is governed by a 3-clause BSD license that can be +found in the LICENSE file. + +============================================================================*/ + +#ifndef MITKSphereInteractor_H +#define MITKSphereInteractor_H + +#include "mitkDataInteractor.h" + + + +namespace mitk +{ + class Surface; + class DataNode; + + /** + * \brief DataInteractor for creating a sphere at a specific coordinate. + * The origin is set by mitk::SphereInteractor::AddCenter() and then the + * radius can be updated by mitk::SphereInteractor::ChangeRadius(). An + * updated sphere is rendered every time the radius changes. + * + * DataNode attributes set by this class: + * * zone.size (float) - the radius of the sphere + * * zone.created (bool) - determines if the interactor reached its final state + * + * Two state machines for this interactor are available as resources of the + * USNavigation module. + * * USZoneInteractions.xml: Create a sphere by clicking left, moving the mouse + * and clicking left againg. Aborting is possible by right mouse click. + * * USZoneInteractionsHold.xml: Create a sphere by pressing the left mouse button, + * moving the mouse while holding it pressed and finally release the button. + * Aborting is possible by right mouse click. + */ + class SphereInteractor : public DataInteractor + { + public: + static const char* DATANODE_PROPERTY_SIZE; + static const char* DATANODE_PROPERTY_CREATED; + + mitkClassMacro(SphereInteractor, DataInteractor); + + itkNewMacro(Self); + + /** + * \brief Creates Vtk Sphere according to current radius. + * The radius is gotten from the float property "zone.size" of the + * data node. + */ + static void UpdateSurface(itk::SmartPointer); + + protected: + SphereInteractor(); + ~SphereInteractor() override; + + /** + * \brief Connects the functions from the state machine to methods of this class. + */ + void ConnectActionsAndFunctions() override; + + /** + * \brief Sets empty surface as data for the new data node. + * This is necessary as data nodes without data do not work + * with data interactors. + */ + void DataNodeChanged() override; + + /** + * \brief Sets origin of the data node to the coordinates of the position event. + * \return false if interaction event isn't a position event, true otherwise + */ + void AddCenter(StateMachineAction*, InteractionEvent*); + + /** + * \brief Updates radius attribute according to position event. + * Calculates distance between the data node origin and the current position + * event and updates the data node attribue "zone.size" accordingly. The + * mitk::SphereInteractor::UpdateSurface() function is called then. + * + * \return false if interaction event isn't a position event, true otherwise + */ + void ChangeRadius(StateMachineAction*, InteractionEvent*); + + /** + * \brief Sets the property "zone.created" of the data node to true. + * \return always true + */ + void EndCreation(StateMachineAction*, InteractionEvent*); + + /** + * \brief Removes Vtk Sphere from data node. + * \return always true + */ + void AbortCreation(StateMachineAction*, InteractionEvent*); + }; +} // namespace mitk + +#endif // MITKSphereInteractor_H diff --git a/Modules/FiberDissection/resource/Interactions/SphereInteractionsStates.xml b/Modules/FiberDissection/resource/Interactions/SphereInteractionsStates.xml new file mode 100644 index 0000000..3420e03 --- /dev/null +++ b/Modules/FiberDissection/resource/Interactions/SphereInteractionsStates.xml @@ -0,0 +1,19 @@ + + + + + + + + + + + + + + + + + + + diff --git a/Plugins/org.mitk.gui.qt.diffusionimaging.fiberprocessing/src/internal/QmitkInteractiveFiberDissectionView.cpp b/Plugins/org.mitk.gui.qt.diffusionimaging.fiberprocessing/src/internal/QmitkInteractiveFiberDissectionView.cpp index fc994d6..ea353a7 100644 --- a/Plugins/org.mitk.gui.qt.diffusionimaging.fiberprocessing/src/internal/QmitkInteractiveFiberDissectionView.cpp +++ b/Plugins/org.mitk.gui.qt.diffusionimaging.fiberprocessing/src/internal/QmitkInteractiveFiberDissectionView.cpp @@ -1,1720 +1,1720 @@ /*=================================================================== The Medical Imaging Interaction Toolkit (MITK) Copyright (c) German Cancer Research Center. 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 #include // Qmitk #include "QmitkInteractiveFiberDissectionView.h" #include #include #include #include #include #include #include #include "mitkNodePredicateDataType.h" #include #include #include #include #include #include #include #include #include #include //#include #include #include "usModuleRegistry.h" //#include #include #include #include #include #include #include #include #include #include #include #include #include #include #include #include #include #include #include #include #include #include #include const std::string QmitkInteractiveFiberDissectionView::VIEW_ID = "org.mitk.views.interactivefiberdissection"; const std::string id_DataManager = "org.mitk.views.datamanager"; using namespace mitk; QmitkInteractiveFiberDissectionView::QmitkInteractiveFiberDissectionView() : QmitkAbstractView() , m_Controls( 0 ) , m_IterationCounter(0) , m_RandomExtractionCounter(0) , m_activeCycleCounter(0) , m_createdStreamlineCounter(0) , m_StreamlineInteractor(nullptr) { } // Destructor QmitkInteractiveFiberDissectionView::~QmitkInteractiveFiberDissectionView() { //disable interactor if (m_StreamlineInteractor != nullptr) { // m_StreamlineInteractor->SetStreamlineNode(nullptr); m_StreamlineInteractor->EnableInteraction(false); } } void QmitkInteractiveFiberDissectionView::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::QmitkInteractiveFiberDissectionViewControls; m_Controls->setupUi( parent ); m_Controls->m_BundleBox->SetDataStorage(this->GetDataStorage()); mitk::TNodePredicateDataType::Pointer isBundle= mitk::TNodePredicateDataType::New(); m_Controls->m_BundleBox->SetPredicate( isBundle ); m_Controls->m_PrototypeBox->SetDataStorage(this->GetDataStorage()); mitk::TNodePredicateDataType::Pointer isPrototype = mitk::TNodePredicateDataType::New(); m_Controls->m_PrototypeBox->SetPredicate( isPrototype ); m_Controls->m_PredictionBox->SetDataStorage(this->GetDataStorage()); mitk::TNodePredicateDataType::Pointer isPrediction = mitk::TNodePredicateDataType::New(); m_Controls->m_PredictionBox->SetPredicate( isPrediction ); m_Controls->m_GroundtruthBox->SetDataStorage(this->GetDataStorage()); mitk::TNodePredicateDataType::Pointer isGroundtruth = mitk::TNodePredicateDataType::New(); m_Controls->m_GroundtruthBox->SetPredicate( isGroundtruth ); m_Controls->m_TestBundleBox->SetDataStorage(this->GetDataStorage()); mitk::TNodePredicateDataType::Pointer isTestBundle = mitk::TNodePredicateDataType::New(); m_Controls->m_TestBundleBox->SetPredicate( isTestBundle); connect(m_Controls->m_ErazorButton, SIGNAL(toggled(bool)), this, SLOT( RemovefromBundle(bool) ) ); connect(m_Controls->m_BrushButton, SIGNAL(toggled(bool)), this, SLOT( RemovefromBundleBrush(bool) ) ); connect(m_Controls->m_StreamlineCreation, SIGNAL( clicked() ), this, SLOT( CreateStreamline())); connect(m_Controls->m_AddRandomFibers, SIGNAL( clicked() ), this, SLOT( ExtractRandomFibersFromTractogram() ) ); //need connect(m_Controls->m_TrainClassifier, SIGNAL( clicked() ), this, SLOT( StartAlgorithm( ))); connect(m_Controls->m_CreatePrediction, SIGNAL( clicked() ), this, SLOT( CreatePredictionNode( ))); connect(m_Controls->m_certainData, SIGNAL( clicked() ), this, SLOT( CreateCertainNode( ))); connect(m_Controls->m_AddUncertainFibers, SIGNAL( clicked() ), this, SLOT( CreateUncertaintySampleNode( ))); connect(m_Controls->m_AddDistanceFibers, SIGNAL( clicked() ), this, SLOT( CreateDistanceSampleNode( ))); connect(m_Controls->m_unclabeling, SIGNAL(toggled(bool)), this, SLOT( RemovefromUncertainty(bool) ) ); //need connect(m_Controls->m_unclabelingBrush, SIGNAL(toggled(bool)), this, SLOT( RemovefromUncertaintyBrush(bool) ) ); //need connect(m_Controls->m_distlabeling, SIGNAL(toggled(bool)), this, SLOT( RemovefromDistance(bool) ) ); //need connect(m_Controls->m_predlabeling, SIGNAL(toggled(bool)), this, SLOT( RemovefromPrediction(bool) ) ); //need connect(m_Controls->m_predlabelingBrush, SIGNAL(toggled(bool)), this, SLOT( RemovefromPredictionBrush(bool) ) ); //need connect(m_Controls->m_sellabeling, SIGNAL(toggled(bool)), this, SLOT( RemovefromSelection(bool) ) ); //need connect(m_Controls->m_ResampleButton, SIGNAL( clicked() ), this, SLOT( ResampleTractogram( ) ) ); connect(m_Controls->m_RandomPrototypesButton, SIGNAL( clicked() ), this, SLOT( RandomPrototypes( ) ) ); connect(m_Controls->m_SFFPrototypesButton, SIGNAL( clicked() ), this, SLOT( SFFPrototypes( ) ) ); connect(m_Controls->m_validate, SIGNAL( clicked() ), this, SLOT( StartValidation( ) ) ); connect(m_Controls->m_automaticLabelling, SIGNAL( clicked() ), this, SLOT( AutomaticLabelling( ) ) ); connect(m_Controls->m_RemoveCertainData, SIGNAL( clicked() ), this, SLOT( RemoveCertainData( ) ) ); connect(m_Controls->m_resetClassifier, SIGNAL( clicked() ), this, SLOT( ResetClassifier( ) ) ); } UpdateGui(); } void QmitkInteractiveFiberDissectionView::SetFocus() { m_Controls->toolBoxx->setFocus(); UpdateGui(); } void QmitkInteractiveFiberDissectionView::UpdateGui() { m_Controls->m_FibLabel->setText("nothing selected"); m_Controls->m_InputData->setTitle("Please Select Input Data"); // disable alle frames m_Controls->m_ErazorButton->setCheckable(true); m_Controls->m_ErazorButton->setEnabled(false); m_Controls->m_BrushButton->setCheckable(true); m_Controls->m_BrushButton->setEnabled(false); m_Controls->m_unclabeling->setCheckable(true); m_Controls->m_unclabeling->setEnabled(false); m_Controls->m_predlabeling->setCheckable(true); m_Controls->m_predlabeling->setEnabled(false); m_Controls->m_unclabelingBrush->setCheckable(true); m_Controls->m_unclabelingBrush->setEnabled(false); m_Controls->m_predlabelingBrush->setCheckable(true); m_Controls->m_predlabelingBrush->setEnabled(false); m_Controls->m_distlabeling->setCheckable(true); m_Controls->m_distlabeling->setEnabled(false); m_Controls->m_sellabeling->setCheckable(true); m_Controls->m_sellabeling->setEnabled(false); m_Controls->m_StreamlineCreation->setEnabled(true); m_Controls->m_TrainClassifier->setEnabled(false); m_Controls->m_CreatePrediction->setEnabled(false); m_Controls->m_CreateUncertantyMap->setEnabled(false); m_Controls->m_Numtolabel->setEnabled(false); m_Controls->m_Numtolabel2->setEnabled(false); m_Controls->m_AddRandomFibers->setEnabled(false); m_Controls->m_AddDistanceFibers->setEnabled(false); m_Controls->m_AddUncertainFibers->setEnabled(false); // m_Controls->m_PrototypeBox->setEditable(false); // m_Controls->m_useStandardP-> mitk::DataNode::Pointer curtestnode = m_Controls->m_TestBundleBox->GetSelectedNode(); bool testnodeSelected = curtestnode.IsNotNull(); MITK_INFO << testnodeSelected; bool fibSelected = !m_SelectedFB.empty(); bool multipleFibsSelected = (m_SelectedFB.size()>1); // bool nfibSelected = !m_newfibersBundleNode.empty(); // bool posSelected = !m_positiveBundleNode.empty(); bool nfibSelected = m_newfibersBundleNode.IsNotNull(); // bool posSelected = !m_positiveBundleNode.IsNotNull(); // bool negSelected = !m_negativeBundleNode.IsNotNull(); bool posSelected = this->GetDataStorage()->Exists(m_positiveBundleNode); bool negSelected = this->GetDataStorage()->Exists(m_negativeBundleNode); bool indexSelected = !m_index.empty(); bool uncertaintySelected = this->GetDataStorage()->Exists(m_UncertaintyLabelNode); // bool distanceSelected = this->GetDataStorage()->Exists(m_DistanceLabelNode); bool predictionSelected = this->GetDataStorage()->Exists(m_PredictionNode); // toggle visibility of elements according to selected method // are fiber bundles selected? if ( testnodeSelected ) { m_Controls->m_AddRandomFibers->setEnabled(true); m_Controls->m_sellabeling->setEnabled(true); } if (fibSelected) { m_Controls->m_FibLabel->setText(QString(m_SelectedFB.at(0)->GetName().c_str())); // more than two bundles needed to join/subtract if (multipleFibsSelected ) { m_Controls->m_FibLabel->setText("multiple bundles selected"); } } // is image selected if (nfibSelected && posSelected) { m_Controls->m_ErazorButton->setEnabled(true); m_Controls->m_BrushButton->setEnabled(true); } if (posSelected && negSelected) { m_Controls->m_TrainClassifier->setEnabled(true); } if (indexSelected) { m_Controls->m_CreatePrediction->setEnabled(true); m_Controls->m_AddUncertainFibers->setEnabled(true); m_Controls->m_Numtolabel->setEnabled(true); m_Controls->m_AddDistanceFibers->setEnabled(true); m_Controls->m_Numtolabel2->setEnabled(true); } if (uncertaintySelected) { m_Controls->m_unclabeling->setEnabled(true); m_Controls->m_unclabelingBrush->setEnabled(true); } if (predictionSelected) { m_Controls->m_predlabeling->setEnabled(true); m_Controls->m_predlabelingBrush->setEnabled(true); } // if (distanceSelected) // { m_Controls->m_distlabeling->setEnabled(true); // } // if (m_Controls->m_useStandardP->isChecked()) // { // m_Controls->m_PrototypeBox->setEditable(true); // } } void QmitkInteractiveFiberDissectionView::OnEndInteraction() { } void QmitkInteractiveFiberDissectionView::ResampleTractogram() { mitk::DataNode::Pointer node = m_Controls->m_BundleBox->GetSelectedNode(); auto tractogram = dynamic_cast(node->GetData()); mitk::FiberBundle::Pointer tempfib = tractogram->GetDeepCopy(); std::vector myvec; for (unsigned int k=0; kGetNumFibers(); k++) { myvec.push_back(k); } // auto rng = std::default_random_engine {}; std::random_shuffle(std::begin(myvec), std::end(myvec)); vtkSmartPointer vNewPolyData = vtkSmartPointer::New(); vtkSmartPointer vNewLines = vtkSmartPointer::New(); vtkSmartPointer vNewPoints = vtkSmartPointer::New(); vtkSmartPointer weights = vtkSmartPointer::New(); /* Check wether all Streamlines of the bundles are labeled... If all are labeled Skip for Loop*/ unsigned int counter = 0; for (unsigned int i=0; iGetNumFibers(); i++) { vtkCell* cell = tempfib->GetFiberPolyData()->GetCell(myvec.at(i)); auto numPoints = cell->GetNumberOfPoints(); vtkPoints* points = cell->GetPoints(); vtkSmartPointer container = vtkSmartPointer::New(); for (unsigned int j=0; jGetPoint(j, p); vtkIdType id = vNewPoints->InsertNextPoint(p); - container->GetPointIds()->InsertNextId(id);PointSet + container->GetPointIds()->InsertNextId(id); } weights->InsertValue(counter, tempfib->GetFiberWeight(myvec.at(i))); vNewLines->InsertNextCell(container); counter++; } vNewPolyData->SetLines(vNewLines); vNewPolyData->SetPoints(vNewPoints); mitk::FiberBundle::Pointer ShuffledBundle = mitk::FiberBundle::New(vNewPolyData); ShuffledBundle->SetFiberWeights(weights); ShuffledBundle->ResampleToNumPoints(40); MITK_INFO << "Resampling Done"; mitk::DataNode::Pointer newnode = mitk::DataNode::New(); newnode->SetData( ShuffledBundle ); newnode->SetName( node->GetName() + "_" + std::to_string(40) ); this->GetDataStorage()->Add(newnode); UpdateGui(); } void QmitkInteractiveFiberDissectionView::RandomPrototypes() { // MITK_INFO << "Number of Fibers to use as Prototypes: "; // MITK_INFO << m_Controls->m_NumPrototypes->value(); // mitk::FiberBundle::Pointer fib = dynamic_cast(m_Controls->m_BundleBox->GetSelectedNode()->GetData()); // MITK_INFO << fib->GetNumFibers(); // std::vector myvec; // for (unsigned int k=0; kGetNumFibers(); k++) // { // myvec.push_back(k); // } // std::random_shuffle(std::begin(myvec), std::end(myvec)); // vtkSmartPointer vNewPolyData = vtkSmartPointer::New(); // vtkSmartPointer vNewLines = vtkSmartPointer::New(); // vtkSmartPointer vNewPoints = vtkSmartPointer::New(); // vtkSmartPointer weights = vtkSmartPointer::New(); // /* Check wether all Streamlines of the bundles are labeled... If all are labeled Skip for Loop*/ // unsigned int counter = 0; // for (int i=0; im_NumPrototypes->value(); i++) // { // vtkCell* cell = fib->GetFiberPolyData()->GetCell(myvec.at(i)); // auto numPoints = cell->GetNumberOfPoints(); // vtkPoints* points = cell->GetPoints(); // vtkSmartPointer container = vtkSmartPointer::New(); // for (unsigned int j=0; jGetPoint(j, p); // vtkIdType id = vNewPoints->InsertNextPoint(p); // container->GetPointIds()->InsertNextId(id); // } // weights->InsertValue(counter, fib->GetFiberWeight(myvec.at(i))); // vNewLines->InsertNextCell(container); // counter++; // } // vNewPolyData->SetLines(vNewLines); // vNewPolyData->SetPoints(vNewPoints); // mitk::FiberBundle::Pointer PrototypesBundle = mitk::FiberBundle::New(vNewPolyData); // PrototypesBundle->SetFiberWeights(weights); // mitk::DataNode::Pointer node = mitk::DataNode::New(); // node->SetData(PrototypesBundle); // node->SetName("Random_Prototypes"); //// MITK_INFO << "Number of Streamlines in first function"; //// MITK_INFO << m_newfibersBundleNode->GetData()->GetFiberPolyData()->GetNumberOfCells(); // m_Controls->m_PrototypeBox->SetAutoSelectNewItems (true); // this->GetDataStorage()->Add(node); // m_Controls->m_PrototypeBox->SetAutoSelectNewItems (false); // m_Controls->m_useStandardP->setChecked(false); // node->SetVisibility(false); // Get the number of fibers to use as prototypes from the user interface const int numPrototypes = m_Controls->m_NumPrototypes->value(); MITK_INFO << "Number of Fibers to use as Prototypes: " << numPrototypes; // Get the bundle of fibers to extract prototypes from mitk::DataNode::Pointer selectedNode = m_Controls->m_BundleBox->GetSelectedNode(); if (!selectedNode) { MITK_ERROR << "No fiber bundle selected"; return; } mitk::FiberBundle::Pointer fiberBundle = dynamic_cast(selectedNode->GetData()); if (!fiberBundle) { MITK_ERROR << "Selected node does not contain a fiber bundle"; return; } MITK_INFO << "Number of fibers in the selected bundle: " << fiberBundle->GetNumFibers(); // Randomly shuffle the indices of fibers in the bundle std::vector indices(fiberBundle->GetNumFibers()); std::iota(std::begin(indices), std::end(indices), 0); // fill the vector with 0 to n-1 std::random_shuffle(std::begin(indices), std::end(indices)); // Create new PolyData to hold the prototype fibers vtkSmartPointer prototypePolyData = vtkSmartPointer::New(); vtkSmartPointer prototypeLines = vtkSmartPointer::New(); vtkSmartPointer prototypePoints = vtkSmartPointer::New(); vtkSmartPointer prototypeWeights = vtkSmartPointer::New(); // Extract a subset of fibers as prototypes for (int i = 0; i < numPrototypes; i++) { if (indices.empty()) break; const int index = indices.back(); indices.pop_back(); vtkCell* cell = fiberBundle->GetFiberPolyData()->GetCell(index); auto numPoints = cell->GetNumberOfPoints(); vtkPoints* points = cell->GetPoints(); vtkSmartPointer container = vtkSmartPointer::New(); for (unsigned int j = 0; j < numPoints; j++) { double p[3]; points->GetPoint(j, p); vtkIdType id = prototypePoints->InsertNextPoint(p); container->GetPointIds()->InsertNextId(id); } prototypeWeights->InsertNextValue(fiberBundle->GetFiberWeight(index)); prototypeLines->InsertNextCell(container); } // Create a new FiberBundle containing the prototype fibers prototypePolyData->SetLines(prototypeLines); prototypePolyData->SetPoints(prototypePoints); mitk::FiberBundle::Pointer prototypesBundle = mitk::FiberBundle::New(prototypePolyData); prototypesBundle->SetFiberWeights(prototypeWeights); auto node = mitk::DataNode::New(); node->SetData(prototypesBundle); node->SetName("Random_Prototypes"); node->SetVisibility(false); GetDataStorage()->Add(node); m_Controls->m_PrototypeBox->SetAutoSelectNewItems(true); m_Controls->m_PrototypeBox->SetSelectedNode(node); m_Controls->m_PrototypeBox->SetAutoSelectNewItems(false); m_Controls->m_useStandardP->setChecked(false); MITK_INFO << "Created new node with " << numPrototypes << " random prototypes"; } void QmitkInteractiveFiberDissectionView::SFFPrototypes() { MITK_INFO << "Number of Fibers to use as Prototypes: "; MITK_INFO << m_Controls->m_NumPrototypes->value(); MITK_INFO << "Start Creating Prototypes based on SFF"; mitk::FiberBundle::Pointer fib = dynamic_cast(m_Controls->m_BundleBox->GetSelectedNode()->GetData()); /* Get Subset of Tractogram*/ int size_subset = std::max(1.0, ceil(3.0 * m_Controls->m_NumPrototypes->value() * std::log(m_Controls->m_NumPrototypes->value()))); MITK_INFO << fib->GetNumFibers(); std::vector myvec; for (unsigned int k=0; kGetNumFibers(); k++) { myvec.push_back(k); } // std::random_shuffle(std::begin(myvec), std::end(myvec)); vtkSmartPointer vNewPolyData = vtkSmartPointer::New(); vtkSmartPointer vNewLines = vtkSmartPointer::New(); vtkSmartPointer vNewPoints = vtkSmartPointer::New(); vtkSmartPointer weights = vtkSmartPointer::New(); unsigned int counter = 0; for (int i=0; iGetFiberPolyData()->GetCell(myvec.at(i)); auto numPoints = cell->GetNumberOfPoints(); vtkPoints* points = cell->GetPoints(); vtkSmartPointer container = vtkSmartPointer::New(); for (unsigned int j=0; jGetPoint(j, p); vtkIdType id = vNewPoints->InsertNextPoint(p); container->GetPointIds()->InsertNextId(id); } weights->InsertValue(counter, fib->GetFiberWeight(myvec.at(i))); vNewLines->InsertNextCell(container); counter++; } vNewPolyData->SetLines(vNewLines); vNewPolyData->SetPoints(vNewPoints); mitk::FiberBundle::Pointer temp_fib = mitk::FiberBundle::New(vNewPolyData); temp_fib->SetFiberWeights(weights); MITK_INFO << temp_fib->GetFiberPolyData()->GetNumberOfCells(); /* Create std::vector of the SubsetBundle*/ std::vector< vnl_matrix > out_fib(temp_fib->GetFiberPolyData()->GetNumberOfCells()); for (int i=0; iGetFiberPolyData()->GetNumberOfCells(); i++) { vtkCell* cell = temp_fib->GetFiberPolyData()->GetCell(i); int numPoints = cell->GetNumberOfPoints(); vtkPoints* points = cell->GetPoints(); vnl_matrix streamline; streamline.set_size(3, cell->GetNumberOfPoints()); streamline.fill(0.0); for (int j=0; jGetPoint(j, cand); vnl_vector_fixed< float, 3 > candV; candV[0]=cand[0]; candV[1]=cand[1]; candV[2]=cand[2]; streamline.set_column(j, candV); } // out_fib.push_back(streamline); out_fib.at(i)=streamline; } /* Calculate the distancematrix of Subset*/ std::vector< vnl_matrix > dist_vec(out_fib.size());// cv::parallel_for_(cv::Range(0, out_fib.size()), [&](const cv::Range &range) { for (int i = range.start; i < range.end; i++) // for (unsigned int i=0; i distances; distances.set_size(1, out_fib.size()); distances.fill(0.0); for (unsigned int j=0; j single_distances; single_distances.set_size(1, out_fib.at(0).cols()); single_distances.fill(0.0); vnl_matrix single_distances_flip; single_distances_flip.set_size(1, out_fib.at(0).cols()); single_distances_flip.fill(0.0); for (unsigned int ik=0; ik single_distances.mean()) { distances.put(0,j, single_distances.mean()); } else { distances.put(0,j, single_distances_flip.mean()); } } // dist_vec.push_back(distances); dist_vec.at(i) = distances; } }); /*Index to find values in distancematrix*/ std::vector myidx; /*Index to find actual streamlines using indexUnc*/ std::vector indexUncDist; /*Start with the Streamline of the highest entropy, which is in distance_matrix at idx 0*/ myidx.push_back(0); /*Vecotr that stores minvalues of current iteration*/ vnl_matrix cur_vec; cur_vec.set_size(1, size_subset); cur_vec.fill(0.0); for (int i=0; im_NumPrototypes->value(); i++) { // unsigned int cur_i = indexUnc.at(myidx.at(i)); /*Save mean distance of all used Samples*/ vnl_matrix sum_matrix; sum_matrix.set_size(myidx.size(), size_subset); sum_matrix.fill(0); for (unsigned int ii=0; ii vNewPolyData2 = vtkSmartPointer::New(); vtkSmartPointer vNewLines2 = vtkSmartPointer::New(); vtkSmartPointer vNewPoints2 = vtkSmartPointer::New(); vtkSmartPointer weights2 = vtkSmartPointer::New(); /* Check wether all Streamlines of the bundles are labeled... If all are labeled Skip for Loop*/ counter = 0; for (int i=0; im_NumPrototypes->value(); i++) { vtkCell* cell = fib->GetFiberPolyData()->GetCell(myidx.at(i)); auto numPoints = cell->GetNumberOfPoints(); vtkPoints* points = cell->GetPoints(); vtkSmartPointer container = vtkSmartPointer::New(); for (unsigned int j=0; jGetPoint(j, p); vtkIdType id = vNewPoints2->InsertNextPoint(p); container->GetPointIds()->InsertNextId(id); } weights2->InsertValue(counter, fib->GetFiberWeight(myvec.at(i))); vNewLines2->InsertNextCell(container); counter++; } vNewPolyData2->SetLines(vNewLines2); vNewPolyData2->SetPoints(vNewPoints2); mitk::FiberBundle::Pointer PrototypesBundle = mitk::FiberBundle::New(vNewPolyData2); PrototypesBundle->SetFiberWeights(weights2); MITK_INFO << PrototypesBundle->GetFiberPolyData()->GetNumberOfCells(); mitk::DataNode::Pointer node = mitk::DataNode::New(); node->SetData(PrototypesBundle); node->SetName("SFF_Prototypes"); //// MITK_INFO << "Number of Streamlines in first function"; //// MITK_INFO << m_newfibersBundleNode->GetData()->GetFiberPolyData()->GetNumberOfCells(); m_Controls->m_PrototypeBox->SetAutoSelectNewItems (true); this->GetDataStorage()->Add(node); m_Controls->m_PrototypeBox->SetAutoSelectNewItems (false); m_Controls->m_useStandardP->setChecked(false); node->SetVisibility(false); } void QmitkInteractiveFiberDissectionView::OnSelectionChanged(berry::IWorkbenchPart::Pointer /*part*/, const QList& nodes) { m_SelectedFB.clear(); if (nodes.empty() || nodes.front().IsNull()) { m_SelectedImageNode = nullptr; } else { m_SelectedImageNode = nodes.front(); } for (auto node: nodes) { if (dynamic_cast(node->GetData())) m_SelectedImage = dynamic_cast(node->GetData()); else if ( dynamic_cast(node->GetData()) ) m_SelectedFB.push_back(node); } UpdateGui(); } void QmitkInteractiveFiberDissectionView::CreateStreamline() { // initialize figure's geometry with empty geometry // mitk::PlanarCircle::Pointer figure = mitk::PlanarCircle::New(); // mitk::PlaneGeometry::Pointer emptygeometry = mitk::PlaneGeometry::New(); // figure->SetPlaneGeometry( emptygeometry ); // //set desired data to DataNode where Planarfigure is stored //// mitk::DataNode::Pointer circleNode = mitk::DataNode::New(); // circleNode->SetName(QString("Ball").toStdString()); // circleNode->SetData(figure); // circleNode->SetBoolProperty("planarfigure.3drendering", true); // circleNode->SetBoolProperty("planarfigure.3drendering.fill", true); // mitk::PlanarFigureInteractor::Pointer figureInteractor = dynamic_cast(circleNode->GetDataInteractor().GetPointer()); // if(figureInteractor.IsNull()) // { // figureInteractor = mitk::PlanarFigureInteractor::New(); // us::Module* planarFigureModule = us::ModuleRegistry::GetModule( "MitkPlanarFigure" ); // figureInteractor->LoadStateMachine("PlanarFigureInteraction.xml", planarFigureModule ); // figureInteractor->SetEventConfig( "PlanarFigureConfig.xml", planarFigureModule ); // figureInteractor->SetDataNode(circleNode); // } // // figure drawn on the topmost layer / image // GetDataStorage()->Add(circleNode ); // UpdateGui(); // circleNode->SetSelected(true); // vtkSmartPointer sphereSource = vtkSmartPointer::New(); //// sphereSource->SetRadius(circleNode->GetData()->GetProperty("radius")->GetDoubleValue()); // sphereSource->SetRadius(5.0); // sphereSource->SetCenter(0,0,0); // sphereSource->SetPhiResolution(30); // sphereSource->SetThetaResolution(30); // sphereSource->Update(); // // Convert the VTK sphere to a MITK surface // mitk::Surface::Pointer sphereSurface = mitk::Surface::New(); // sphereSurface->SetVtkPolyData(sphereSource->GetOutput()); // // Add the surface to the DataStorage // mitk::DataNode::Pointer sphereNode = mitk::DataNode::New(); // sphereNode->SetData(sphereSurface); // sphereNode->SetName("Sphere"); // sphereNode->SetVisibility(true); // sphereNode->SetOpacity(1.0); // sphereNode->SetColor(1.0, 0.0, 0.0); // GetDataStorage()->Add(sphereNode); // vtkSmartPointer sphereSource = vtkSmartPointer::New(); // sphereSource->SetCenter(0, 0, 0); // sphereSource->SetRadius(5.0); // auto mapper = GetDataNode()->GetMapper(BaseRenderer::Standard3D); // vtkSmartPointer mapper = vtkSmartPointer::New(); // vtkmapper->SetInputConnection(sphereSource->GetOutputPort()); // vtkSmartPointer actor = vtkSmartPointer::New(); // actor->SetMapper(mapper); // actor->GetProperty()->SetColor(1,0,0); // mitk::Surface::Pointer sphereSurface = mitk::Surface::New(); // sphereSurface->SetVtkPolyData(sphereSource->GetOutput()); // mitk::DataNode::Pointer m_SphereNode = mitk::DataNode::New(); // m_SphereNode->SetName("Sphere"); // m_SphereNode->SetData(sphereSurface); // m_SphereNode->SetOpacity(1.0); // m_SphereNode->SetColor(1.0, 0.0, 0.0); // m_SphereNode->SetVisibility(true); // GetDataStorage()->Add(m_SphereNode); // mitk::RenderingManager::GetInstance()->RequestUpdateAll(); // mitk::VtkPropRenderer::Pointer m_Renderer = mitk::VtkPropRenderer::New(); // m_Renderer->SetMapperID(mitk::BaseRenderer::Standard3D); // m_Renderer->SetDataStorage(GetDataStorage()); // m_Renderer->SetDataNode(m_SphereNode); // GetDataStorage()->Add(m_Renderer->GetRendererAsDataNode()); // mitk::DataNode::Pointer rendererNode = mitk::DataNode::New(); // rendererNode->SetData(m_Renderer); // m_SphereNode->SetData(sphereSurface); // m_SphereNode->SetVisibility(true); // // Set a name for the renderer node // rendererNode->SetName("RendererNode"); // // Add the renderer node to the DataStorage // GetDataStorage()->Add(rendererNode); // RenderingManager::GetInstance()->RequestUpdateAll(); // workaround for bug 16407 - m_Interactor = mitk::SphereInteractor::New(); - m_Interactor->LoadStateMachine("SphereInteractionsStates.xml", us::ModuleRegistry::GetModule("MitkFiberDissection")); - m_Interactor->SetEventConfig("globalConfig.xml"); - - mitk::DataNode::Pointer dataNode = mitk::DataNode::New(); - // zone number is added to zone name (padding one zero) - dataNode->SetName("HI"); - dataNode->SetColor(0.9, 0.9, 0); - this->GetDataStorage()->Add(dataNode); - m_Interactor->SetDataNode(dataNode); +// m_Interactor = mitk::SphereInteractor::New(); +// m_Interactor->LoadStateMachine("SphereInteractionsStates.xml", us::ModuleRegistry::GetModule("MitkFiberDissection")); +// m_Interactor->SetEventConfig("globalConfig.xml"); + +// mitk::DataNode::Pointer dataNode = mitk::DataNode::New(); +// // zone number is added to zone name (padding one zero) +// dataNode->SetName("HI"); +// dataNode->SetColor(0.9, 0.9, 0); +// this->GetDataStorage()->Add(dataNode); +// m_Interactor->SetDataNode(dataNode); UpdateGui(); } void QmitkInteractiveFiberDissectionView::ExtractRandomFibersFromTractogram() { // Hide the selected node. m_testnode = m_Controls->m_TestBundleBox->GetSelectedNode(); m_testnode->SetVisibility(false); // Uncheck the Brush and Erazor buttons. m_Controls->m_ErazorButton->setChecked(false); m_Controls->m_BrushButton->setChecked(false); // Print the number of fibers to extract. MITK_INFO << "Number of Fibers to extract from Tractogram: "; MITK_INFO << m_Controls->m_NumRandomFibers->value(); MITK_INFO << this->GetDataStorage()->GetAll(); // If a newfibersBundleNode exists, remove it from the data storage. if (m_newfibersBundleNode) { MITK_INFO << "To Label Bundle Exists"; mitk::FiberBundle::Pointer Stack = dynamic_cast(m_newfibersBundleNode->GetData()); // Create a new data node and set it to an empty FiberBundle. mitk::DataNode::Pointer node = mitk::DataNode::New(); m_newfibersFibersData = vtkSmartPointer::New(); m_newfibersFibersData->SetPoints(vtkSmartPointer::New()); m_newfibersBundle = mitk::FiberBundle:: New(m_newfibersFibersData); m_newfibersFibersData->SetLines(vtkSmartPointer::New()); // Print a message to indicate the creation of the FiberBundle. MITK_INFO << "Create Bundle"; } // Get the selected node, which is assumed to be a FiberBundle. mitk::FiberBundle::Pointer fib = dynamic_cast(m_testnode->GetData()); // Create a new PolyData object, and its associated points and cell arrays. vtkSmartPointer vNewPolyData = vtkSmartPointer::New(); vtkSmartPointer vNewLines = vtkSmartPointer::New(); vtkSmartPointer vNewPoints = vtkSmartPointer::New(); vtkSmartPointer weights = vtkSmartPointer::New(); // Initialize a counter variable. unsigned int counter = 0; if (m_Controls->m_NumRandomFibers->value() != fib->GetFiberPolyData()->GetNumberOfCells()) { for (int i = 0; i < m_Controls->m_NumRandomFibers->value(); i++) { // Get the i-th fiber in the input dataset vtkCell* cell = fib->GetFiberPolyData()->GetCell(i); // Get the number of points in the fiber auto numPoints = cell->GetNumberOfPoints(); // Get the points in the fiber vtkPoints* points = cell->GetPoints(); // Create a new vtkPolyLine container to store the new fiber vtkSmartPointer container = vtkSmartPointer::New(); // Loop through each point in the fiber for (unsigned int j = 0; j < numPoints; j++) { double p[3]; points->GetPoint(j, p); // Insert the new point into the vtkPoints object and get its ID vtkIdType id = vNewPoints->InsertNextPoint(p); // Add the ID to the container object to create a new fiber container->GetPointIds()->InsertNextId(id); } // Insert the fiber weight into the vtkDoubleArray object weights->InsertValue(counter, fib->GetFiberWeight(i)); // Insert the new fiber into the vtkCellArray object vNewLines->InsertNextCell(container); // Increment the counter variable counter++; } // Delete the old fibers from the input dataset for (int i = 0; i < m_Controls->m_NumRandomFibers->value(); i++) { fib->GetFiberPolyData()->DeleteCell(i); } // Remove any deleted cells from the input dataset fib->GetFiberPolyData()->RemoveDeletedCells(); // Output the number of fibers in the new dataset to the console MITK_INFO << fib->GetFiberPolyData()->GetNumberOfCells(); // Set the vtkPolyData object to the new fibers vNewPolyData->SetLines(vNewLines); vNewPolyData->SetPoints(vNewPoints); // Create a new vtkPolyData object and set it to the new fibers m_newfibersFibersData = vtkSmartPointer::New(); m_newfibersFibersData->SetPoints(vtkSmartPointer::New()); m_newfibersFibersData->SetLines(vtkSmartPointer::New()); m_newfibersFibersData->SetPoints(vNewPoints); m_newfibersFibersData->SetLines(vNewLines); // Create a new mitk::FiberBundle object and set it to the new fibers m_newfibersBundle = mitk::FiberBundle::New(vNewPolyData); m_newfibersBundle->SetFiberColors(255, 255, 255); m_newfibersBundle->SetFiberWeights(weights); mitk::DataNode::Pointer node = mitk::DataNode::New(); node->SetData(m_newfibersBundle); node->SetName("ToLabel"); m_newfibersBundleNode = node; this->GetDataStorage()->Add(m_newfibersBundleNode); // Create a new data node for the negativeBundle object if (!m_negativeBundleNode) { mitk::FiberBundle::Pointer m_negativeBundle = mitk::FiberBundle::New(); mitk::DataNode::Pointer node2 = mitk::DataNode::New(); node2->SetName("-Bundle"); node2->SetData(m_negativeBundle); m_negativeBundleNode = node2; this->GetDataStorage()->Add(m_negativeBundleNode); } // Increment the RandomExtractionCounter m_RandomExtractionCounter++; } UpdateGui(); } void QmitkInteractiveFiberDissectionView::RemovefromBundle( bool checked ) { if (checked) { m_Controls->m_BrushButton->setChecked(false); // if (m_StreamlineInteractor.IsNull()) // { this->CreateStreamlineInteractorBrush(); this->CreateStreamlineInteractor(); // } m_StreamlineInteractor->EnableInteraction(true); m_StreamlineInteractor->LabelfromPrediction(false); m_StreamlineInteractor->SetNegativeNode(m_negativeBundleNode); m_StreamlineInteractor->SetPositiveNode(m_positiveBundleNode); m_StreamlineInteractor->SetToLabelNode(m_newfibersBundleNode); m_StreamlineInteractor->EnableInteraction(true); // m_StreamlineInteractor->EnableInteraction(true); // m_StreamlineInteractor->LabelfromPrediction(false); // m_StreamlineInteractor->SetNegativeNode(m_negativeBundleNode); // m_StreamlineInteractor->SetPositiveNode(m_positiveBundleNode); // m_StreamlineInteractor->SetToLabelNode(m_newfibersBundleNode); // } // else // { // m_StreamlineInteractor->EnableInteraction(true); // m_StreamlineInteractor->LabelfromPrediction(false); // m_StreamlineInteractor->SetPositiveNode(m_positiveBundleNode); // m_StreamlineInteractor->SetToLabelNode(m_newfibersBundleNode); // } } else { m_StreamlineInteractor->EnableInteraction(false); // m_StreamlineInteractor = nullptr; } UpdateGui(); } void QmitkInteractiveFiberDissectionView::RemovefromBundleBrush( bool checked ) { if (checked) { m_Controls->m_ErazorButton->setChecked(false); // if (m_StreamlineInteractorBrush.IsNull()) // { this->CreateStreamlineInteractor(); this->CreateStreamlineInteractorBrush(); // } m_StreamlineInteractorBrush->EnableInteraction(true); m_StreamlineInteractorBrush->LabelfromPrediction(false); m_StreamlineInteractorBrush->SetNegativeNode(m_negativeBundleNode); m_StreamlineInteractorBrush->SetPositiveNode(m_positiveBundleNode); m_StreamlineInteractorBrush->SetToLabelNode(m_newfibersBundleNode); m_StreamlineInteractorBrush->EnableInteraction(true); // m_StreamlineInteractorBrush->EnableInteraction(true); // m_StreamlineInteractorBrush->LabelfromPrediction(false); // m_StreamlineInteractorBrush->SetNegativeNode(m_negativeBundleNode); // m_StreamlineInteractorBrush->SetPositiveNode(m_positiveBundleNode); // m_StreamlineInteractorBrush->SetToLabelNode(m_newfibersBundleNode); // } // else // { // m_StreamlineInteractorBrush->EnableInteraction(true); // m_StreamlineInteractorBrush->LabelfromPrediction(false); // m_StreamlineInteractorBrush->SetPositiveNode(m_positiveBundleNode); // m_StreamlineInteractorBrush->SetToLabelNode(m_newfibersBundleNode); // } } else { m_StreamlineInteractorBrush->EnableInteraction(false); // m_StreamlineInteractor = nullptr; } UpdateGui(); } void QmitkInteractiveFiberDissectionView::CreateStreamlineInteractor() { m_StreamlineInteractor = mitk::StreamlineInteractor::New(); m_StreamlineInteractor->LoadStateMachine("Streamline3DStates.xml", us::ModuleRegistry::GetModule("MitkFiberDissection")); m_StreamlineInteractor->SetEventConfig("Streamline3DConfig.xml", us::ModuleRegistry::GetModule("MitkFiberDissection")); // m_StreamlineInteractor->SetRotationEnabled(rotationEnabled); } void QmitkInteractiveFiberDissectionView::CreateStreamlineInteractorBrush() { m_StreamlineInteractorBrush = mitk::StreamlineInteractorBrush::New(); m_StreamlineInteractorBrush->LoadStateMachine("StreamlineBrush3DStates.xml", us::ModuleRegistry::GetModule("MitkFiberDissection")); m_StreamlineInteractorBrush->SetEventConfig("StreamlineBrush3DConfig.xml", us::ModuleRegistry::GetModule("MitkFiberDissection")); // m_StreamlineInteractor->SetRotationEnabled(rotationEnabled); } void QmitkInteractiveFiberDissectionView::StartAlgorithm() { m_negativeBundle = dynamic_cast(m_negativeBundleNode->GetData()); m_positiveBundle = dynamic_cast(m_positiveBundleNode->GetData()); this->GetDataStorage()->Remove(m_UncertaintyLabelNode); this->GetDataStorage()->Remove(m_DistanceLabelNode); MITK_INFO << "Clean Test Data"; // this->CleanTestArray(); m_testnode = m_Controls->m_TestBundleBox->GetSelectedNode(); // mitk::FiberBundle::Pointer fib = dynamic_cast(m_SelectedFB.at(0)->GetData()); mitk::FiberBundle::Pointer fib = dynamic_cast(m_testnode->GetData()); MITK_INFO << fib->GetFiberPolyData()->GetNumberOfCells(); fib->GetFiberPolyData()->RemoveDeletedCells(); MITK_INFO << fib->GetFiberPolyData()->GetNumberOfCells(); m_Controls->m_unclabeling->setChecked(false); m_Controls->m_distlabeling->setChecked(false); m_Controls->m_unclabelingBrush->setChecked(false); m_Controls->m_predlabeling->setChecked(false); m_Controls->m_predlabelingBrush->setChecked(false); m_uncCounter = 0; // classifier.reset(); MITK_INFO << "Extract Features"; classifier = std::make_shared(); classifier->SetActiveCycle(m_activeCycleCounter); classifier->SetTractogramPlus(m_positiveBundle); classifier->SetTractogramMinus(m_negativeBundle); classifier->SetTractogramPrototypes(dynamic_cast(m_Controls->m_PrototypeBox->GetSelectedNode()->GetData()), m_Controls->m_useStandardP->isChecked()); // classifier->SetTractogramTest(dynamic_cast(m_SelectedFB.at(0)->GetData()), m_SelectedFB.at(0)->GetName()); classifier->SetTractogramTest(dynamic_cast(m_testnode->GetData()), m_testnode->GetName()); // classifier->SetTractogramTest(dynamic_cast(m_trainbundle->GetData()), m_trainbundle->GetName()); classifier->Update(); m_index = classifier->m_index; MITK_INFO << "Number of Cycles"; MITK_INFO << m_activeCycleCounter; m_activeCycleCounter += 1; MITK_INFO << "Algorithm run succesfully"; // mitk::DataNode::Pointer node = mitk::DataNode::New(); // this->GetDataStorage()->Add(node); m_Controls->m_CreatePrediction->setEnabled(true); UpdateGui(); } void QmitkInteractiveFiberDissectionView::CreatePredictionNode() { MITK_INFO << "Create Prediction"; m_Prediction = classifier->CreatePrediction(m_index.at(0), false); // m_Prediction->ColorFibersByFiberWeights(false, mitk::LookupTable::JET); mitk::DataNode::Pointer node = mitk::DataNode::New(); node->SetData(m_Prediction); auto s = std::to_string(m_activeCycleCounter); node->SetName("Prediction"+s); m_PredictionNode = node; this->GetDataStorage()->Add(m_PredictionNode); UpdateGui(); } void QmitkInteractiveFiberDissectionView::CreateCertainNode() { MITK_INFO << "Create Certain Data"; m_CertainMinus = classifier->CreatePrediction(m_index.at(2), false); mitk::DataNode::Pointer node = mitk::DataNode::New(); node->SetData(m_CertainMinus); auto s = std::to_string(m_activeCycleCounter); node->SetName("m_CertainMinus"+s); m_CertainMinusNode = node; this->GetDataStorage()->Add(m_CertainMinusNode); // m_CertainPlus = classifier->CreatePrediction(m_index.at(4)); // mitk::DataNode::Pointer node2= mitk::DataNode::New(); // node2->SetData(m_CertainPlus); // node2->SetName("m_CertainPlus"+s); // m_CertainPlusNode = node2; // this->GetDataStorage()->Add(m_CertainPlusNode); // m_CertainBetweenMinus = classifier->CreatePrediction(m_index.at(4)); // mitk::DataNode::Pointer node3 = mitk::DataNode::New(); // node3->SetData(m_CertainBetweenMinus); // node3->SetName("m_CertainBetweenMinus"+s); // m_CertainBetweenMinusNode = node3; // this->GetDataStorage()->Add(m_CertainBetweenMinusNode); // m_CertainBetweenPlus = classifier->CreatePrediction(m_index.at(6)); // mitk::DataNode::Pointer node4= mitk::DataNode::New(); // node4->SetData(m_CertainBetweenPlus); // node4->SetName("m_CertainBetweenPlus"+s); // m_CertainBetweenPlusNode = node4; // this->GetDataStorage()->Add(m_CertainBetweenPlusNode); } void QmitkInteractiveFiberDissectionView::RemoveCertainData() { // mitk::FiberBundle::Pointer fib = dynamic_cast(m_SelectedFB.at(0)->GetData()); mitk::FiberBundle::Pointer fib = dynamic_cast(m_testnode->GetData()); MITK_INFO << "Length of certain negativ data:"; MITK_INFO << m_index.at(2).size(); MITK_INFO << "Length of Testdata"; MITK_INFO << fib->GetFiberPolyData()->GetNumberOfCells(); for (unsigned int i=0; i< m_index.at(2).size(); i++) { fib->GetFiberPolyData()->DeleteCell(m_index.at(2).at(i)); } // fib->GetFiberPolyData()->RemoveDeletedCells(); MITK_INFO << "Length of Testdata"; MITK_INFO << fib->GetFiberPolyData()->GetNumberOfCells(); } void QmitkInteractiveFiberDissectionView::CreateUncertaintySampleNode() { this->GetDataStorage()->Remove(m_UncertaintyLabelNode); MITK_INFO << "Create Fibers to label based on Uncertainty"; std::vector vec = m_index.at(1); std::vector myvec = {vec.begin() + m_uncCounter, vec.begin() + m_uncCounter + m_Controls->m_Numtolabel->value()}; m_uncCounter = m_uncCounter + m_Controls->m_Numtolabel->value(); MITK_INFO << m_index.at(1).size(); MITK_INFO << myvec.size(); m_UncertaintyLabel = classifier->CreatePrediction(myvec, true); mitk::DataNode::Pointer node = mitk::DataNode::New(); node->SetData(m_UncertaintyLabel); float d = 5.0; auto s = std::to_string(m_activeCycleCounter); node->SetName("UncertaintyLabel"+s); m_UncertaintyLabelNode = node; m_UncertaintyLabelNode->SetProperty("Fiber2DSliceThickness", mitk::FloatProperty::New(d)); this->GetDataStorage()->Add(m_UncertaintyLabelNode); UpdateGui(); } void QmitkInteractiveFiberDissectionView::CreateDistanceSampleNode() { // MITK_INFO << "Create Fibers to label based on Distance in Features-Space"; // std::vector myvec = m_index.at(2); // myvec.resize(m_Controls->m_Numtolabel2->value()); // MITK_INFO << m_index.at(2).size(); // MITK_INFO << myvec.size(); float myval = m_Controls->m_subsetfft->value() * 0.01; MITK_INFO << myval; std::vector> curidx; curidx = classifier->GetDistanceData(myval); std::vector myvec = curidx.at(0); myvec.resize(m_Controls->m_Numtolabel2->value()); MITK_INFO << m_index.at(2).size(); MITK_INFO << myvec.size(); m_DistanceLabel = classifier->CreatePrediction(myvec, true); mitk::DataNode::Pointer node = mitk::DataNode::New(); node->SetData(m_DistanceLabel); auto s = std::to_string(m_activeCycleCounter); node->SetName("DistanceLabel"+s); m_DistanceLabelNode = node; this->GetDataStorage()->Add(m_DistanceLabelNode); UpdateGui(); } void QmitkInteractiveFiberDissectionView::RemovefromUncertainty( bool checked ) { if (checked) { m_Controls->m_unclabelingBrush->setChecked(false); m_Controls->m_predlabelingBrush->setChecked(false); m_Controls->m_predlabeling->setChecked(false); m_UncertaintyLabel->SetFiberColors(255, 255, 255); this->CreateStreamlineInteractor(); m_StreamlineInteractor->EnableInteraction(true); m_StreamlineInteractor->LabelfromPrediction(false); m_StreamlineInteractor->SetNegativeNode(m_negativeBundleNode); m_StreamlineInteractor->SetPositiveNode(m_positiveBundleNode); m_StreamlineInteractor->SetToLabelNode(m_UncertaintyLabelNode); } else { m_StreamlineInteractor->EnableInteraction(false); // m_StreamlineInteractor = nullptr; } RenderingManager::GetInstance()->RequestUpdateAll(); } void QmitkInteractiveFiberDissectionView::RemovefromUncertaintyBrush( bool checked ) { if (checked) { m_Controls->m_unclabeling->setChecked(false); m_Controls->m_predlabelingBrush->setChecked(false); m_Controls->m_predlabeling->setChecked(false); m_UncertaintyLabel->SetFiberColors(255, 255, 255); this->CreateStreamlineInteractorBrush(); m_StreamlineInteractorBrush->EnableInteraction(true); m_StreamlineInteractorBrush->LabelfromPrediction(false); m_StreamlineInteractorBrush->SetNegativeNode(m_negativeBundleNode); m_StreamlineInteractorBrush->SetPositiveNode(m_positiveBundleNode); m_StreamlineInteractorBrush->SetToLabelNode(m_UncertaintyLabelNode); } else { m_StreamlineInteractorBrush->EnableInteraction(false); // m_StreamlineInteractor = nullptr; } RenderingManager::GetInstance()->RequestUpdateAll(); } void QmitkInteractiveFiberDissectionView::RemovefromDistance( bool checked ) { if (checked) { m_DistanceLabel->SetFiberColors(255, 255, 255); m_StreamlineInteractor->EnableInteraction(true); m_StreamlineInteractor->LabelfromPrediction(false); m_StreamlineInteractor->SetToLabelNode(m_DistanceLabelNode); } else { m_StreamlineInteractor->EnableInteraction(false); // m_StreamlineInteractor = nullptr; } RenderingManager::GetInstance()->RequestUpdateAll(); } void QmitkInteractiveFiberDissectionView::RemovefromPrediction( bool checked ) { if (checked) { m_Controls->m_predlabelingBrush->setChecked(false); m_Controls->m_unclabelingBrush->setChecked(false); m_Controls->m_unclabeling->setChecked(false); // m_Prediction->SetFiberColors(255, 255, 255); this->CreateStreamlineInteractor(); m_StreamlineInteractor->EnableInteraction(true); m_StreamlineInteractor->LabelfromPrediction(true); m_StreamlineInteractor->SetNegativeNode(m_negativeBundleNode); m_StreamlineInteractor->SetPositiveNode(m_positiveBundleNode); m_StreamlineInteractor->SetToLabelNode(m_PredictionNode); } else { m_StreamlineInteractor->EnableInteraction(false); // m_StreamlineInteractor = nullptr; // this->CleanTestArray(); } } void QmitkInteractiveFiberDissectionView::RemovefromPredictionBrush( bool checked ) { if (checked) { m_Controls->m_predlabeling->setChecked(false); m_Controls->m_unclabelingBrush->setChecked(false); m_Controls->m_unclabeling->setChecked(false); // m_Prediction->SetFiberColors(255, 255, 255); this->CreateStreamlineInteractorBrush(); m_StreamlineInteractorBrush->EnableInteraction(true); m_StreamlineInteractorBrush->LabelfromPrediction(true); m_StreamlineInteractorBrush->SetNegativeNode(m_negativeBundleNode); m_StreamlineInteractorBrush->SetPositiveNode(m_positiveBundleNode); m_StreamlineInteractorBrush->SetToLabelNode(m_PredictionNode); } else { m_StreamlineInteractorBrush->EnableInteraction(false); // m_StreamlineInteractor = nullptr; // this->CleanTestArray(); } } void QmitkInteractiveFiberDissectionView::RemovefromSelection( bool checked ) { if (checked) { // m_Prediction->SetFiberColors(255, 255, 255); m_StreamlineInteractor->EnableInteraction(true); m_StreamlineInteractor->LabelfromPrediction(true); // m_StreamlineInteractor->SetToLabelNode(m_SelectedFB.at(0)); m_StreamlineInteractor->SetToLabelNode(m_testnode); } else { m_StreamlineInteractor->EnableInteraction(false); // m_StreamlineInteractor = nullptr; } } void QmitkInteractiveFiberDissectionView::StartValidation() { validater.reset(); // mitk::DataNode::Pointer prednode = m_Controls->m_BundleBox->GetSelectedNode(); // mitk::FiberBundle::Pointer pred = dynamic_cast(prednode->GetData()); // mitk::DataNode::Pointer gtnode = m_Controls->m_BundleBox->GetSelectedNode(); // mitk::FiberBundle::Pointer gt = dynamic_cast(gtnode->GetData()); // mitk::FiberBundle::Pointer pred = dynamic_cast(m_Controls->m_PredictionBox->GetSelectedNode()->GetData()); // mitk::FiberBundle::Pointer gt = dynamic_cast(m_Controls->m_GroundtruthBox->GetSelectedNode()->GetData()); validater= std::make_shared(); validater->SetTractogramPrototypes(dynamic_cast(m_Controls->m_PrototypeBox->GetSelectedNode()->GetData()), m_Controls->m_useStandardP->isChecked()); MITK_INFO << "Prototypes loaded"; validater->SetTractogramPrediction(dynamic_cast(m_Controls->m_PredictionBox->GetSelectedNode()->GetData())); MITK_INFO << "Prediction loaded"; validater->SetTractogramGroundtruth(dynamic_cast(m_Controls->m_GroundtruthBox->GetSelectedNode()->GetData())); MITK_INFO << "Groundtruth loaded"; validater->SetActiveCycle(m_activeCycleCounter); // validater->SetTractogramTest(dynamic_cast(m_SelectedFB.at(0)->GetData()), m_SelectedFB.at(0)->GetName()); validater->SetTractogramTest(dynamic_cast(m_testnode->GetData()), m_testnode->GetName()); // classifier->SetTractogramTest(dynamic_cast(m_trainbundle->GetData()), m_trainbundle->GetName()); MITK_INFO << "Testdata loaded"; vnl_vector metrics; metrics = validater->ValidationPipe(); m_metrics.push_back(metrics); MITK_INFO << "Validation run succesfully"; UpdateGui(); } void QmitkInteractiveFiberDissectionView::AutomaticLabelling() { // mitk::FiberBundle::Pointer fib = dynamic_cast(m_SelectedFB.at(0)->GetData()); // mitk::FiberBundle::Pointer fib_true = dynamic_cast(m_Controls->m_GroundtruthBox->GetSelectedNode()->GetData()); // vtkCell* cell; // vtkCell* cell2; // for (int i=0; iGetFiberPolyData()->GetNumberOfCells(); i++) // { // cell = fib->GetFiberPolyData()->GetCell(i); // for (int k=0; kGetFiberPolyData()->GetNumberOfCells(); k++ ) // { // cell2 = fib_true->GetFiberPolyData()->GetCell(i); // if (cell==cell2) // MITK_INFO << "Same"; // } // } mitk::FiberBundle::Pointer fib = dynamic_cast(m_PredictionNode->GetData()); mitk::FiberBundle::Pointer fib_true = dynamic_cast(m_positiveBundleNode->GetData()); vtkSmartPointer vNewPolyData = vtkSmartPointer::New(); vtkSmartPointer vNewLines = vtkSmartPointer::New(); vtkSmartPointer vNewPoints = vtkSmartPointer::New(); vtkSmartPointer weights = vtkSmartPointer::New(); /* Check wether all Streamlines of the bundles are labeled... If all are labeled Skip for Loop*/ unsigned int counter = 0; for (int i=0; iGetFiberPolyData()->GetNumberOfCells(); i++) { vtkCell* cell = fib->GetFiberPolyData()->GetCell(i); auto numPoints = cell->GetNumberOfPoints(); vtkPoints* points = cell->GetPoints(); vtkSmartPointer container = vtkSmartPointer::New(); for (unsigned int j=0; jGetPoint(j, p); vtkIdType id = vNewPoints->InsertNextPoint(p); container->GetPointIds()->InsertNextId(id); } weights->InsertValue(counter, fib->GetFiberWeight(i)); vNewLines->InsertNextCell(container); counter++; } for (int i=0; iGetFiberPolyData()->GetNumberOfCells(); i++) { vtkCell* cell = fib_true->GetFiberPolyData()->GetCell(i); auto numPoints = cell->GetNumberOfPoints(); vtkPoints* points = cell->GetPoints(); vtkSmartPointer container = vtkSmartPointer::New(); for (unsigned int j=0; jGetPoint(j, p); vtkIdType id = vNewPoints->InsertNextPoint(p); container->GetPointIds()->InsertNextId(id); } weights->InsertValue(counter, fib_true->GetFiberWeight(i)); vNewLines->InsertNextCell(container); counter++; } vNewPolyData->SetLines(vNewLines); vNewPolyData->SetPoints(vNewPoints); mitk::FiberBundle::Pointer MergedPrediction = mitk::FiberBundle::New(vNewPolyData); MergedPrediction->SetFiberWeights(weights); mitk::DataNode::Pointer node = mitk::DataNode::New(); node->SetData(MergedPrediction); node->SetName("MergedPrediction"); this->GetDataStorage()->Add(node); } void QmitkInteractiveFiberDissectionView::CleanTestArray() { mitk::FiberBundle::Pointer fib_pos = dynamic_cast(m_positiveBundleNode->GetData()); mitk::FiberBundle::Pointer fib_neg = dynamic_cast(m_negativeBundleNode->GetData()); // mitk::FiberBundle::Pointer fib = dynamic_cast(m_SelectedFB.at(0)->GetData()); mitk::FiberBundle::Pointer fib = dynamic_cast(m_testnode->GetData()); vtkCell* cur_cell; vtkCell* cur_cell2; MITK_INFO << fib_neg->GetFiberPolyData()->GetNumberOfCells(); MITK_INFO << fib_pos->GetFiberPolyData()->GetNumberOfCells(); MITK_INFO << fib->GetFiberPolyData()->GetNumberOfCells(); std::vector array; std::vector array2; // cv::parallel_for_(cv::Range(0, fib->GetFiberPolyData()->GetNumberOfCells()), [&](const cv::Range &range) // { // for (int i = range.start; i < range.end; i++) for (int i=0; iGetFiberPolyData()->GetNumberOfCells(); i++) { cur_cell = fib->GetFiberPolyData()->GetCell(i); auto numPoints = cur_cell->GetNumberOfPoints(); vtkPoints* points = cur_cell->GetPoints(); for (unsigned int j=0; jGetPoint(j, p); array.push_back(*p); } for (int ik=0; ikGetFiberPolyData()->GetNumberOfCells(); ik++) { cur_cell2 = fib_neg->GetFiberPolyData()->GetCell(ik); auto numPoints2 = cur_cell2->GetNumberOfPoints(); vtkPoints* points2 = cur_cell2->GetPoints(); for (unsigned int j2=0; j2GetPoint(j2, p2); array2.push_back(*p2); } if (array==array2) { fib->GetFiberPolyData()->DeleteCell(i); MITK_INFO << "Delete Cell"; } array2.clear(); } for (int ik=0; ikGetFiberPolyData()->GetNumberOfCells(); ik++) { cur_cell2 = fib_pos->GetFiberPolyData()->GetCell(ik); auto numPoints2 = cur_cell2->GetNumberOfPoints(); vtkPoints* points2 = cur_cell2->GetPoints(); for (unsigned int j2=0; j2GetPoint(j2, p2); array2.push_back(*p2); } if (array==array2) { fib->GetFiberPolyData()->DeleteCell(i); MITK_INFO << "Delete Cell"; } array2.clear(); } array.clear(); } // }); // fib->GetFiberPolyData()->RemoveDeletedCells(); MITK_INFO << fib->GetFiberPolyData()->GetNumberOfCells(); } void QmitkInteractiveFiberDissectionView::ResetClassifier() { m_IterationCounter = 0; m_RandomExtractionCounter = 0; m_activeCycleCounter = 0; m_createdStreamlineCounter = 0; classifier.reset(); this->GetDataStorage()->Remove(m_positiveBundleNode); this->GetDataStorage()->Remove(m_negativeBundleNode); this->GetDataStorage()->Remove(m_negativeBundleNode); m_positiveBundleNode = NULL; m_negativeBundleNode = NULL; m_negativeBundleNode = NULL; m_positiveBundle = NULL; m_negativeBundle = NULL; m_negativeBundle = NULL; m_Controls->m_TrainClassifier->setEnabled(false); m_Controls->m_CreatePrediction->setEnabled(false); m_Controls->m_CreateUncertantyMap->setEnabled(false); } diff --git a/Plugins/org.mitk.gui.qt.diffusionimaging.fiberprocessing/src/internal/QmitkInteractiveFiberDissectionView.h b/Plugins/org.mitk.gui.qt.diffusionimaging.fiberprocessing/src/internal/QmitkInteractiveFiberDissectionView.h index 2491444..afbc609 100644 --- a/Plugins/org.mitk.gui.qt.diffusionimaging.fiberprocessing/src/internal/QmitkInteractiveFiberDissectionView.h +++ b/Plugins/org.mitk.gui.qt.diffusionimaging.fiberprocessing/src/internal/QmitkInteractiveFiberDissectionView.h @@ -1,198 +1,187 @@ /*=================================================================== The Medical Imaging Interaction Toolkit (MITK) Copyright (c) German Cancer Research Center. 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 QmitkInteractiveFiberDissectionView_h #define QmitkInteractiveFiberDissectionView_h #include "ui_QmitkInteractiveFiberDissectionViewControls.h" -#include //Pointset -#include //Pointset - -#include //Pointset -#include //Pointset #include #include -#include //Pointset #include #include #include #include #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, fiber resampling, mirroring, join and subtract bundles and much more. +\brief View to dissect fiber bundles with active learning */ class QmitkInteractiveFiberDissectionView : public QmitkAbstractView, public mitk::IRenderWindowPartListener { // 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; typedef itk::Image< float, 3 > ItkFloatImageType; static const std::string VIEW_ID; QmitkInteractiveFiberDissectionView(); virtual ~QmitkInteractiveFiberDissectionView(); - virtual void CreateQtPartControl(QWidget *parent) override; /// /// Sets the focus to an internal widget. /// virtual void SetFocus() override; protected slots: - void RenderWindowPartActivated(mitk::IRenderWindowPart* renderWindowPart) override; //Pointset - void RenderWindowPartDeactivated(mitk::IRenderWindowPart* renderWindowPart) override; //Pointset - void OnAddPointSetClicked();//Pointset void CreateStreamline(); void RemovefromBundle( bool checked ); void RemovefromBundleBrush( bool checked ); void ExtractRandomFibersFromTractogram(); void StartAlgorithm(); void CreatePredictionNode(); void CreateCertainNode(); void CreateUncertaintySampleNode(); void CreateDistanceSampleNode(); void RemovefromUncertainty( bool checked ); void RemovefromUncertaintyBrush( bool checked ); void RemovefromDistance( bool checked ); void RemovefromPrediction( bool checked ); void RemovefromPredictionBrush( bool checked ); void RemovefromSelection( bool checked ); void ResampleTractogram(); void RandomPrototypes(); void SFFPrototypes(); void StartValidation(); void AutomaticLabelling(); void RemoveCertainData(); void ResetClassifier(); void UpdateGui(); ///< update button activity etc. dpending on current datamanager selection protected: - void OnCurrentSelectionChanged(QmitkSingleNodeSelectionWidget::NodeList nodes);//Pointset virtual void OnSelectionChanged(berry::IWorkbenchPart::Pointer part, const QList& nodes) override; void OnEndInteraction(); void CreateStreamlineInteractor(); void CreateStreamlineInteractorBrush(); void CleanTestArray(); Ui::QmitkInteractiveFiberDissectionViewControls* m_Controls; int m_IterationCounter; ///< used for data node naming int m_RandomExtractionCounter; ///< used for random extracton of different Streamlines int m_activeCycleCounter; int m_newpos; int m_newneg; int m_startneg; int m_createdStreamlineCounter; int m_uncCounter; // int m_thresh2; std::vector m_SelectedFB; ///< selected fiber bundle nodes mitk::DataNode::Pointer m_testnode; // mitk::DataNode::Pointer m_trainbundle; mitk::Image::Pointer m_SelectedImage; mitk::DataNode::Pointer m_SelectedPS; mitk::DataNode::Pointer m_SelectedImageNode; mitk::FiberBundle::Pointer m_positiveBundle; mitk::FiberBundle::Pointer m_newfibersBundle; mitk::FiberBundle::Pointer m_negativeBundle; mitk::FiberBundle::Pointer m_Prediction; mitk::FiberBundle::Pointer m_CertainPlus; mitk::FiberBundle::Pointer m_CertainMinus; mitk::FiberBundle::Pointer m_CertainBetweenPlus; mitk::FiberBundle::Pointer m_CertainBetweenMinus; mitk::FiberBundle::Pointer m_UncertaintyLabel; mitk::FiberBundle::Pointer m_DistanceLabel; mitk::DataNode::Pointer m_positiveBundleNode; mitk::DataNode::Pointer m_newfibersBundleNode; mitk::DataNode::Pointer m_negativeBundleNode; mitk::DataNode::Pointer m_PredictionNode; mitk::DataNode::Pointer m_CertainPlusNode; mitk::DataNode::Pointer m_CertainMinusNode; mitk::DataNode::Pointer m_CertainBetweenPlusNode; mitk::DataNode::Pointer m_CertainBetweenMinusNode; mitk::DataNode::Pointer m_UncertaintyLabelNode; mitk::DataNode::Pointer m_DistanceLabelNode; vtkSmartPointer m_positiveFibersData; vtkSmartPointer m_newfibersFibersData; mitk::DataNode::Pointer circleNode; vtkSmartPointer m_picker1; mitk::StreamlineInteractor::Pointer m_StreamlineInteractor; mitk::StreamlineInteractorBrush::Pointer m_StreamlineInteractorBrush; std::shared_ptr< mitk::StreamlineFeatureExtractor > classifier; std::shared_ptr< mitk::StreamlineFeatureExtractor > validater; std::vector> m_metrics; std::vector> m_index; }; #endif // _QMITKFIBERTRACKINGVIEW_H_INCLUDED diff --git a/Plugins/org.mitk.gui.qt.diffusionimaging.fiberprocessing/src/internal/QmitkInteractiveFiberDissectionViewControls.ui b/Plugins/org.mitk.gui.qt.diffusionimaging.fiberprocessing/src/internal/QmitkInteractiveFiberDissectionViewControls.ui index 5a53e8f..ea99477 100644 --- a/Plugins/org.mitk.gui.qt.diffusionimaging.fiberprocessing/src/internal/QmitkInteractiveFiberDissectionViewControls.ui +++ b/Plugins/org.mitk.gui.qt.diffusionimaging.fiberprocessing/src/internal/QmitkInteractiveFiberDissectionViewControls.ui @@ -1,1105 +1,975 @@ QmitkInteractiveFiberDissectionViewControls 0 0 417 711 Form QCommandLinkButton:disabled { border: none; } QGroupBox { background-color: transparent; } 9 9 9 9 true true Label Fibers QFrame::NoFrame - 4 + 1 6 0 0 399 439 Generate Prototypes 0 0 0 0 381 359 Defaults Extract from SFF Extraction Qt::Vertical 20 40 0 0 273 171 Advanced Settings Number of Prototypes 10 200 100 Random Extraction Resample Bundle true Use Standard Prototypes true Choose own Prototypes Qt::Vertical 20 170 0 0 399 439 Fiber Creation - - - QFrame::StyledPanel - - - QFrame::Raised + + + Create Streamline - - - - - Selected Streamline Pointset - - - - - - - Qt::Horizontal - - - - 40 - 20 - - - - - - - - Streamline Points - - - - - - - - - Qt::Vertical - - - - 20 - 40 - - - - - - - - - - - Qt::Horizontal - - - - 40 - 20 - - - - - - - - Qt::Horizontal - - - - 40 - 20 - - - - - - - - Add new Streamline Pointset - - - - - - - - 0 - 0 - - - - - 0 - 40 - - - - - - - - Qt::Vertical - - - - 20 - 40 - - - - - - - - Create Streamline - - - - true 0 0 399 439 Fiber Labelling Dissect/Eraze Fibers by Erasion and Highlighting true ArrowCursor QFrame::NoFrame QFrame::Raised Label individual Streamlines Qt::Vertical 20 40 Streamlines to be labeled QFrame::StyledPanel QFrame::Raised Label Streamlines Unlabel: Leftclick + shift/alt Reject: Rightclick + shift 30 30 :/org.mitk.gui.qt.diffusionimaging.fiberprocessing/resources/eraze.png:/org.mitk.gui.qt.diffusionimaging.fiberprocessing/resources/eraze.png 32 32 true Qt::Horizontal 40 20 Accept: Rightclick + alt 1 2000 20 Random Streamlines Qt::Vertical 20 40 Add 30 30 :/org.mitk.gui.qt.diffusionimaging.fiberprocessing/resources/brush.png:/org.mitk.gui.qt.diffusionimaging.fiberprocessing/resources/brush.png 32 32 true 0 0 399 439 Active Learning 0 0 381 391 QFrame::StyledPanel QFrame::Raised 0 0 0 361 309 Default 30 30 :/org.mitk.gui.qt.diffusionimaging.fiberprocessing/resources/brush.png:/org.mitk.gui.qt.diffusionimaging.fiberprocessing/resources/brush.png 32 32 true Qt::Horizontal 57 20 30 30 :/org.mitk.gui.qt.diffusionimaging.fiberprocessing/resources/eraze.png:/org.mitk.gui.qt.diffusionimaging.fiberprocessing/resources/eraze.png 32 32 true Add 30 30 :/org.mitk.gui.qt.diffusionimaging.fiberprocessing/resources/eraze.png:/org.mitk.gui.qt.diffusionimaging.fiberprocessing/resources/eraze.png 32 32 true Train Classifier 30 30 :/org.mitk.gui.qt.diffusionimaging.fiberprocessing/resources/brush.png:/org.mitk.gui.qt.diffusionimaging.fiberprocessing/resources/brush.png 32 32 true Reset Classifier Qt::Horizontal 40 20 Annotate from Prediction Qt::Horizontal 57 20 Annotate ShowPrediction 1 2000 0 10 Qt::Horizontal 57 20 0 0 337 173 Advanced Label from Current Selection Create Uncertanty Map Qt::Horizontal 40 20 Unc_dis_Label Add 100 95 Certain Data 100 1 500 20 Dist: to label Qt::Vertical 20 40 Label Remove 0 0 399 439 Validation 10 20 351 371 QFrame::StyledPanel QFrame::Raised Qt::Vertical 20 40 Prediction Groundtrouth Validate Merge Prediction with Labled Data Please Select Input Data Training Fiber Bundle: <html><head/><body><p><span style=" color:#ff0000;">mandatory</span></p></body></html> true Input DTI Selectd Fiber Bundle: QmitkDataStorageComboBox QComboBox
QmitkDataStorageComboBox.h
 - - QmitkSingleNodeSelectionWidget - QWidget -
QmitkSingleNodeSelectionWidget.h
- 1 - - - QmitkPointListWidget - QWidget -
QmitkPointListWidget.h
-