diff --git a/Modules/Bundles/org.mitk.gui.qt.diffusionimaging/src/internal/QmitkFiberBundleDeveloperView.cpp b/Modules/Bundles/org.mitk.gui.qt.diffusionimaging/src/internal/QmitkFiberBundleDeveloperView.cpp index 288b69e0bd..aefb54c38e 100644 --- a/Modules/Bundles/org.mitk.gui.qt.diffusionimaging/src/internal/QmitkFiberBundleDeveloperView.cpp +++ b/Modules/Bundles/org.mitk.gui.qt.diffusionimaging/src/internal/QmitkFiberBundleDeveloperView.cpp @@ -1,797 +1,798 @@ /*========================================================================= Program: Medical Imaging & Interaction Toolkit Language: C++ Date: $Date: 2010-03-31 16:40:27 +0200 (Mi, 31 Mrz 2010) $ Version: $Revision: 21975 $ Copyright (c) German Cancer Research Center, Division of Medical and Biological Informatics. All rights reserved. See MITKCopyright.txt or http://www.mitk.org/copyright.html for details. This software is distributed WITHOUT ANY WARRANTY; without even the implied warranty of MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the above copyright notices for more information. =========================================================================*/ //=========FOR TESTING========== //random generation, number of points equal requested points // Blueberry application and interaction service #include #include // Qmitk #include "QmitkFiberBundleDeveloperView.h" #include // Qt #include // MITK //#include //for fiberStructure //===needed when timeSlicedGeometry is null to invoke rendering mechansims ==== #include #include // VTK #include //for randomized FiberStructure #include //for fiberStructure #include //for fiberStructure #include //for geometry //ITK #include /*=================================================================================== * THIS METHOD IMPLEMENTS THE ACTIONS WHICH SHALL BE EXECUTED by the according THREAD * --generate FiberIDs--*/ QmitkFiberIDWorker::QmitkFiberIDWorker(QThread* hostingThread, Package4WorkingThread itemPackage) : m_itemPackage(itemPackage), m_hostingThread(hostingThread) { } void QmitkFiberIDWorker::run() { //accurate time measurement using ITK timeProbe itk::TimeProbe clock; clock.Start(); + m_itemPackage.st_Controls->infoTimerGenerateFiberIds->setText(QString::number(0)); //set GUI representation of timer to 0 + m_itemPackage.st_idGenerateTimer->start(); m_itemPackage.st_FBX->DoGenerateFiberIds(); clock.Stop(); m_itemPackage.st_idGenerateTimer->stop(); //stop fancy Qt-timer in GUI m_itemPackage.st_Controls->infoTimerGenerateFiberIds->setText( QString::number(clock.GetTotal()) ); + delete m_itemPackage.st_idGenerateTimer; // fancy timer is not needed anymore m_hostingThread->quit(); } //=================================================================================== /*=================================================================================== * THIS METHOD IMPLEMENTS THE ACTIONS WHICH SHALL BE EXECUTED by the according THREAD */ QmitkFiberGenerateRandomWorker::QmitkFiberGenerateRandomWorker(QThread* hostingThread, Package4WorkingThread itemPackage) : m_itemPackage(itemPackage), m_hostingThread(hostingThread) { } void QmitkFiberGenerateRandomWorker::run() { //accurate time measurement using ITK timeProbe //itk::TimeProbe clock; //clock.Start(); MITK_INFO << "GENERATE RANDOM WORKER .. run()"; // generateRandomFibers int numOfFibers = m_itemPackage.st_Controls->boxFiberNumbers->value(); int distrRadius = m_itemPackage.st_Controls->boxDistributionRadius->value(); int numOfPoints = numOfFibers * distrRadius; // // std::vector< std::vector > fiberStorage; for (int i=0; i a; fiberStorage.push_back( a ); } /* Generate Point Cloud */ vtkSmartPointer randomPoints = vtkSmartPointer::New(); randomPoints->SetCenter(0.0, 0.0, 0.0); randomPoints->SetNumberOfPoints(numOfPoints); randomPoints->SetRadius(distrRadius); randomPoints->Update(); // vtkPoints* pnts = randomPoints->GetOutput()->GetPoints(); // // /*====== checkpoint: compare initialized and required points ============================= INCLUDE IN TEST */ // if (numOfPoints != pnts->GetNumberOfPoints()) { // MITK_INFO << "VTK POINT ERROR, WRONG AMOUNT OF GENRERATED POINTS... COULD BE VTK BUG OR BITFLIP DUE TO COSMIC RADIATION!"; // return ; // }/* ================================= */ // // /* ASSIGN EACH POINT TO A RANDOM FIBER */ srand((unsigned)time(0)); // init randomizer for (int i=0; iGetNumberOfPoints(); ++i) { //generate random number between 0 and numOfFibers-1 int random_integer; random_integer = (rand()%numOfFibers); //add current point to random fiber fiberStorage.at(random_integer).push_back(i); // MITK_INFO << "point" << i << " |" << pnts->GetPoint(random_integer)[0] << "|" << pnts->GetPoint(random_integer)[1]<< "|" << pnts->GetPoint(random_integer)[2] << "| into fiber" << random_integer; } //=====timer measurement==== itk::TimeProbe clock; clock.Start(); //========================== /* GENERATE VTK POLYLINES OUT OF FIBERSTORAGE */ vtkSmartPointer linesCell = vtkSmartPointer::New(); // Host vtkPolyLines linesCell->Allocate(pnts->GetNumberOfPoints()*2); //allocate for each cellindex also space for the pointId, e.g. [idx | pntID] for (unsigned long i=0; i singleFiber = fiberStorage.at(i); vtkSmartPointer fiber = vtkSmartPointer::New(); fiber->GetPointIds()->SetNumberOfIds((int)singleFiber.size()); for (unsigned long si=0; siGetPointIds()->SetId( si, singleFiber.at(si) ); } linesCell->InsertNextCell(fiber); } /* =======checkpoint for cellarray allocation ==========*/ if ( (linesCell->GetSize()/pnts->GetNumberOfPoints()) != 2 ) { MITK_INFO << "RANDOM FIBER ALLOCATION CAN NOT BE TRUSTED ANYMORE! Correct leak or remove command: linesCell->Allocate(pnts->GetNumberOfPoints()*2) but be aware of possible loss in performance."; }/* ====================================================*/ /* HOSTING POLYDATA FOR RANDOM FIBERSTRUCTURE */ vtkPolyData* PDRandom = vtkPolyData::New(); PDRandom->SetPoints(pnts); PDRandom->SetLines(linesCell); //====timer measurement======== clock.Stop(); m_itemPackage.st_Controls->infoTimerGenerateFiberBundle->setText( QString::number(clock.GetTotal()) ); MITK_INFO << "=====Assambling random Fibers to Polydata======\nMean: " << clock.GetMean() << std::endl; MITK_INFO << "Total: " << clock.GetTotal() << std::endl; MITK_INFO << "in thread pnts: "<< PDRandom->GetNumberOfPoints() << " in thread lines: " << PDRandom->GetNumberOfLines(); //============================= // write random generated fiberstructure to datastorage (m_itemPackage.st_host->*m_itemPackage.st_pntr_to_Method_PutFibersToDataStorage)(PDRandom); // clock.Stop(); // m_itemPackage.st_idGenerateTimer->stop(); //stop fancy Qt-timer in GUI // m_itemPackage.st_Controls->infoTimerGenerateFiberIds->setText( QString::number(clock.GetTotal()) ); m_hostingThread->quit(); } //=================================================================================== // ========= HERE STARTS THE ACTUAL FIBERBUNDLE DEVELOPER VIEW IMPLEMENTATION ====== const std::string QmitkFiberBundleDeveloperView::VIEW_ID = "org.mitk.views.fiberbundledeveloper"; const std::string id_DataManager = "org.mitk.views.datamanager"; using namespace berry; QmitkFiberBundleDeveloperView::QmitkFiberBundleDeveloperView() : QmitkFunctionality() , m_Controls( 0 ) , m_MultiWidget( NULL ) { m_hostThread = new QThread; m_threadInProgress = false; } // Destructor QmitkFiberBundleDeveloperView::~QmitkFiberBundleDeveloperView() { m_FiberBundleX->Delete(); delete m_hostThread; delete m_FiberIDGenerator; - - // m_idGenerateTimer: no need to delete, is not initialized using "new" - + } void QmitkFiberBundleDeveloperView::CreateQtPartControl( QWidget *parent ) { // build up qt view, unless already done in QtDesigner, etc. if ( !m_Controls ) { // create GUI widgets from the Qt Designer's .ui file m_Controls = new Ui::QmitkFiberBundleDeveloperViewControls; m_Controls->setupUi( parent ); /*=========INITIALIZE BUTTON CONFIGURATION ================*/ m_Controls->radioButton_directionX->setEnabled(false); m_Controls->radioButton_directionY->setEnabled(false); m_Controls->radioButton_directionZ->setEnabled(false); m_Controls->buttonGenerateFiberIds->setEnabled(false); m_Controls->buttonGenerateFibers->setEnabled(true); m_Controls->buttonColorFibers->setEnabled(false);//not yet implemented m_Controls->buttonSMFibers->setEnabled(false);//not yet implemented m_Controls->buttonVtkDecimatePro->setEnabled(false);//not yet implemented m_Controls->buttonVtkSmoothPD->setEnabled(false);//not yet implemented m_Controls->buttonGenerateTubes->setEnabled(false);//not yet implemented connect( m_Controls->buttonGenerateFibers, SIGNAL(clicked()), this, SLOT(DoGenerateFibers()) ); connect( m_Controls->buttonGenerateFiberIds, SIGNAL(pressed()), this, SLOT(DoGenerateFiberIDs()) ); connect( m_Controls->radioButton_directionRandom, SIGNAL(clicked()), this, SLOT(DoUpdateGenerateFibersWidget()) ); connect( m_Controls->radioButton_directionX, SIGNAL(clicked()), this, SLOT(DoUpdateGenerateFibersWidget()) ); connect( m_Controls->radioButton_directionY, SIGNAL(clicked()), this, SLOT(DoUpdateGenerateFibersWidget()) ); connect( m_Controls->radioButton_directionZ, SIGNAL(clicked()), this, SLOT(DoUpdateGenerateFibersWidget()) ); connect( m_Controls->toolBox, SIGNAL(currentChanged ( int ) ), this, SLOT(SelectionChangedToolBox(int)) ); } // Checkpoint for fiber ORIENTATION if ( m_DirectionRadios.empty() ) { m_DirectionRadios.insert(0, m_Controls->radioButton_directionRandom); m_DirectionRadios.insert(1, m_Controls->radioButton_directionX); m_DirectionRadios.insert(2, m_Controls->radioButton_directionY); m_DirectionRadios.insert(3, m_Controls->radioButton_directionZ); } // set GUI elements of FiberGenerator to according configuration DoUpdateGenerateFibersWidget(); } /* THIS METHOD UPDATES ALL GUI ELEMENTS OF QGroupBox DEPENDING ON CURRENTLY SELECTED * RADIO BUTTONS */ void QmitkFiberBundleDeveloperView::DoUpdateGenerateFibersWidget() { //get selected radioButton QString fibDirection; //stores the object_name of selected radiobutton QVector::const_iterator i; for (i = m_DirectionRadios.begin(); i != m_DirectionRadios.end(); ++i) { QRadioButton* rdbtn = *i; if (rdbtn->isChecked()) fibDirection = rdbtn->objectName(); } if ( fibDirection == FIB_RADIOBUTTON_DIRECTION_RANDOM ) { // disable radiobuttons if (m_Controls->boxFiberMinLength->isEnabled()) m_Controls->boxFiberMinLength->setEnabled(false); if (m_Controls->labelFiberMinLength->isEnabled()) m_Controls->labelFiberMinLength->setEnabled(false); if (m_Controls->boxFiberMaxLength->isEnabled()) m_Controls->boxFiberMaxLength->setEnabled(false); if (m_Controls->labelFiberMaxLength->isEnabled()) m_Controls->labelFiberMaxLength->setEnabled(false); //enable radiobuttons if (!m_Controls->labelFibersTotal->isEnabled()) m_Controls->labelFibersTotal->setEnabled(true); if (!m_Controls->boxFiberNumbers->isEnabled()) m_Controls->boxFiberNumbers->setEnabled(true); if (!m_Controls->labelDistrRadius->isEnabled()) m_Controls->labelDistrRadius->setEnabled(true); if (!m_Controls->boxDistributionRadius->isEnabled()) m_Controls->boxDistributionRadius->setEnabled(true); } else { // disable radiobuttons if (m_Controls->labelDistrRadius->isEnabled()) m_Controls->labelDistrRadius->setEnabled(false); if (m_Controls->boxDistributionRadius->isEnabled()) m_Controls->boxDistributionRadius->setEnabled(false); //enable radiobuttons if (!m_Controls->labelFibersTotal->isEnabled()) m_Controls->labelFibersTotal->setEnabled(true); if (!m_Controls->boxFiberNumbers->isEnabled()) m_Controls->boxFiberNumbers->setEnabled(true); if (!m_Controls->boxFiberMinLength->isEnabled()) m_Controls->boxFiberMinLength->setEnabled(true); if (!m_Controls->labelFiberMinLength->isEnabled()) m_Controls->labelFiberMinLength->setEnabled(true); if (!m_Controls->boxFiberMaxLength->isEnabled()) m_Controls->boxFiberMaxLength->setEnabled(true); if (!m_Controls->labelFiberMaxLength->isEnabled()) m_Controls->labelFiberMaxLength->setEnabled(true); } } void QmitkFiberBundleDeveloperView::DoGenerateFibers() { // GET SELECTED FIBER DIRECTION QString fibDirection; //stores the object_name of selected radiobutton QVector::const_iterator i; for (i = m_DirectionRadios.begin(); i != m_DirectionRadios.end(); ++i) { QRadioButton* rdbtn = *i; if (rdbtn->isChecked()) fibDirection = rdbtn->objectName(); } // vtkPolyData* output; // FiberPD stores the generated PolyData... going to be generated in thread if ( fibDirection == FIB_RADIOBUTTON_DIRECTION_RANDOM ) { // build polydata with random lines and fibers // output = GenerateVtkFibersRandom(); } else if ( fibDirection == FIB_RADIOBUTTON_DIRECTION_X ) { // build polydata with XDirection fibers //output = GenerateVtkFibersDirectionX(); } else if ( fibDirection == FIB_RADIOBUTTON_DIRECTION_Y ) { // build polydata with YDirection fibers // output = GenerateVtkFibersDirectionY(); } else if ( fibDirection == FIB_RADIOBUTTON_DIRECTION_Z ) { // build polydata with ZDirection fibers // output = GenerateVtkFibersDirectionZ(); } } void QmitkFiberBundleDeveloperView::PutFibersToDataStorage( vtkPolyData* threadOutput) { MITK_INFO << "YEHAAAAAAAAA WHAT A GREAT DAY!!!!!!"; MITK_INFO << "lines: " << threadOutput->GetNumberOfLines() << "pnts: " << threadOutput->GetNumberOfPoints(); //qthread mutex lock mitk::FiberBundleX::Pointer FB = mitk::FiberBundleX::New(); FB->SetFibers(threadOutput); FB->SetGeometry(this->GenerateStandardGeometryForMITK()); mitk::DataNode::Pointer FBNode; FBNode = mitk::DataNode::New(); FBNode->SetName("FiberBundleX"); FBNode->SetData(FB); FBNode->SetVisibility(true); GetDataStorage()->Add(FBNode); //output->Delete(); const mitk::PlaneGeometry * tsgeo = m_MultiWidget->GetTimeNavigationController()->GetCurrentPlaneGeometry(); if (tsgeo == NULL) { /* GetDataStorage()->Modified etc. have no effect, therefore proceed as followed below */ // get all nodes that have not set "includeInBoundingBox" to false mitk::NodePredicateNot::Pointer pred = mitk::NodePredicateNot::New(mitk::NodePredicateProperty::New("includeInBoundingBox" , mitk::BoolProperty::New(false))); mitk::DataStorage::SetOfObjects::ConstPointer rs = GetDataStorage()->GetSubset(pred); // calculate bounding geometry of these nodes mitk::TimeSlicedGeometry::Pointer bounds = GetDataStorage()->ComputeBoundingGeometry3D(rs); // initialize the views to the bounding geometry mitk::RenderingManager::GetInstance()->InitializeViews(bounds); } else { GetDataStorage()->Modified(); m_MultiWidget->RequestUpdate(); //necessary?? } //qthread mutex unlock } /* * Generate polydata of random fibers */ void QmitkFiberBundleDeveloperView::GenerateVtkFibersRandom() { struct Package4WorkingThread ItemPackageForRandomGenerator; ItemPackageForRandomGenerator.st_FBX = m_FiberBundleX; - //ItemPackageForRandomGenerator.st_idGenerateTimer = &m_idGenerateTimer; set to randomTimer ItemPackageForRandomGenerator.st_Controls = m_Controls; ItemPackageForRandomGenerator.st_host = this; ItemPackageForRandomGenerator.st_pntr_to_Method_PutFibersToDataStorage = &QmitkFiberBundleDeveloperView::PutFibersToDataStorage; m_GeneratorFibersRandom = new QmitkFiberGenerateRandomWorker(m_hostThread, ItemPackageForRandomGenerator); m_GeneratorFibersRandom->moveToThread(m_hostThread); connect(m_hostThread, SIGNAL(started()), this, SLOT( BeforeThread_GenerateFibersRandom()) ); connect(m_hostThread, SIGNAL(started()), m_GeneratorFibersRandom, SLOT(run()) ); connect(m_hostThread, SIGNAL(finished()), this, SLOT(AfterThread_GenerateFibersRandom()) ); connect(m_hostThread, SIGNAL(terminated()), this, SLOT(AfterThread_GenerateFibersRandom()) ); m_hostThread->start(QThread::LowestPriority); } void QmitkFiberBundleDeveloperView::BeforeThread_GenerateFibersRandom() { } void QmitkFiberBundleDeveloperView::AfterThread_GenerateFibersRandom() { m_threadInProgress = false; disconnect(m_hostThread, 0, 0, 0); m_hostThread->disconnect(); } vtkSmartPointer QmitkFiberBundleDeveloperView::GenerateVtkFibersDirectionX() { int numOfFibers = m_Controls->boxFiberNumbers->value(); vtkSmartPointer linesCell = vtkSmartPointer::New(); vtkSmartPointer points = vtkSmartPointer::New(); //insert Origin point, this point has index 0 in point array double originX = 0.0; double originY = 0.0; double originZ = 0.0; //after each iteration the origin of the new fiber increases //here you set which direction is affected. double increaseX = 0.0; double increaseY = 1.0; double increaseZ = 0.0; //walk along X axis //length of fibers increases in each iteration for (int i=0; i newFiber = vtkSmartPointer::New(); newFiber->GetPointIds()->SetNumberOfIds(i+2); //create starting point and add it to pointset points->InsertNextPoint(originX + (double)i * increaseX , originY + (double)i * increaseY, originZ + (double)i * increaseZ); //add starting point to fiber newFiber->GetPointIds()->SetId(0,points->GetNumberOfPoints()-1); //insert remaining points for fiber for (int pj=0; pj<=i ; ++pj) { //generate next point on X axis points->InsertNextPoint( originX + (double)pj+1 , originY + (double)i * increaseY, originZ + (double)i * increaseZ ); newFiber->GetPointIds()->SetId(pj+1,points->GetNumberOfPoints()-1); } linesCell->InsertNextCell(newFiber); } vtkSmartPointer PDX = vtkSmartPointer::New(); PDX->SetPoints(points); PDX->SetLines(linesCell); return PDX; } vtkSmartPointer QmitkFiberBundleDeveloperView::GenerateVtkFibersDirectionY() { vtkSmartPointer PDY = vtkSmartPointer::New(); //todo return PDY; } vtkSmartPointer QmitkFiberBundleDeveloperView::GenerateVtkFibersDirectionZ() { vtkSmartPointer PDZ = vtkSmartPointer::New(); //todo return PDZ; } /* === OutSourcedMethod: THIS METHOD GENERATES ESSENTIAL GEOMETRY PARAMETERS FOR THE MITK FRAMEWORK === * WITHOUT, the rendering mechanism will ignore objects without valid Geometry * for each object, MITK requires: ORIGIN, SPACING, TRANSFORM MATRIX, BOUNDING-BOX */ mitk::Geometry3D::Pointer QmitkFiberBundleDeveloperView::GenerateStandardGeometryForMITK() { mitk::Geometry3D::Pointer geometry = mitk::Geometry3D::New(); // generate origin mitk::Point3D origin; origin[0] = 0; origin[1] = 0; origin[2] = 0; geometry->SetOrigin(origin); // generate spacing float spacing[3] = {1,1,1}; geometry->SetSpacing(spacing); // generate identity transform-matrix vtkMatrix4x4* m = vtkMatrix4x4::New(); geometry->SetIndexToWorldTransformByVtkMatrix(m); // generate boundingbox // for an usable bounding-box use gui parameters to estimate the boundingbox float bounds[] = {500, 500, 500, -500, -500, -500}; // GET SELECTED FIBER DIRECTION QString fibDirection; //stores the object_name of selected radiobutton QVector::const_iterator i; for (i = m_DirectionRadios.begin(); i != m_DirectionRadios.end(); ++i) { QRadioButton* rdbtn = *i; if (rdbtn->isChecked()) fibDirection = rdbtn->objectName(); } if ( fibDirection == FIB_RADIOBUTTON_DIRECTION_RANDOM ) { // use information about distribution parameter to calculate bounding box int distrRadius = m_Controls->boxDistributionRadius->value(); bounds[0] = distrRadius; bounds[1] = distrRadius; bounds[2] = distrRadius; bounds[3] = -distrRadius; bounds[4] = -distrRadius; bounds[5] = -distrRadius; } else { // so far only X,Y,Z directions are available MITK_INFO << "_______GEOMETRY ISSUE_____\n***BoundingBox for X, Y, Z fiber directions are not optimized yet!***"; int maxFibLength = m_Controls->boxFiberMaxLength->value(); bounds[0] = maxFibLength; bounds[1] = maxFibLength; bounds[2] = maxFibLength; bounds[3] = -maxFibLength; bounds[4] = -maxFibLength; bounds[5] = -maxFibLength; } geometry->SetFloatBounds(bounds); geometry->SetImageGeometry(true); //?? return geometry; } void QmitkFiberBundleDeveloperView::UpdateFiberIDTimer() { //MAKE SURE by yourself THAT NOTHING ELSE THAN A NUMBER IS SET IN THAT LABEL QString crntValue = m_Controls->infoTimerGenerateFiberIds->text(); int tmpVal = crntValue.toInt(); m_Controls->infoTimerGenerateFiberIds->setText(QString::number(++tmpVal)); m_Controls->infoTimerGenerateFiberIds->update(); } /* Initialie ID dataset in FiberBundleX */ void QmitkFiberBundleDeveloperView::DoGenerateFiberIDs() { + /* ===== TIMER CONFIGURATIONS for visual effect ====== + * start and stop is called in Thread */ + QTimer *localTimer = new QTimer; // timer must be initialized here, otherwise timer is not fancy enough + localTimer->setInterval( 10 ); + connect( localTimer, SIGNAL(timeout()), this, SLOT(UpdateFiberIDTimer()) ); + + + // pack items which are needed by thread processing struct Package4WorkingThread FiberIdPackage; FiberIdPackage.st_FBX = m_FiberBundleX; - FiberIdPackage.st_idGenerateTimer = &m_idGenerateTimer; + FiberIdPackage.st_idGenerateTimer = localTimer; FiberIdPackage.st_Controls = m_Controls; - /* ===== TIMER CONFIGURATIONS for visual effect ====== - * start and stop is called in Thread pre- and postprocessing methods */ - m_idGenerateTimer.setInterval( 10 ); - connect( &m_idGenerateTimer, SIGNAL(timeout()), this, SLOT(UpdateFiberIDTimer()) ); - + if (m_threadInProgress) return; //maybe popup window saying, working thread still in progress...pls wait // THREAD CONFIGURATION m_FiberIDGenerator = new QmitkFiberIDWorker(m_hostThread, FiberIdPackage); m_FiberIDGenerator->moveToThread(m_hostThread); connect(m_hostThread, SIGNAL(started()), this, SLOT( BeforeThread_IdGenerate()) ); connect(m_hostThread, SIGNAL(started()), m_FiberIDGenerator, SLOT(run())); connect(m_hostThread, SIGNAL(finished()), this, SLOT(AfterThread_IdGenerate())); connect(m_hostThread, SIGNAL(terminated()), this, SLOT(AfterThread_IdGenerate())); m_hostThread->start(QThread::LowestPriority); // m_Controls->infoTimerGenerateFiberIds->setText(QString::number(clock.GetTotal())); } void QmitkFiberBundleDeveloperView::BeforeThread_IdGenerate() { - m_Controls->infoTimerGenerateFiberIds->setText(QString::number(0)); //set GUI representation of timer to 0 m_threadInProgress = true; - m_idGenerateTimer.start(); } void QmitkFiberBundleDeveloperView::AfterThread_IdGenerate() { - if (m_idGenerateTimer.isActive()) - m_idGenerateTimer.stop(); + m_threadInProgress = false; disconnect(m_hostThread, 0, 0, 0); m_hostThread->disconnect(); } /* THE WORKER ACCESS THIS METHOD TO PASS GENERATED FIBERBUNDLE * TO DATASTORAGE */ void QmitkFiberBundleDeveloperView::SetGeneratedFBX() { } void QmitkFiberBundleDeveloperView::ResetFiberInfoWidget() { if (m_Controls->infoAnalyseNumOfFibers->isEnabled()) { m_Controls->infoAnalyseNumOfFibers->setText("-"); m_Controls->infoAnalyseNumOfPoints->setText("-"); m_Controls->infoAnalyseNumOfFibers->setEnabled(false); } } void QmitkFiberBundleDeveloperView::FeedFiberInfoWidget() { if (!m_Controls->infoAnalyseNumOfFibers->isEnabled()) m_Controls->infoAnalyseNumOfFibers->setEnabled(true); QString numOfFibers; numOfFibers.setNum( m_FiberBundleX->GetFibers()->GetNumberOfLines() ); QString numOfPoints; numOfPoints.setNum( m_FiberBundleX->GetFibers()->GetNumberOfPoints() ); m_Controls->infoAnalyseNumOfFibers->setText( numOfFibers ); m_Controls->infoAnalyseNumOfPoints->setText( numOfPoints ); } void QmitkFiberBundleDeveloperView::SelectionChangedToolBox(int idx) { MITK_INFO << "printtoolbox: " << idx; if (m_Controls->page_FiberInfo->isVisible() && m_FiberBundleX != NULL) { FeedFiberInfoWidget(); } else { //if infolables are disabled: return //else set info back to - and set label and info to disabled if (!m_Controls->page_FiberInfo->isVisible()) { return; } else { ResetFiberInfoWidget(); } } } void QmitkFiberBundleDeveloperView::FBXDependendGUIElementsConfigurator(bool isVisible) { // ==== FIBER PROCESSING ELEMENTS ====== m_Controls->buttonGenerateFiberIds->setEnabled(isVisible); } void QmitkFiberBundleDeveloperView::StdMultiWidgetAvailable (QmitkStdMultiWidget &stdMultiWidget) { m_MultiWidget = &stdMultiWidget; } void QmitkFiberBundleDeveloperView::StdMultiWidgetNotAvailable() { m_MultiWidget = NULL; } /* OnSelectionChanged is registered to SelectionService, therefore no need to implement SelectionService Listener explicitly */ void QmitkFiberBundleDeveloperView::OnSelectionChanged( std::vector nodes ) { /* ==== reset everyhing related to FiberBundleX ====== * - variable m_FiberBundleX * - visualization of analysed fiberbundle */ m_FiberBundleX = NULL; //reset pointer, so that member does not point to depricated locations ResetFiberInfoWidget(); FBXDependendGUIElementsConfigurator(false); m_Controls->infoTimerGenerateFiberIds->setText("-"); //set GUI representation of timer to - m_Controls->infoTimerGenerateFiberBundle->setText( "-" ); //==================================================== if (nodes.empty()) return; for( std::vector::iterator it = nodes.begin(); it != nodes.end(); ++it ) { mitk::DataNode::Pointer node = *it; /* CHECKPOINT: FIBERBUNDLE*/ if( node.IsNotNull() && dynamic_cast(node->GetData()) ) { m_FiberBundleX = dynamic_cast(node->GetData()); if (m_FiberBundleX == NULL) MITK_INFO << "========ATTENTION=========\n unable to load selected FiberBundleX to FiberBundleDeveloper-plugin \n"; // ==== FIBERBUNDLE_INFO ELEMENTS ==== if ( m_Controls->page_FiberInfo->isVisible() ) FeedFiberInfoWidget(); // enable FiberBundleX related Gui Elements, such as buttons etc. FBXDependendGUIElementsConfigurator(true); } } } void QmitkFiberBundleDeveloperView::Activated() { MITK_INFO << "FB DevelopersV ACTIVATED()"; } diff --git a/Modules/Bundles/org.mitk.gui.qt.diffusionimaging/src/internal/QmitkFiberBundleDeveloperView.h b/Modules/Bundles/org.mitk.gui.qt.diffusionimaging/src/internal/QmitkFiberBundleDeveloperView.h index 9936127c69..561cb27911 100644 --- a/Modules/Bundles/org.mitk.gui.qt.diffusionimaging/src/internal/QmitkFiberBundleDeveloperView.h +++ b/Modules/Bundles/org.mitk.gui.qt.diffusionimaging/src/internal/QmitkFiberBundleDeveloperView.h @@ -1,225 +1,224 @@ /*========================================================================= Program: Medical Imaging & Interaction Toolkit Language: C++ Date: $Date: 2010-03-31 16:40:27 +0200 (Mi, 31 Mrz 2010) $ Version: $Revision: 21975 $ Copyright (c) German Cancer Research Center, Division of Medical and Biological Informatics. All rights reserved. See MITKCopyright.txt or http://www.mitk.org/copyright.html for details. This software is distributed WITHOUT ANY WARRANTY; without even the implied warranty of MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the above copyright notices for more information. =========================================================================*/ #ifndef QmitkFiberBundleDeveloperView_h #define QmitkFiberBundleDeveloperView_h #include #include #include #include "ui_QmitkFiberBundleDeveloperViewControls.h" #include #include // Qt #include #include #include // VTK #include #include #include #include #include #include class QmitkFiberBundleDeveloperView; //this include is needed for the struct element, especially for functors to QmitkFiberBundleDeveloperView /* ==== THIS STRUCT CONTAINS ALL NECESSARY VARIABLES * TO EXECUTE AND UPDATE GUI ELEMENTS DURING PROCESSING OF A THREAD * why? either you add tons of friendclasses (e.g. FiberWorker objects), or you create a package containing all items needed. Otherwise you have to set all members etc. to public! */ struct Package4WorkingThread { mitk::FiberBundleX* st_FBX; QTimer* st_idGenerateTimer; Ui::QmitkFiberBundleDeveloperViewControls* st_Controls; //functors to outdoor methods QmitkFiberBundleDeveloperView* st_host; void (QmitkFiberBundleDeveloperView::*st_pntr_to_Method_PutFibersToDataStorage) (vtkPolyData*); }; // ==================================================================== // ============= WORKER WHICH IS PASSED TO THREAD ===================== // ==================================================================== class QmitkFiberIDWorker : public QObject { Q_OBJECT public: QmitkFiberIDWorker( QThread*, Package4WorkingThread ); public slots: void run(); private: //mitk::FiberBundleX* m_FBX; Package4WorkingThread m_itemPackage; QThread* m_hostingThread; }; // ==================================================================== // ============= WORKER WHICH IS PASSED TO THREAD ===================== // ==================================================================== class QmitkFiberGenerateRandomWorker : public QObject { Q_OBJECT public: QmitkFiberGenerateRandomWorker( QThread*, Package4WorkingThread ); public slots: void run(); private: //mitk::FiberBundleX* m_FBX; Package4WorkingThread m_itemPackage; QThread* m_hostingThread; }; // ========= HERE STARTS THE ACTUAL FIBERBUNDLE DEVELOPER VIEW ======= const QString FIB_RADIOBUTTON_DIRECTION_RANDOM = "radioButton_directionRandom"; const QString FIB_RADIOBUTTON_DIRECTION_X = "radioButton_directionX"; const QString FIB_RADIOBUTTON_DIRECTION_Y = "radioButton_directionY"; const QString FIB_RADIOBUTTON_DIRECTION_Z = "radioButton_directionZ"; /*! \brief QmitkFiberBundleView \warning This application module is not yet documented. Use "svn blame/praise/annotate" and ask the author to provide basic documentation. \sa QmitkFunctionality \ingroup Functionalities */ class QmitkFiberBundleDeveloperView : 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: static const std::string VIEW_ID; QmitkFiberBundleDeveloperView(); virtual ~QmitkFiberBundleDeveloperView(); virtual void CreateQtPartControl(QWidget *parent); virtual void StdMultiWidgetAvailable (QmitkStdMultiWidget &stdMultiWidget); virtual void StdMultiWidgetNotAvailable(); virtual void Activated(); protected slots: void DoGenerateFibers(); void DoGenerateFiberIDs(); void DoUpdateGenerateFibersWidget(); void UpdateFiberIDTimer(); void SelectionChangedToolBox(int); //SLOTS FOR THREADS void BeforeThread_IdGenerate(); void AfterThread_IdGenerate(); void BeforeThread_GenerateFibersRandom(); void AfterThread_GenerateFibersRandom(); protected: /// \brief called by QmitkFunctionality when DataManager's selection has changed virtual void OnSelectionChanged( std::vector nodes ); Ui::QmitkFiberBundleDeveloperViewControls* m_Controls; QmitkStdMultiWidget* m_MultiWidget; private: /* METHODS GENERATING FIBERSTRUCTURES */ void GenerateVtkFibersRandom(); vtkSmartPointer GenerateVtkFibersDirectionX(); vtkSmartPointer GenerateVtkFibersDirectionY(); vtkSmartPointer GenerateVtkFibersDirectionZ(); void PutFibersToDataStorage( vtkPolyData* ); /* METHODS FOR FIBER PROCESSING OR PREPROCESSING */ /* HELPERMETHODS */ mitk::Geometry3D::Pointer GenerateStandardGeometryForMITK(); void ResetFiberInfoWidget(); void FeedFiberInfoWidget(); void FBXDependendGUIElementsConfigurator(bool); void SetGeneratedFBX(); //contains the selected FiberBundle mitk::FiberBundleX* m_FiberBundleX; // radiobutton groups QVector< QRadioButton* > m_DirectionRadios; QVector< QRadioButton* > m_FARadios; QVector< QRadioButton* > m_GARadios; - // timer for updating fiber id generation - QTimer m_idGenerateTimer; + // Thread based Workers which do some processing of fibers QmitkFiberIDWorker * m_FiberIDGenerator; QmitkFiberGenerateRandomWorker * m_GeneratorFibersRandom; QThread * m_hostThread; bool m_threadInProgress; }; #endif // _QMITKFIBERTRACKINGVIEW_H_INCLUDED diff --git a/Modules/DiffusionImaging/IODataStructures/FiberBundleX/mitkFiberBundleX.cpp b/Modules/DiffusionImaging/IODataStructures/FiberBundleX/mitkFiberBundleX.cpp index af98444c92..b8dd5fb014 100644 --- a/Modules/DiffusionImaging/IODataStructures/FiberBundleX/mitkFiberBundleX.cpp +++ b/Modules/DiffusionImaging/IODataStructures/FiberBundleX/mitkFiberBundleX.cpp @@ -1,310 +1,310 @@ /*========================================================================= Program: Medical Imaging & Interaction Toolkit Language: C++ Date: $Date: 2010-03-31 16:40:27 +0200 (Mi, 31 Mrz 2010) $ Version: $Revision: 21975 $ Copyright (c) German Cancer Research Center, Division of Medical and Biological Informatics. All rights reserved. See MITKCopyright.txt or http://www.mitk.org/copyright.html for details. This software is distributed WITHOUT ANY WARRANTY; without even the implied warranty of MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the above copyright notices for more information. =========================================================================*/ #include "mitkFiberBundleX.h" /* musthave */ #include // without geometry, fibers are not rendered #include #include #include #include #include // baptize array names const char* mitk::FiberBundleX::COLORCODING_ORIENTATION_BASED = "Color_Orient"; const char* mitk::FiberBundleX::COLORCODING_FA_BASED = "Color_FA"; const char* mitk::FiberBundleX::FIBER_ID_ARRAY = "Fiber_IDs"; mitk::FiberBundleX::FiberBundleX() { /* ====== GEOMETRY IS ESSENTIAL ======= * by default set a standard geometry, usually geometry is * set by the user on initializing a mitkFiberBundle Object */ // mitk::Geometry3D::Pointer fbgeometry = mitk::Geometry3D::New(); // fbgeometry->SetIdentity(); // this->SetGeometry(fbgeometry); /* ==================================== */ } mitk::FiberBundleX::~FiberBundleX() { // Memory Management m_FiberStructureData->Delete(); } /* === main input method ==== * set computed fibers from tractography algorithms */ void mitk::FiberBundleX::SetFibers(vtkPolyData* fiberPD) { if (fiberPD == NULL){ MITK_INFO << "passed FiberBundleX is NULL, exit!"; return; } m_FiberStructureData = fiberPD; } /* === main output method === * return fiberbundle as vtkPolyData * Depending on processing of input fibers, this method returns * the latest processed fibers. */ vtkPolyData* mitk::FiberBundleX::GetFibers() { return m_FiberStructureData; } /*============================================== *++++ PROCESSING WITH FIBER INFORMATION +++++++ =============================================*/ 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_FiberStructureData->GetPointData()->HasArray(COLORCODING_ORIENTATION_BASED) && m_FiberStructureData->GetNumberOfPoints() == m_FiberStructureData->GetPointData()->GetArray(COLORCODING_ORIENTATION_BASED)->GetNumberOfTuples() ) { // fiberstructure is already colorcoded MITK_INFO << " NO NEED TO REGENERATE COLORCODING!"; return; } /* Finally, execute color calculation */ vtkPoints* extrPoints = m_FiberStructureData->GetPoints(); int 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); vtkUnsignedCharArray *colorsT = vtkUnsignedCharArray::New(); colorsT->Allocate(numOfPoints * componentSize); colorsT->SetNumberOfComponents(componentSize); colorsT->SetName(COLORCODING_ORIENTATION_BASED); /* checkpoint: does polydata contain any fibers */ int numOfFibers = m_FiberStructureData->GetNumberOfLines(); if (numOfFibers < 1) { MITK_INFO << "\n ========= Number of Fibers is below 1 ========= \n"; return; } /* extract single fibers of fiberBundle */ vtkCellArray* fiberList = m_FiberStructureData->GetLines(); for (int fi=0; fiGetNextCell(numOfPoints, idList); /* single fiber checkpoints: is number of points valid */ if (numOfPoints > 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; diff1.normalize(); vnl_vector_fixed< double, 3 > diff2; diff2 = currentPntvtk - prevPntvtk; diff2.normalize(); vnl_vector_fixed< double, 3 > diff; diff = (diff1 - diff2) / 2.0; rgba[0] = (unsigned char) (255.0 * std::abs(diff[0])); rgba[1] = (unsigned char) (255.0 * std::abs(diff[1])); rgba[2] = (unsigned char) (255.0 * std::abs(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::abs(diff1[0])); rgba[1] = (unsigned char) (255.0 * std::abs(diff1[1])); rgba[2] = (unsigned char) (255.0 * std::abs(diff1[2])); rgba[3] = (unsigned char) (255.0); } else if (i==numOfPoints-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::abs(diff2[0])); rgba[1] = (unsigned char) (255.0 * std::abs(diff2[1])); rgba[2] = (unsigned char) (255.0 * std::abs(diff2[2])); rgba[3] = (unsigned char) (255.0); } colorsT->InsertTupleValue(idList[i], rgba); } //end for loop } else if (numOfPoints == 1) { /* a single point does not define a fiber (use vertex mechanisms instead */ continue; // colorsT->InsertTupleValue(0, rgba); } else { MITK_INFO << "Fiber with 0 points detected... please check your tractography algorithm!" ; continue; } }//end for loop m_FiberStructureData->GetPointData()->AddArray(colorsT); //mini test, shall be ported to MITK TESTINGS! if (colorsT->GetSize() != numOfPoints*componentSize) { MITK_INFO << "ALLOCATION ERROR IN INITIATING COLOR ARRAY"; } //===== clean memory ===== colorsT->Delete(); //======================== } void mitk::FiberBundleX::DoGenerateFiberIds() { if (m_FiberStructureData == NULL) return; -// for (int i=0; i<10000000; ++i) -// { -// if(i%500 == 0) -// MITK_INFO << i; -// } + for (int i=0; i<10000000; ++i) + { + if(i%500 == 0) + MITK_INFO << i; + } MITK_INFO << "Generating Fiber Ids"; vtkSmartPointer idFiberFilter = vtkSmartPointer::New(); idFiberFilter->SetInput(m_FiberStructureData); idFiberFilter->CellIdsOn(); // idFiberFilter->PointIdsOn(); // point id's are not needed idFiberFilter->SetIdsArrayName(FIBER_ID_ARRAY); idFiberFilter->FieldDataOn(); idFiberFilter->Update(); m_FiberIdDataSet = idFiberFilter->GetOutput(); MITK_INFO << "Generating Fiber Ids...[done] | " << m_FiberIdDataSet->GetNumberOfCells(); } /* COMPUTE BOUND OF FiberBundle */ double* mitk::FiberBundleX::DoComputeFiberStructureBoundingBox() { m_FiberStructureData->ComputeBounds(); double* bounds = m_FiberStructureData->GetBounds(); return bounds; } ////private repairMechanism for orientationbased colorcoding //bool mitk::FiberBundleX::doSelfHealingColorOrient(vtkPolyData* healMe) //{ // bool hasHealingSucceeded = false; // MITK_INFO << "FiberBundleX self repair mechanism is called, but not yet implemented"; //// check type of healMe // if (healMe == m_ImportedFiberData) // { // //todo // } // // return hasHealingSucceeded; //} /* 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( itk::DataObject *data ) { } \ No newline at end of file