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 3caadf2687..6fadf068bd 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 @@ -1,1648 +1,1651 @@ /*========================================================================= 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 #include #include //===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 //============================================== //======== W O R K E R S ____ S T A R T ======== //============================================== /*=================================================================================== * 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() { if(m_itemPackage.st_Controls->checkBoxMonitorFiberThreads->isChecked()) m_itemPackage.st_fiberThreadMonitorWorker->setThreadStatus(FBX_STATUS_RUNNING); /* MEASUREMENTS AND FANCY GUI EFFECTS * accurate time measurement using ITK timeProbe*/ itk::TimeProbe clock; clock.Start(); //set GUI representation of timer to 0, is essential for correct timer incrementation m_itemPackage.st_Controls->infoTimerGenerateFiberIds->setText(QString::number(0)); m_itemPackage.st_FancyGUITimer1->start(); //do processing m_itemPackage.st_FBX->DoGenerateFiberIds(); /* MEASUREMENTS AND FANCY GUI EFFECTS CLEANUP */ clock.Stop(); m_itemPackage.st_FancyGUITimer1->stop(); m_itemPackage.st_Controls->infoTimerGenerateFiberIds->setText( QString::number(clock.GetTotal()) ); delete m_itemPackage.st_FancyGUITimer1; // fancy timer is not needed anymore m_hostingThread->quit(); } /*=================================================================================== * THIS METHOD IMPLEMENTS THE ACTIONS WHICH SHALL BE EXECUTED by the according THREAD * -- extract fibers by given PlanarFigure --*/ QmitkFiberExtractorWorker::QmitkFiberExtractorWorker(QThread* hostingThread, Package4WorkingThread itemPackage) : m_itemPackage(itemPackage), m_hostingThread(hostingThread) { } void QmitkFiberExtractorWorker::run() { if(m_itemPackage.st_Controls->checkBoxMonitorFiberThreads->isChecked()) m_itemPackage.st_fiberThreadMonitorWorker->setThreadStatus(FBX_STATUS_RUNNING); /* MEASUREMENTS AND FANCY GUI EFFECTS * accurate time measurement using ITK timeProbe*/ itk::TimeProbe clock; clock.Start(); //set GUI representation of timer to 0, is essential for correct timer incrementation - m_itemPackage.st_Controls->infoTimerGenerateFiberIds->setText(QString::number(0)); + m_itemPackage.st_Controls->infoTimerExtractFibers->setText(QString::number(0)); m_itemPackage.st_FancyGUITimer1->start(); //do processing m_itemPackage.st_FBX->DoExtractFiberIds(m_itemPackage.st_PlanarFigure); + //generate new fiberbundle by fiber iDs +// m_itemPackage.st_FBX->CreateNewFiberbundleByIds(std::vector desiredFiberIds); + /* MEASUREMENTS AND FANCY GUI EFFECTS CLEANUP */ clock.Stop(); m_itemPackage.st_FancyGUITimer1->stop(); - m_itemPackage.st_Controls->infoTimerGenerateFiberIds->setText( QString::number(clock.GetTotal()) ); + m_itemPackage.st_Controls->infoTimerExtractFibers->setText( QString::number(clock.GetTotal()) ); delete m_itemPackage.st_FancyGUITimer1; // fancy timer is not needed anymore m_hostingThread->quit(); } /*=================================================================================== * THIS METHOD IMPLEMENTS THE ACTIONS WHICH SHALL BE EXECUTED by the according THREAD * --do color coding--*/ QmitkFiberColoringWorker::QmitkFiberColoringWorker(QThread* hostingThread, Package4WorkingThread itemPackage) : m_itemPackage(itemPackage) , m_hostingThread(hostingThread) { } void QmitkFiberColoringWorker::run() { if(m_itemPackage.st_Controls->checkBoxMonitorFiberThreads->isChecked()) m_itemPackage.st_fiberThreadMonitorWorker->setThreadStatus(FBX_STATUS_RUNNING); /* MEASUREMENTS AND FANCY GUI EFFECTS * accurate time measurement using ITK timeProbe*/ itk::TimeProbe clock; clock.Start(); //set GUI representation of timer to 0, is essential for correct timer incrementation m_itemPackage.st_Controls->infoTimerColorCoding->setText(QString::number(0)); m_itemPackage.st_FancyGUITimer1->start(); //do processing //TODO check which colorcoding option is checked! m_itemPackage.st_FBX->DoColorCodingOrientationbased(); /* MEASUREMENTS AND FANCY GUI EFFECTS CLEANUP */ clock.Stop(); m_itemPackage.st_FancyGUITimer1->stop(); m_itemPackage.st_Controls->infoTimerColorCoding->setText( QString::number(clock.GetTotal()) ); delete m_itemPackage.st_FancyGUITimer1; // fancy timer is not needed anymore m_hostingThread->quit(); } /*=================================================================================== * THIS METHOD IMPLEMENTS THE ACTIONS WHICH SHALL BE EXECUTED by the according THREAD * --generate random fibers--*/ QmitkFiberGenerateRandomWorker::QmitkFiberGenerateRandomWorker(QThread* hostingThread, Package4WorkingThread itemPackage) : m_itemPackage(itemPackage), m_hostingThread(hostingThread) { } void QmitkFiberGenerateRandomWorker::run() { if(m_itemPackage.st_Controls->checkBoxMonitorFiberThreads->isChecked()) m_itemPackage.st_fiberThreadMonitorWorker->setThreadStatus(FBX_STATUS_RUNNING); /* MEASUREMENTS AND FANCY GUI EFFECTS */ //MAKE SURE by yourself THAT NOTHING ELSE THAN A NUMBER IS SET IN THAT LABEL m_itemPackage.st_Controls->infoTimerGenerateFiberBundle->setText(QString::number(0)); m_itemPackage.st_FancyGUITimer1->start(); //do processing, 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(); /* 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; } // initialize accurate time 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 ) //e.g. size: 12, number of points:6 .... each cell hosts point ids (6 ids) + cell index for each idPoint. 6 * 2 = 12 { 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 */ vtkSmartPointer PDRandom = vtkPolyData::New(); //could also be a standard pointer instead of smartpointer cuz ther is no need to delete because data is managed in datastorage. PDRandom->SetPoints(pnts); PDRandom->SetLines(linesCell); // accurate timer measurement stop clock.Stop(); //MITK_INFO << "=====Assambling random Fibers to Polydata======\nMean: " << clock.GetMean() << " Total: " << clock.GetTotal() << std::endl; // call function to convert fiberstructure into fiberbundleX and pass it to datastorage (m_itemPackage.st_host->*m_itemPackage.st_pntr_to_Method_PutFibersToDataStorage)(PDRandom); /* MEASUREMENTS AND FANCY GUI EFFECTS CLEANUP */ m_itemPackage.st_FancyGUITimer1->stop(); m_itemPackage.st_Controls->infoTimerGenerateFiberBundle->setText( QString::number(clock.GetTotal()) ); delete m_itemPackage.st_FancyGUITimer1; // fancy timer is not needed anymore m_hostingThread->quit(); } /*=================================================================================== * THIS METHOD IMPLEMENTS THE ACTIONS WHICH SHALL BE EXECUTED by the according THREAD * --update GUI elements of thread monitor-- * implementation not thread safe, not needed so far because * there exists only 1 thread for fiberprocessing * for threadsafety, you need to implement checking mechanisms in methods "::threadFor...." */ QmitkFiberThreadMonitorWorker::QmitkFiberThreadMonitorWorker( QThread* hostingThread, Package4WorkingThread itemPackage ) : m_itemPackage(itemPackage) , m_hostingThread(hostingThread) , m_pixelstepper(10) //for next rendering call, move object 10px , m_steppingDistance(220) //use only a multiple value of pixelstepper, x-axis border for fancy stuff { //set timers m_thtimer_initMonitor = new QTimer; m_thtimer_initMonitor->setInterval(10); m_thtimer_initMonitorSetFinalPosition = new QTimer; m_thtimer_initMonitorSetFinalPosition->setInterval(10); m_thtimer_initMonitorSetMasks = new QTimer; m_thtimer_initMonitorSetFinalPosition->setInterval(10); m_thtimer_threadStarted = new QTimer; m_thtimer_threadStarted->setInterval(50); m_thtimer_threadFinished = new QTimer; m_thtimer_threadFinished->setInterval(50); m_thtimer_threadTerminated = new QTimer; m_thtimer_threadTerminated->setInterval(50); connect (m_thtimer_initMonitor, SIGNAL( timeout()), this, SLOT( fancyMonitorInitialization() ) ); connect ( m_thtimer_initMonitorSetFinalPosition, SIGNAL( timeout() ), this, SLOT( fancyMonitorInitializationFinalPos() ) ); connect ( m_thtimer_initMonitorSetMasks, SIGNAL( timeout() ), this, SLOT( fancyMonitorInitializationMask() ) ); connect (m_thtimer_threadStarted, SIGNAL( timeout()), this, SLOT( fancyTextFading_threadStarted() ) ); connect (m_thtimer_threadFinished, SIGNAL( timeout()), this, SLOT( fancyTextFading_threadFinished() ) ); connect (m_thtimer_threadTerminated, SIGNAL( timeout()), this, SLOT( fancyTextFading_threadTerminated() ) ); //first, the current text shall turn transparent m_decreaseOpacity_threadStarted = true; m_decreaseOpacity_threadFinished = true; m_decreaseOpacity_threadTerminated = true; } void QmitkFiberThreadMonitorWorker::run() { } void QmitkFiberThreadMonitorWorker::initializeMonitor() { //fancy configuration of animation start mitk::Point2D pntOpen; pntOpen[0] = 118; pntOpen[1] = 10; mitk::Point2D headPos; headPos[0] = 19; headPos[1] = 10; mitk::Point2D statusPos; statusPos[0] = 105; statusPos[1] = 23; mitk::Point2D startedPos; startedPos[0] = 68; startedPos[1] = 10; mitk::Point2D finishedPos; finishedPos[0] = 143; finishedPos[1] = 10; mitk::Point2D terminatedPos; terminatedPos[0] = 240; terminatedPos[1] = 10; m_itemPackage.st_FBX_Monitor->setBracketClosePosition(pntOpen); m_itemPackage.st_FBX_Monitor->setBracketOpenPosition(pntOpen); m_itemPackage.st_FBX_Monitor->setHeadingPosition(headPos); m_itemPackage.st_FBX_Monitor->setMaskPosition(headPos); m_itemPackage.st_FBX_Monitor->setStatusPosition(statusPos); m_itemPackage.st_FBX_Monitor->setStartedPosition(startedPos); m_itemPackage.st_FBX_Monitor->setFinishedPosition(finishedPos); m_itemPackage.st_FBX_Monitor->setTerminatedPosition(terminatedPos); m_thtimer_initMonitor->start(); } void QmitkFiberThreadMonitorWorker::setThreadStatus(QString status) { m_itemPackage.st_FBX_Monitor->setStatus(status); m_itemPackage.st_ThreadMonitorDataNode->Modified(); m_itemPackage.st_MultiWidget->RequestUpdate(); } /* Methods to set status of running threads * Following three methods are usually called - before a thread starts and - a thread is finished or terminated */ void QmitkFiberThreadMonitorWorker::threadForFiberProcessingStarted() { if(!m_thtimer_threadStarted->isActive()) { m_thtimer_threadStarted->start(); } else { //fast change without fancy stuff, needed to keep threaddebugger info up to date int counter = m_itemPackage.st_FBX_Monitor->getStarted(); m_itemPackage.st_FBX_Monitor->setStarted(++counter); } } void QmitkFiberThreadMonitorWorker::threadForFiberProcessingFinished() { if(!m_thtimer_threadFinished->isActive()) { m_thtimer_threadFinished->start(); } else { //fast change without fancy stuff int counter = m_itemPackage.st_FBX_Monitor->getFinished(); m_itemPackage.st_FBX_Monitor->setFinished(++counter); } } void QmitkFiberThreadMonitorWorker::threadForFiberProcessingTerminated() { if(!m_thtimer_threadTerminated->isActive()) { m_thtimer_threadTerminated->start(); } else { //fast change without fancy stuff int counter = m_itemPackage.st_FBX_Monitor->getTerminated(); m_itemPackage.st_FBX_Monitor->setTerminated(++counter); } } /* Helper methods for fancy fading efx for thread monitor */ void QmitkFiberThreadMonitorWorker::fancyTextFading_threadStarted() { if (m_decreaseOpacity_threadStarted) { int startedOpacity = m_itemPackage.st_FBX_Monitor->getStartedOpacity(); m_itemPackage.st_FBX_Monitor->setStartedOpacity( --startedOpacity ); if (startedOpacity == 0) { int counter = m_itemPackage.st_FBX_Monitor->getStarted(); m_itemPackage.st_FBX_Monitor->setStarted(++counter); m_decreaseOpacity_threadStarted = false; } m_itemPackage.st_ThreadMonitorDataNode->Modified(); m_itemPackage.st_MultiWidget->RequestUpdate(); } else { int startedOpacity = m_itemPackage.st_FBX_Monitor->getStartedOpacity(); m_itemPackage.st_FBX_Monitor->setStartedOpacity( ++startedOpacity ); if (startedOpacity >= 10) { m_thtimer_threadStarted->stop(); m_decreaseOpacity_threadStarted = true; //set back to true, cuz next iteration shall decrease opacity as well } m_itemPackage.st_ThreadMonitorDataNode->Modified(); m_itemPackage.st_MultiWidget->RequestUpdate(); } } void QmitkFiberThreadMonitorWorker::fancyTextFading_threadFinished() { if (m_decreaseOpacity_threadFinished) { int finishedOpacity = m_itemPackage.st_FBX_Monitor->getFinishedOpacity(); m_itemPackage.st_FBX_Monitor->setFinishedOpacity( --finishedOpacity ); if (finishedOpacity == 0) { int counter = m_itemPackage.st_FBX_Monitor->getFinished(); m_itemPackage.st_FBX_Monitor->setFinished(++counter); m_decreaseOpacity_threadFinished = false; } m_itemPackage.st_ThreadMonitorDataNode->Modified(); m_itemPackage.st_MultiWidget->RequestUpdate(); } else { int finishedOpacity = m_itemPackage.st_FBX_Monitor->getFinishedOpacity(); m_itemPackage.st_FBX_Monitor->setFinishedOpacity( ++finishedOpacity ); if (finishedOpacity >= 10) { m_thtimer_threadFinished->stop(); m_decreaseOpacity_threadFinished = true; //set back to true, cuz next iteration shall decrease opacity as well } m_itemPackage.st_ThreadMonitorDataNode->Modified(); m_itemPackage.st_MultiWidget->RequestUpdate(); } } void QmitkFiberThreadMonitorWorker::fancyTextFading_threadTerminated() { if (m_decreaseOpacity_threadTerminated) { int terminatedOpacity = m_itemPackage.st_FBX_Monitor->getTerminatedOpacity(); m_itemPackage.st_FBX_Monitor->setTerminatedOpacity( --terminatedOpacity ); if (terminatedOpacity == 0) { int counter = m_itemPackage.st_FBX_Monitor->getTerminated(); m_itemPackage.st_FBX_Monitor->setTerminated(++counter); m_decreaseOpacity_threadTerminated = false; } m_itemPackage.st_ThreadMonitorDataNode->Modified(); m_itemPackage.st_MultiWidget->RequestUpdate(); } else { int terminatedOpacity = m_itemPackage.st_FBX_Monitor->getTerminatedOpacity(); m_itemPackage.st_FBX_Monitor->setTerminatedOpacity( ++terminatedOpacity ); if (terminatedOpacity >= 10) { m_thtimer_threadTerminated->stop(); m_decreaseOpacity_threadTerminated = true; //set back to true, cuz next iteration shall decrease opacity as well } m_itemPackage.st_ThreadMonitorDataNode->Modified(); m_itemPackage.st_MultiWidget->RequestUpdate(); } } void QmitkFiberThreadMonitorWorker::fancyMonitorInitialization() { mitk::Point2D pntClose = m_itemPackage.st_FBX_Monitor->getBracketClosePosition(); //possible bottleneck, set pntClose to member mitk::Point2D pntOpen = m_itemPackage.st_FBX_Monitor->getBracketOpenPosition(); //possible bottleneck, set pntClose to member pntClose[0] += m_pixelstepper; pntOpen[0] -= m_pixelstepper; //MITK_INFO << pntClose[0] << " " << pntOpen[0]; m_itemPackage.st_FBX_Monitor->setBracketClosePosition(pntClose); m_itemPackage.st_FBX_Monitor->setBracketOpenPosition(pntOpen); int opacity = m_itemPackage.st_FBX_Monitor->getHeadingOpacity() + 1; if (opacity > 10) opacity = 10; m_itemPackage.st_FBX_Monitor->setHeadingOpacity(opacity); if (pntClose[0] >= m_steppingDistance) { if (m_itemPackage.st_FBX_Monitor->getHeadingOpacity() != 10 ) { m_itemPackage.st_FBX_Monitor->setHeadingOpacity(10); m_itemPackage.st_ThreadMonitorDataNode->Modified(); m_itemPackage.st_MultiWidget->RequestUpdate(); } m_thtimer_initMonitor->stop(); //position them to obt y=25 m_thtimer_initMonitorSetFinalPosition->start(); } m_itemPackage.st_ThreadMonitorDataNode->Modified(); m_itemPackage.st_MultiWidget->RequestUpdate(); } void QmitkFiberThreadMonitorWorker::fancyMonitorInitializationFinalPos() { //get y pos of mitk::Point2D pntClose = m_itemPackage.st_FBX_Monitor->getBracketClosePosition(); mitk::Point2D pntOpen = m_itemPackage.st_FBX_Monitor->getBracketOpenPosition(); mitk::Point2D pntHead = m_itemPackage.st_FBX_Monitor->getHeadingPosition(); pntClose[1] += 5; pntOpen[1] += 5; pntHead[1] += 5; m_itemPackage.st_FBX_Monitor->setBracketClosePosition(pntClose); m_itemPackage.st_FBX_Monitor->setBracketOpenPosition(pntOpen); m_itemPackage.st_FBX_Monitor->setHeadingPosition(pntHead); if (pntClose[1] >= 35) { //35 = y position m_thtimer_initMonitorSetFinalPosition->stop(); //now init mask of labels m_thtimer_initMonitorSetMasks->start(); } m_itemPackage.st_ThreadMonitorDataNode->Modified(); m_itemPackage.st_MultiWidget->RequestUpdate(); } void QmitkFiberThreadMonitorWorker::fancyMonitorInitializationMask() { //increase opacity int opacity = m_itemPackage.st_FBX_Monitor->getMaskOpacity(); opacity++; m_itemPackage.st_FBX_Monitor->setMaskOpacity(opacity); m_itemPackage.st_FBX_Monitor->setStartedOpacity(opacity); m_itemPackage.st_FBX_Monitor->setFinishedOpacity(opacity); m_itemPackage.st_FBX_Monitor->setTerminatedOpacity(opacity); m_itemPackage.st_FBX_Monitor->setStatusOpacity(opacity); if (opacity >=10) { m_thtimer_initMonitorSetMasks->stop(); } m_itemPackage.st_ThreadMonitorDataNode->Modified(); m_itemPackage.st_MultiWidget->RequestUpdate(); } //============================================== //======== W O R K E R S ________ E N D ======== //============================================== //========#########################===============###########################=====================######################### //========#########################===============###########################=====================######################### //========#########################===============###########################=====================######################### //========#########################===============###########################=====================######################### //========#########################===============###########################=====================######################### // 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_FiberIDGenerator( NULL) , m_GeneratorFibersRandom( NULL ) , m_fiberMonitorIsOn( false ) , m_CircleCounter( 0 ) { m_hostThread = new QThread; m_threadInProgress = false; } // Destructor QmitkFiberBundleDeveloperView::~QmitkFiberBundleDeveloperView() { //m_FiberBundleX->Delete(); using weakPointer, therefore no delete necessary delete m_hostThread; if (m_FiberIDGenerator != NULL) delete m_FiberIDGenerator; if (m_GeneratorFibersRandom != NULL) delete m_GeneratorFibersRandom; } 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); m_Controls->ddAvailableColorcodings->setEnabled(false); m_Controls->buttonExtractFibers->setEnabled(false); 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->buttonExtractFibers, SIGNAL(clicked()), this, SLOT(DoExtractFibers()) ); 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)) ); connect( m_Controls->tabWidget, SIGNAL(currentChanged ( int ) ), this, SLOT(SelectionChangedToolBox(int)) ); //needed to update GUI elements when tab selection of fiberProcessing page changes connect( m_Controls->m_CircleButton, SIGNAL( clicked() ), this, SLOT( ActionDrawEllipseTriggered() ) ); connect( m_Controls->buttonColorFibers, SIGNAL(clicked()), this, SLOT(DoColorFibers()) ); connect( m_Controls->ddAvailableColorcodings, SIGNAL(currentIndexChanged(int)), this, SLOT(SetCurrentColorCoding(int) )); connect( m_Controls->checkBoxMonitorFiberThreads, SIGNAL(stateChanged(int)), this, SLOT(DoMonitorFiberThreads(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::DoExtractFibers() { /* ===== 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( UpdateExtractFibersTimer()) ); struct Package4WorkingThread ItemPackageForExtractor; ItemPackageForExtractor.st_FBX = m_FiberBundleX; ItemPackageForExtractor.st_Controls = m_Controls; ItemPackageForExtractor.st_FancyGUITimer1 = localTimer; ItemPackageForExtractor.st_host = this; //needed to access method "PutFibersToDataStorage()" ItemPackageForExtractor.st_pntr_to_Method_PutFibersToDataStorage = &QmitkFiberBundleDeveloperView::PutFibersToDataStorage; //actual functor calling method putFibersToDataStorage ItemPackageForExtractor.st_PlanarFigure = m_PlanarFigure; //set element for thread monitoring if (m_fiberMonitorIsOn) ItemPackageForExtractor.st_fiberThreadMonitorWorker = m_fiberThreadMonitorWorker; if (m_threadInProgress) return; //maybe popup window saying, working thread still in progress...pls wait m_FiberExtractor = new QmitkFiberExtractorWorker(m_hostThread, ItemPackageForExtractor); m_FiberExtractor->moveToThread(m_hostThread); //connections connect(m_hostThread, SIGNAL(started()), this, SLOT( BeforeThread_ExtractFibers() )); connect(m_hostThread, SIGNAL(started()), m_FiberExtractor, SLOT( run() )); connect(m_hostThread, SIGNAL(started()), this, SLOT( AfterThread_ExtractFibers() )); connect(m_hostThread, SIGNAL(started()), this, SLOT( AfterThread_ExtractFibers() )); - m_hostThread->start(QThread::NormalPriority) ; + m_hostThread->start(QThread::HighestPriority) ; } void QmitkFiberBundleDeveloperView::UpdateExtractFibersTimer() { // Make sure that thread has set according info-label to number! here we do not check if value is numeric! shall be done in beforeThreadstarted() - QString crntValue = m_Controls->infoTimerColorCoding->text(); + QString crntValue = m_Controls->infoTimerExtractFibers->text(); int tmpVal = crntValue.toInt(); m_Controls->infoTimerExtractFibers->setText(QString::number(++tmpVal)); m_Controls->infoTimerExtractFibers->update(); } void QmitkFiberBundleDeveloperView::BeforeThread_FiberExtraction() { m_threadInProgress = true; if (m_fiberMonitorIsOn){ m_fiberThreadMonitorWorker->threadForFiberProcessingStarted(); //m_fiberThreadMonitorWorker->setThreadStatus(FBX_STATUS_STARTED); } } void QmitkFiberBundleDeveloperView::AfterThread_FiberExtraction() { m_threadInProgress = false; if (m_fiberMonitorIsOn){ m_fiberThreadMonitorWorker->threadForFiberProcessingFinished(); m_fiberThreadMonitorWorker->setThreadStatus(FBX_STATUS_IDLE); } disconnect(m_hostThread, 0, 0, 0); m_hostThread->disconnect(); } void QmitkFiberBundleDeveloperView::PutFibersToDataStorage( vtkSmartPointer threadOutput) { MITK_INFO << "lines: " << threadOutput->GetNumberOfLines() << "pnts: " << threadOutput->GetNumberOfPoints(); //qthread mutex lock mitk::FiberBundleX::Pointer FB = mitk::FiberBundleX::New(threadOutput); 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 } void QmitkFiberBundleDeveloperView::PutFigureToDataStorage(mitk::PlanarFigure* figure, const QString& name) { mitk::DataNode::Pointer newNode = mitk::DataNode::New(); newNode->SetName(name.toStdString()); newNode->SetData(figure); std::vector selectedNodes = GetDataManagerSelection(); for(unsigned int i = 0; i < selectedNodes.size(); i++) { selectedNodes[i]->SetSelected(false); } newNode->SetSelected(true); newNode->AddProperty( "planarfigure.default.line.color", mitk::ColorProperty::New(1.0,0.0,0.0)); newNode->AddProperty( "planarfigure.line.width", mitk::FloatProperty::New(2.0)); newNode->AddProperty( "planarfigure.drawshadow", mitk::BoolProperty::New(true)); newNode->AddProperty( "selected", mitk::BoolProperty::New(true) ); newNode->AddProperty( "planarfigure.ishovering", mitk::BoolProperty::New(true) ); newNode->AddProperty( "planarfigure.drawoutline", mitk::BoolProperty::New(true) ); newNode->AddProperty( "planarfigure.drawquantities", mitk::BoolProperty::New(false) ); newNode->AddProperty( "planarfigure.drawshadow", mitk::BoolProperty::New(true) ); newNode->AddProperty( "planarfigure.line.width", mitk::FloatProperty::New(3.0) ); newNode->AddProperty( "planarfigure.shadow.widthmodifier", mitk::FloatProperty::New(2.0) ); newNode->AddProperty( "planarfigure.outline.width", mitk::FloatProperty::New(2.0) ); newNode->AddProperty( "planarfigure.helperline.width", mitk::FloatProperty::New(2.0) ); newNode->AddProperty( "planarfigure.default.line.color", mitk::ColorProperty::New(1.0,1.0,1.0) ); newNode->AddProperty( "planarfigure.default.line.opacity", mitk::FloatProperty::New(2.0) ); newNode->AddProperty( "planarfigure.default.outline.color", mitk::ColorProperty::New(1.0,0.0,0.0) ); newNode->AddProperty( "planarfigure.default.outline.opacity", mitk::FloatProperty::New(2.0) ); newNode->AddProperty( "planarfigure.default.helperline.color", mitk::ColorProperty::New(1.0,0.0,0.0) ); newNode->AddProperty( "planarfigure.default.helperline.opacity", mitk::FloatProperty::New(2.0) ); newNode->AddProperty( "planarfigure.default.markerline.color", mitk::ColorProperty::New(0.0,0.0,0.0) ); newNode->AddProperty( "planarfigure.default.markerline.opacity", mitk::FloatProperty::New(2.0) ); newNode->AddProperty( "planarfigure.default.marker.color", mitk::ColorProperty::New(1.0,1.0,1.0) ); newNode->AddProperty( "planarfigure.default.marker.opacity",mitk::FloatProperty::New(2.0) ); newNode->AddProperty( "planarfigure.hover.line.color", mitk::ColorProperty::New(1.0,0.0,0.0) ); newNode->AddProperty( "planarfigure.hover.line.opacity", mitk::FloatProperty::New(2.0) ); newNode->AddProperty( "planarfigure.hover.outline.color", mitk::ColorProperty::New(1.0,0.0,0.0) ); newNode->AddProperty( "planarfigure.hover.outline.opacity", mitk::FloatProperty::New(2.0) ); newNode->AddProperty( "planarfigure.hover.helperline.color", mitk::ColorProperty::New(1.0,0.0,0.0) ); newNode->AddProperty( "planarfigure.hover.helperline.opacity", mitk::FloatProperty::New(2.0) ); newNode->AddProperty( "planarfigure.hover.markerline.color", mitk::ColorProperty::New(1.0,0.0,0.0) ); newNode->AddProperty( "planarfigure.hover.markerline.opacity", mitk::FloatProperty::New(2.0) ); newNode->AddProperty( "planarfigure.hover.marker.color", mitk::ColorProperty::New(1.0,0.0,0.0) ); newNode->AddProperty( "planarfigure.hover.marker.opacity", mitk::FloatProperty::New(2.0) ); newNode->AddProperty( "planarfigure.selected.line.color", mitk::ColorProperty::New(1.0,0.0,0.0) ); newNode->AddProperty( "planarfigure.selected.line.opacity",mitk::FloatProperty::New(2.0) ); newNode->AddProperty( "planarfigure.selected.outline.color", mitk::ColorProperty::New(1.0,0.0,0.0) ); newNode->AddProperty( "planarfigure.selected.outline.opacity", mitk::FloatProperty::New(2.0)); newNode->AddProperty( "planarfigure.selected.helperline.color", mitk::ColorProperty::New(1.0,0.0,0.0) ); newNode->AddProperty( "planarfigure.selected.helperline.opacity",mitk::FloatProperty::New(2.0) ); newNode->AddProperty( "planarfigure.selected.markerline.color", mitk::ColorProperty::New(1.0,0.0,0.0) ); newNode->AddProperty( "planarfigure.selected.markerline.opacity", mitk::FloatProperty::New(2.0) ); newNode->AddProperty( "planarfigure.selected.marker.color", mitk::ColorProperty::New(1.0,0.0,0.0) ); newNode->AddProperty( "planarfigure.selected.marker.opacity",mitk::FloatProperty::New(2.0)); // figure drawn on the topmost layer / image this->GetDataStorage()->Add(newNode); } /* * Generate polydata of random fibers */ void QmitkFiberBundleDeveloperView::GenerateVtkFibersRandom() { /* ===== 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(UpdateGenerateRandomFibersTimer()) ); struct Package4WorkingThread ItemPackageForRandomGenerator; ItemPackageForRandomGenerator.st_FBX = m_FiberBundleX; ItemPackageForRandomGenerator.st_Controls = m_Controls; ItemPackageForRandomGenerator.st_FancyGUITimer1 = localTimer; ItemPackageForRandomGenerator.st_host = this; //needed to access method "PutFibersToDataStorage()" ItemPackageForRandomGenerator.st_pntr_to_Method_PutFibersToDataStorage = &QmitkFiberBundleDeveloperView::PutFibersToDataStorage; //actual functor calling method putFibersToDataStorage //set element for thread monitoring if (m_fiberMonitorIsOn) ItemPackageForRandomGenerator.st_fiberThreadMonitorWorker = m_fiberThreadMonitorWorker; if (m_threadInProgress) return; //maybe popup window saying, working thread still in progress...pls wait 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::UpdateColorFibersTimer() { // Make sure that thread has set according info-label to number! here we do not check if value is numeric! QString crntValue = m_Controls->infoTimerColorCoding->text(); int tmpVal = crntValue.toInt(); m_Controls->infoTimerColorCoding->setText(QString::number(++tmpVal)); m_Controls->infoTimerColorCoding->update(); } void QmitkFiberBundleDeveloperView::UpdateGenerateRandomFibersTimer() { // Make sure that thread has set according info-label to number! here we do not check if value is numeric! QString crntValue = m_Controls->infoTimerGenerateFiberBundle->text(); int tmpVal = crntValue.toInt(); m_Controls->infoTimerGenerateFiberBundle->setText(QString::number(++tmpVal)); m_Controls->infoTimerGenerateFiberBundle->update(); } void QmitkFiberBundleDeveloperView::BeforeThread_GenerateFibersRandom() { m_threadInProgress = true; if (m_fiberMonitorIsOn){ m_fiberThreadMonitorWorker->threadForFiberProcessingStarted(); //m_fiberThreadMonitorWorker->setThreadStatus(FBX_STATUS_STARTED); } } void QmitkFiberBundleDeveloperView::AfterThread_GenerateFibersRandom() { m_threadInProgress = false; if (m_fiberMonitorIsOn){ m_fiberThreadMonitorWorker->threadForFiberProcessingFinished(); m_fiberThreadMonitorWorker->setThreadStatus(FBX_STATUS_IDLE); } 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; } void QmitkFiberBundleDeveloperView::DoColorFibers() { // MITK_INFO << "call fibercoloring in fiberBundleX"; QTimer *localTimer = new QTimer; // timer must be initialized here, otherwise timer is not fancy enough localTimer->setInterval( 10 ); connect( localTimer, SIGNAL(timeout()), this, SLOT( UpdateColorFibersTimer() ) ); // pack items which are needed by thread processing struct Package4WorkingThread ItemPackageForFiberColoring; ItemPackageForFiberColoring.st_FBX = m_FiberBundleX; ItemPackageForFiberColoring.st_FancyGUITimer1 = localTimer; ItemPackageForFiberColoring.st_Controls = m_Controls; //needed to catch up some selections and set options in GUI if (m_fiberMonitorIsOn) ItemPackageForFiberColoring.st_fiberThreadMonitorWorker = m_fiberThreadMonitorWorker; if (m_threadInProgress) return; //maybe popup window saying, working thread still in progress...pls wait m_FiberColoringSlave = new QmitkFiberColoringWorker(m_hostThread, ItemPackageForFiberColoring); m_FiberColoringSlave->moveToThread(m_hostThread); connect(m_hostThread, SIGNAL(started()), this, SLOT( BeforeThread_FiberColorCoding()) ); connect(m_hostThread, SIGNAL(started()), m_FiberColoringSlave, SLOT(run()) ); connect(m_hostThread, SIGNAL(finished()), this, SLOT(AfterThread_FiberColorCoding())); connect(m_hostThread, SIGNAL(terminated()), this, SLOT(AfterThread_FiberColorCoding())); m_hostThread->start(QThread::LowestPriority); } void QmitkFiberBundleDeveloperView::BeforeThread_FiberColorCoding() { m_threadInProgress = true; if (m_fiberMonitorIsOn){ m_fiberThreadMonitorWorker->threadForFiberProcessingStarted(); } } void QmitkFiberBundleDeveloperView::AfterThread_FiberColorCoding() { m_threadInProgress = false; if (m_fiberMonitorIsOn){ m_fiberThreadMonitorWorker->threadForFiberProcessingFinished(); m_fiberThreadMonitorWorker->setThreadStatus(FBX_STATUS_IDLE); } disconnect(m_hostThread, 0, 0, 0); m_hostThread->disconnect(); //update renderer m_MultiWidget->RequestUpdate(); //update QComboBox(dropDown menu) in view of available ColorCodings DoGatherColorCodings(); } void QmitkFiberBundleDeveloperView::DoGatherColorCodings() { QStringList fbxColorCodings = m_FiberBundleX->GetAvailableColorCodings(); //update dropDown Menu //remove all items from menu int ddItems = m_Controls->ddAvailableColorcodings->count(); for(int i=ddItems-1; i>=0; i--) { //note, after each item remove, index in QComboBox is updated, therefore we start from the back which causes less update calculation m_Controls->ddAvailableColorcodings->removeItem(i); } //fill new data into menu m_Controls->ddAvailableColorcodings->addItem("---"); m_Controls->ddAvailableColorcodings->addItems(fbxColorCodings); //highlight current colorcoding QString cc = m_FiberBundleX->GetCurrentColorCoding(); MITK_INFO << "current idx: " << m_Controls->ddAvailableColorcodings->findText(cc); m_Controls->ddAvailableColorcodings->setCurrentIndex( m_Controls->ddAvailableColorcodings->findText(cc) ); } void QmitkFiberBundleDeveloperView::SetCurrentColorCoding(int idx) { QString selectedColorCoding = m_Controls->ddAvailableColorcodings->itemText(idx); m_FiberBundleX->SetColorCoding(selectedColorCoding.toStdString().c_str() ); //QString to char // update rendering m_MultiWidget->RequestUpdate(); } /* === 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 vtkSmartPointer 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_FancyGUITimer1 = localTimer; FiberIdPackage.st_Controls = m_Controls; //set element for thread monitoring if (m_fiberMonitorIsOn) FiberIdPackage.st_fiberThreadMonitorWorker = m_fiberThreadMonitorWorker; 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_threadInProgress = true; if (m_fiberMonitorIsOn){ m_fiberThreadMonitorWorker->threadForFiberProcessingStarted(); m_fiberThreadMonitorWorker->setThreadStatus(FBX_STATUS_STARTED); } } void QmitkFiberBundleDeveloperView::AfterThread_IdGenerate() { m_threadInProgress = false; if (m_fiberMonitorIsOn){ m_fiberThreadMonitorWorker->threadForFiberProcessingFinished(); m_fiberThreadMonitorWorker->setThreadStatus(FBX_STATUS_IDLE); } disconnect(m_hostThread, 0, 0, 0); m_hostThread->disconnect(); } 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->GetFiberPolyData()->GetNumberOfLines() ); QString numOfPoints; numOfPoints.setNum( m_FiberBundleX->GetFiberPolyData()->GetNumberOfPoints() ); m_Controls->infoAnalyseNumOfFibers->setText( numOfFibers ); m_Controls->infoAnalyseNumOfPoints->setText( numOfPoints ); } void QmitkFiberBundleDeveloperView::SelectionChangedToolBox(int idx) { // show/reset items of selected toolbox page FiberInfo if (m_Controls->page_FiberInfo->isVisible()) { if (m_FiberBundleX != NULL) { FeedFiberInfoWidget(); } else { //if infolables are disabled: return //else set info back to - and set label and info to disabled ResetFiberInfoWidget(); } } // show/reset items of selected toolbox page FiberProcessing if (m_Controls->page_FiberProcessing->isVisible()) { if (m_FiberBundleX.IsNotNull() && m_PlanarFigure.IsNotNull() ) { //show fiber extraction button m_Controls->buttonExtractFibers->setEnabled(true); } else { m_Controls->buttonExtractFibers->setEnabled(false); } if (m_FiberBundleX.IsNotNull()) { if (m_Controls->tabColoring->isVisible()){ //show button colorCoding m_Controls->buttonColorFibers->setEnabled(true); m_Controls->ddAvailableColorcodings->setEnabled(true); MITK_INFO << "Color"; }else if(m_Controls->tabCutting->isVisible()){ m_Controls->buttonGenerateFiberIds->setEnabled(true); }else if(m_Controls->tabShape->isVisible()){ // m_Controls->buttonSMFibers->setEnabled(true); // m_Controls->buttonVtkDecimatePro->setEnabled(true); // m_Controls->buttonVtkSmoothPD->setEnabled(true); // m_Controls->buttonGenerateTubes->setEnabled(true); } } else { m_Controls->buttonColorFibers->setEnabled(false); m_Controls->ddAvailableColorcodings->setEnabled(false); m_Controls->buttonGenerateFiberIds->setEnabled(false); m_Controls->buttonSMFibers->setEnabled(false); m_Controls->buttonVtkDecimatePro->setEnabled(false); m_Controls->buttonVtkSmoothPD->setEnabled(false); m_Controls->buttonGenerateTubes->setEnabled(true); } } } void QmitkFiberBundleDeveloperView::FBXDependendGUIElementsConfigurator() { // ==== FIBER PROCESSING ELEMENTS and ALL ELEMENTS WHICH NEED A FBX DATANODE====== // m_Controls->buttonGenerateFiberIds->setEnabled(isVisible); moved to selectionChangedToolBox SelectionChangedToolBox(-1); //set gui elements with respect to active tab, widget, etc. -1 has no effect } void QmitkFiberBundleDeveloperView::DoMonitorFiberThreads(int checkStatus) { //check if in datanode exists already a node of type mitkFiberBundleXThreadMonitor //if not then put node to datastorage //if checkStatus is 1 then start qtimer using fading in starting text in datanode //if checkStatus is 0 then fade out dataNode using qtimer if (checkStatus) { m_fiberMonitorIsOn = true; // Generate Node hosting thread information mitk::FiberBundleXThreadMonitor::Pointer FBXThreadMonitor = mitk::FiberBundleXThreadMonitor::New(); FBXThreadMonitor->SetGeometry(this->GenerateStandardGeometryForMITK()); m_MonitorNode = mitk::DataNode::New(); m_MonitorNode->SetName("FBX_threadMonitor"); m_MonitorNode->SetData(FBXThreadMonitor); m_MonitorNode->SetVisibility(true); m_MonitorNode->SetOpacity(1.0); GetDataStorage()->Add(m_MonitorNode); //following code is needed for rendering text in mitk! without geometry nothing is rendered 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?? } //__GEOMETRY FOR THREADMONITOR GENERATED /* ====== initialize thread for managing fiberThread information ========= */ m_monitorThread = new QThread; // the package needs datastorage, MonitorDatanode, standardmultiwidget, struct Package4WorkingThread ItemPackageForThreadMonitor; ItemPackageForThreadMonitor.st_DataStorage = GetDataStorage(); ItemPackageForThreadMonitor.st_ThreadMonitorDataNode = m_MonitorNode; ItemPackageForThreadMonitor.st_MultiWidget = m_MultiWidget; ItemPackageForThreadMonitor.st_FBX_Monitor = FBXThreadMonitor; m_fiberThreadMonitorWorker = new QmitkFiberThreadMonitorWorker(m_monitorThread, ItemPackageForThreadMonitor); m_fiberThreadMonitorWorker->moveToThread(m_monitorThread); connect ( m_monitorThread, SIGNAL( started() ), m_fiberThreadMonitorWorker, SLOT( run() ) ); m_monitorThread->start(QThread::LowestPriority); m_fiberThreadMonitorWorker->initializeMonitor();//do some init animation ;-) } else { m_fiberMonitorIsOn = false; m_monitorThread->quit(); //think about outsourcing following lines to quit / terminate slot of thread GetDataStorage()->Remove(m_MonitorNode); GetDataStorage()->Modified(); m_MultiWidget->RequestUpdate(); //necessary?? } } 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(); //every gui element which needs a FBX for processing is disabled //timer reset only when no thread is in progress if (!m_threadInProgress) { m_Controls->infoTimerGenerateFiberIds->setText("-"); //set GUI representation of timer to - m_Controls->infoTimerGenerateFiberBundle->setText( "-" ); m_Controls->infoTimerColorCoding->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.IsNull()) 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(); } /* CHECKPOINT: PLANARFIGURE */ else if ( node.IsNotNull() && dynamic_cast(node->GetData()) ) { m_PlanarFigure = dynamic_cast(node->GetData()); MITK_INFO << "PF selected"; if (m_PlanarFigure.IsNull()) MITK_INFO << "========ATTENTION=========\n unable to load selected Planarfigure to FiberBundleDeveloper-plugin \n"; } } } void QmitkFiberBundleDeveloperView::ActionDrawEllipseTriggered() { // bool checked = m_Controls->m_CircleButton->isChecked(); mitk::PlanarCircle::Pointer figure = mitk::PlanarCircle::New(); this->PutFigureToDataStorage(figure, QString("Circle%1").arg(++m_CircleCounter)); MITK_INFO << "PlanarCircle created ..."; mitk::DataStorage::SetOfObjects::ConstPointer _NodeSet = this->GetDefaultDataStorage()->GetAll(); mitk::DataNode* node = 0; mitk::PlanarFigureInteractor::Pointer figureInteractor = 0; mitk::PlanarFigure* figureP = 0; for(mitk::DataStorage::SetOfObjects::ConstIterator it=_NodeSet->Begin(); it!=_NodeSet->End() ; it++) { node = const_cast(it->Value().GetPointer()); figureP = dynamic_cast(node->GetData()); if(figureP) { figureInteractor = dynamic_cast(node->GetInteractor()); if(figureInteractor.IsNull()) figureInteractor = mitk::PlanarFigureInteractor::New("PlanarFigureInteractor", node); mitk::GlobalInteraction::GetInstance()->AddInteractor(figureInteractor); } } } void QmitkFiberBundleDeveloperView::Activated() { MITK_INFO << "FB DevelopersV ACTIVATED()"; } diff --git a/Modules/DiffusionImaging/IODataStructures/FiberBundleX/mitkFiberBundleX.cpp b/Modules/DiffusionImaging/IODataStructures/FiberBundleX/mitkFiberBundleX.cpp index c31133ccbe..64ff3746b0 100644 --- a/Modules/DiffusionImaging/IODataStructures/FiberBundleX/mitkFiberBundleX.cpp +++ b/Modules/DiffusionImaging/IODataStructures/FiberBundleX/mitkFiberBundleX.cpp @@ -1,701 +1,708 @@ /*========================================================================= 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" #include //#include #include #include /* musthave */ //#include // without geometry, fibers are not rendered #include #include #include #include #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(vtkSmartPointer fiberPolyData ) - : m_currentColorCoding(NULL) - , m_isModified(false) + : m_currentColorCoding(NULL) + , m_isModified(false) { - //generate geometry of passed polydata - if (fiberPolyData == NULL) - this->m_FiberPolyData = vtkSmartPointer::New(); - else - this->m_FiberPolyData = fiberPolyData; + //generate geometry of passed polydata + if (fiberPolyData == NULL) + this->m_FiberPolyData = vtkSmartPointer::New(); + else + this->m_FiberPolyData = fiberPolyData; - this->UpdateFiberGeometry(); + this->UpdateFiberGeometry(); } mitk::FiberBundleX::~FiberBundleX() { } /* * set computed fibers from tractography algorithms */ void mitk::FiberBundleX::SetFiberPolyData(vtkSmartPointer fiberPD) { - if (fiberPD == NULL) - this->m_FiberPolyData = vtkSmartPointer::New(); - else - this->m_FiberPolyData = fiberPD; + if (fiberPD == NULL) + this->m_FiberPolyData = vtkSmartPointer::New(); + else + this->m_FiberPolyData = fiberPD; - m_isModified = true; + m_isModified = true; } /* * return fiberbundle as vtkPolyData * Depending on processing of input fibers, this method returns * the latest processed fibers. */ vtkSmartPointer mitk::FiberBundleX::GetFiberPolyData() { - return m_FiberPolyData; + return m_FiberPolyData; } /*=================================== *++++ PROCESSING WITH FIBERS +++++++ ====================================*/ void mitk::FiberBundleX::DoColorCodingOrientationbased() { //===== FOR WRITING A TEST ======================== // colorT size == tupelComponents * tupelElements // compare color results // to cover this code 100% also polydata needed, where colorarray already exists // + one fiber with exactly 1 point // + one fiber with 0 points //================================================= /* make sure that processing colorcoding is only called when necessary */ if ( m_FiberPolyData->GetPointData()->HasArray(COLORCODING_ORIENTATION_BASED) && m_FiberPolyData->GetNumberOfPoints() == m_FiberPolyData->GetPointData()->GetArray(COLORCODING_ORIENTATION_BASED)->GetNumberOfTuples() ) { // fiberstructure is already colorcoded MITK_INFO << " NO NEED TO REGENERATE COLORCODING! " ; return; } - /* Finally, execute color calculation */ - vtkPoints* extrPoints = m_FiberPolyData->GetPoints(); - int numOfPoints = extrPoints->GetNumberOfPoints(); + /* Finally, execute color calculation */ + vtkPoints* extrPoints = m_FiberPolyData->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); + //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); + 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_FiberPolyData->GetNumberOfLines(); - if (numOfFibers < 1) { - MITK_INFO << "\n ========= Number of Fibers is 0 and below ========= \n"; - return; - } + /* checkpoint: does polydata contain any fibers */ + int numOfFibers = m_FiberPolyData->GetNumberOfLines(); + if (numOfFibers < 1) { + MITK_INFO << "\n ========= Number of Fibers is 0 and below ========= \n"; + return; + } - /* extract single fibers of fiberBundle */ - vtkCellArray* fiberList = m_FiberPolyData->GetLines(); - fiberList->InitTraversal(); - for (int fi=0; fiGetLines(); + fiberList->InitTraversal(); + for (int fi=0; fiGetNextCell(pointsPerFiber, idList); + vtkIdType* idList; // contains the point id's of the line + vtkIdType pointsPerFiber; // number of points for current line + fiberList->GetNextCell(pointsPerFiber, idList); // MITK_INFO << "Fib#: " << fi << " of " << numOfFibers << " pnts in fiber: " << pointsPerFiber ; - /* single fiber checkpoints: is number of points valid */ - if (pointsPerFiber > 1) - { - /* operate on points of single fiber */ - for (int i=0; i 0) + /* single fiber checkpoints: is number of points valid */ + if (pointsPerFiber > 1) { - /* 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]); + /* operate on points of single fiber */ + for (int i=0; i 0) + { + /* The color value of the current point is influenced by the previous point and next point. */ + vnl_vector_fixed< double, 3 > currentPntvtk(extrPoints->GetPoint(idList[i])[0], extrPoints->GetPoint(idList[i])[1],extrPoints->GetPoint(idList[i])[2]); + vnl_vector_fixed< double, 3 > nextPntvtk(extrPoints->GetPoint(idList[i+1])[0], extrPoints->GetPoint(idList[i+1])[1], extrPoints->GetPoint(idList[i+1])[2]); + vnl_vector_fixed< double, 3 > prevPntvtk(extrPoints->GetPoint(idList[i-1])[0], extrPoints->GetPoint(idList[i-1])[1], extrPoints->GetPoint(idList[i-1])[2]); - vnl_vector_fixed< double, 3 > diff1; - diff1 = currentPntvtk - nextPntvtk; + vnl_vector_fixed< double, 3 > diff1; + diff1 = currentPntvtk - nextPntvtk; - vnl_vector_fixed< double, 3 > diff2; - diff2 = currentPntvtk - prevPntvtk; + vnl_vector_fixed< double, 3 > diff2; + diff2 = currentPntvtk - prevPntvtk; - vnl_vector_fixed< double, 3 > diff; - diff = (diff1 - diff2) / 2.0; - diff.normalize(); + vnl_vector_fixed< double, 3 > diff; + diff = (diff1 - diff2) / 2.0; + diff.normalize(); - 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); + 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 */ + } 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 > 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(); + 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); + 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==pointsPerFiber-1) { - /* Last point has no next point, therefore only diff2 is taken */ - vnl_vector_fixed< double, 3 > currentPntvtk(extrPoints->GetPoint(idList[i])[0], extrPoints->GetPoint(idList[i])[1],extrPoints->GetPoint(idList[i])[2]); - vnl_vector_fixed< double, 3 > prevPntvtk(extrPoints->GetPoint(idList[i-1])[0], extrPoints->GetPoint(idList[i-1])[1], extrPoints->GetPoint(idList[i-1])[2]); + } else if (i==pointsPerFiber-1) { + /* Last point has no next point, therefore only diff2 is taken */ + vnl_vector_fixed< double, 3 > currentPntvtk(extrPoints->GetPoint(idList[i])[0], extrPoints->GetPoint(idList[i])[1],extrPoints->GetPoint(idList[i])[2]); + vnl_vector_fixed< double, 3 > prevPntvtk(extrPoints->GetPoint(idList[i-1])[0], extrPoints->GetPoint(idList[i-1])[1], extrPoints->GetPoint(idList[i-1])[2]); - vnl_vector_fixed< double, 3 > diff2; - diff2 = currentPntvtk - prevPntvtk; - diff2.normalize(); + 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); + 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); + colorsT->InsertTupleValue(idList[i], rgba); - } //end for loop + } //end for loop - } else if (pointsPerFiber == 1) { - /* a single point does not define a fiber (use vertex mechanisms instead */ - continue; - // colorsT->InsertTupleValue(0, rgba); + } else if (pointsPerFiber == 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; + } else { + MITK_INFO << "Fiber with 0 points detected... please check your tractography algorithm!" ; + continue; - } + } - }//end for loop + }//end for loop m_FiberPolyData->GetPointData()->AddArray(colorsT); /*========================= - this is more relevant for renderer than for fiberbundleX datastructure - think about sourcing this to a explicit method which coordinates colorcoding */ this->SetColorCoding(COLORCODING_ORIENTATION_BASED); m_isModified = true; // =========================== - //mini test, shall be ported to MITK TESTINGS! - if (colorsT->GetSize() != numOfPoints*componentSize) { - MITK_INFO << "ALLOCATION ERROR IN INITIATING COLOR ARRAY"; - } + //mini test, shall be ported to MITK TESTINGS! + if (colorsT->GetSize() != numOfPoints*componentSize) { + MITK_INFO << "ALLOCATION ERROR IN INITIATING COLOR ARRAY"; + } } void mitk::FiberBundleX::DoGenerateFiberIds() { - if (m_FiberPolyData == NULL) - return; - - // 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_FiberPolyData); - idFiberFilter->CellIdsOn(); - // idFiberFilter->PointIdsOn(); // point id's are not needed - idFiberFilter->SetIdsArrayName(FIBER_ID_ARRAY); - idFiberFilter->FieldDataOn(); - idFiberFilter->Update(); - - m_FiberIdDataSet = idFiberFilter->GetOutput(); - - MITK_INFO << "Generating Fiber Ids...[done] | " << m_FiberIdDataSet->GetNumberOfCells(); + if (m_FiberPolyData == NULL) + return; + + // 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_FiberPolyData); + idFiberFilter->CellIdsOn(); + // idFiberFilter->PointIdsOn(); // point id's are not needed + idFiberFilter->SetIdsArrayName(FIBER_ID_ARRAY); + idFiberFilter->FieldDataOn(); + idFiberFilter->Update(); + + m_FiberIdDataSet = idFiberFilter->GetOutput(); + + MITK_INFO << "Generating Fiber Ids...[done] | " << m_FiberIdDataSet->GetNumberOfCells(); } //temporarely include only #include //========================== std::vector mitk::FiberBundleX::DoExtractFiberIds(mitk::PlanarFigure::Pointer pf) { MITK_INFO << "Extracting fiber!"; /* Handle type of planarfigure */ // if incoming pf is a pfc mitk::PlanarFigureComposite::Pointer pfcomp= dynamic_cast(pf.GetPointer()); if (!pfcomp.IsNull()) { // process requested boolean operation of PFC } else { - mitk::PlanarCircle::Pointer circleName = mitk::PlanarCircle::New(); - mitk::PlanarPolygon::Pointer polyName = mitk::PlanarPolygon::New(); - if (pf->GetNameOfClass() == circleName->GetNameOfClass() ) - { - mitk::Geometry2D::ConstPointer pfgeometry = pf->GetGeometry2D(); - const mitk::PlaneGeometry* planeGeometry = dynamic_cast (pfgeometry.GetPointer()); - Vector3D planeNormal = planeGeometry->GetNormal(); - planeNormal.Normalize(); - Point3D planeOrigin = planeGeometry->GetOrigin(); + mitk::Geometry2D::ConstPointer pfgeometry = pf->GetGeometry2D(); + const mitk::PlaneGeometry* planeGeometry = dynamic_cast (pfgeometry.GetPointer()); + Vector3D planeNormal = planeGeometry->GetNormal(); + planeNormal.Normalize(); + Point3D planeOrigin = planeGeometry->GetOrigin(); + + MITK_INFO << "planeOrigin: " << planeOrigin[0] << " | " << planeOrigin[1] << " | " << planeOrigin[2] << endl; + MITK_INFO << "planeNormal: " << planeNormal[0] << " | " << planeNormal[1] << " | " << planeNormal[2] << endl; - MITK_INFO << "planeOrigin: " << planeOrigin[0] << " | " << planeOrigin[1] << " | " << planeOrigin[2] << endl; - MITK_INFO << "planeNormal: " << planeNormal[0] << " | " << planeNormal[1] << " | " << planeNormal[2] << endl; - } - } - /* init necessary vectors hosting pointIds and FiberIds */ - // contains all pointIds which are crossing the cutting plane - std::vector PointsOnPlane; - // based on PointsOnPlane, all ROI relevant point IDs are stored here - std::vector PointsInROI; + /* init necessary vectors hosting pointIds and FiberIds */ + // contains all pointIds which are crossing the cutting plane + std::vector PointsOnPlane; - // vector which is returned, contains all extracted FiberIds - std::vector FibersInROI; + // based on PointsOnPlane, all ROI relevant point IDs are stored here + std::vector PointsInROI; + // vector which is returned, contains all extracted FiberIds + std::vector FibersInROI; - /* Define cutting plane by ROI (PlanarFigure) */ - vtkSmartPointer plane = vtkSmartPointer::New(); - plane->SetOrigin(10.0,5.0,0.0); - plane->SetNormal(0.0,1.0,0.0); - //same plane but opposite normal direction. so point cloud will be reduced -> better performance - vtkSmartPointer planeR = vtkSmartPointer::New(); - planeR->SetOrigin(10.0,5.0,0.0); - planeR->SetNormal(0.0,-1.0,0.0); + /* Define cutting plane by ROI (PlanarFigure) */ + vtkSmartPointer plane = vtkSmartPointer::New(); + plane->SetOrigin(planeOrigin[0],planeOrigin[1],planeOrigin[2]); + plane->SetNormal(planeNormal[0],planeNormal[1],planeNormal[2]); + //same plane but opposite normal direction. so point cloud will be reduced -> better performance + vtkSmartPointer planeR = vtkSmartPointer::New(); + planeR->SetOrigin(10.0,5.0,0.0); + planeR->SetNormal(0.0,-1.0,0.0); - /* get all points/fibers cutting the plane */ - vtkSmartPointer clipper = vtkSmartPointer::New(); - clipper->SetInput(m_FiberIdDataSet); - clipper->SetClipFunction(plane); - clipper->GenerateClipScalarsOn(); - clipper->GenerateClippedOutputOn(); - vtkSmartPointer clipperout1 = clipper->GetClippedOutput(); - /* for some reason clipperoutput is not initialized for futher processing + /* get all points/fibers cutting the plane */ + vtkSmartPointer clipper = vtkSmartPointer::New(); + clipper->SetInput(m_FiberIdDataSet); + clipper->SetClipFunction(plane); + clipper->GenerateClipScalarsOn(); + clipper->GenerateClippedOutputOn(); + vtkSmartPointer clipperout1 = clipper->GetClippedOutput(); + + /* for some reason clipperoutput is not initialized for futher processing * so far only writing out clipped polydata provides requested */ - vtkSmartPointer writerC = vtkSmartPointer::New(); - writerC->SetInput(clipperout1); - writerC->SetFileName("/vtkOutput/Cout1_FbId_clipLineId0+1+2-tests.vtk"); - writerC->SetFileTypeToASCII(); - writerC->Write(); + vtkSmartPointer writerC = vtkSmartPointer::New(); + writerC->SetInput(clipperout1); + writerC->SetFileName("/vtkOutput/Cout1_FbId_clipLineId0+1+2-tests.vtk"); + writerC->SetFileTypeToASCII(); + writerC->Write(); - vtkSmartPointer Rclipper = vtkSmartPointer::New(); - Rclipper->SetInput(clipperout1); - Rclipper->SetClipFunction(planeR); - Rclipper->GenerateClipScalarsOn(); - Rclipper->GenerateClippedOutputOn(); - vtkSmartPointer clipperout = Rclipper->GetClippedOutput(); + vtkSmartPointer Rclipper = vtkSmartPointer::New(); + Rclipper->SetInput(clipperout1); + Rclipper->SetClipFunction(planeR); + Rclipper->GenerateClipScalarsOn(); + Rclipper->GenerateClippedOutputOn(); + vtkSmartPointer clipperout = Rclipper->GetClippedOutput(); - vtkSmartPointer writerC1 = vtkSmartPointer::New(); - writerC1->SetInput(clipperout); - writerC1->SetFileName("/vtkOutput/FbId_clipLineId0+1+2-tests.vtk"); - writerC1->SetFileTypeToASCII(); - writerC1->Write(); + vtkSmartPointer writerC1 = vtkSmartPointer::New(); + writerC1->SetInput(clipperout); + writerC1->SetFileName("/vtkOutput/FbId_clipLineId0+1+2-tests.vtk"); + writerC1->SetFileTypeToASCII(); + writerC1->Write(); - /*======STEP 1====== + /*======STEP 1====== * extract all points, which are crossing the plane */ - // Scalar values describe the distance between each remaining point to the given plane. Values sorted by point index - vtkSmartPointer distanceList = clipperout->GetPointData()->GetScalars(); - vtkIdType sizeOfList = distanceList->GetNumberOfTuples(); - PointsOnPlane.reserve(sizeOfList); /* use reserve for high-performant push_back, no hidden copy procedures are processed then! + // Scalar values describe the distance between each remaining point to the given plane. Values sorted by point index + vtkSmartPointer distanceList = clipperout->GetPointData()->GetScalars(); + vtkIdType sizeOfList = distanceList->GetNumberOfTuples(); + PointsOnPlane.reserve(sizeOfList); /* use reserve for high-performant push_back, no hidden copy procedures are processed then! * size of list can be optimized by reducing allocation, but be aware of iterator and vector size*/ - for (int i=0; iGetTuple(i); - std::cout << "distance of point " << i << " : " << distance[0] << std::endl; + for (int i=0; iGetTuple(i); + std::cout << "distance of point " << i << " : " << distance[0] << std::endl; + + // check if point is on plane. + // 0.01 due to some approximation errors when calculating distance + if (distance[0] >= -0.01 && distance[0] <= 0.01) + { + std::cout << "adding " << i << endl; + PointsOnPlane.push_back(i); //push back in combination with reserve is fastest way to fill vector with various values + } - // check if point is on plane. - // 0.01 due to some approximation errors when calculating distance - if (distance[0] >= -0.01 && distance[0] <= 0.01) - { - std::cout << "adding " << i << endl; - PointsOnPlane.push_back(i); //push back in combination with reserve is fastest way to fill vector with various values } - } + // DEBUG print out all interesting points, stop where array starts with value -1. after -1 no more interesting idx are set! + std::vector::iterator rit = PointsOnPlane.begin(); + while (rit != PointsOnPlane.end() ) { + std::cout << "interesting point: " << *rit << " coord: " << clipperout->GetPoint(*rit)[0] << " | " << clipperout->GetPoint(*rit)[1] << " | " << clipperout->GetPoint(*rit)[2] << endl; + rit++; + } + - // DEBUG print out all interesting points, stop where array starts with value -1. after -1 no more interesting idx are set! - std::vector::iterator rit = PointsOnPlane.begin(); - while (rit != PointsOnPlane.end() ) { - std::cout << "interesting point: " << *rit << " coord: " << clipperout->GetPoint(*rit)[0] << " | " << clipperout->GetPoint(*rit)[1] << " | " << clipperout->GetPoint(*rit)[2] << endl; - rit++; - } - /*=======STEP 2===== + /*=======STEP 2===== * extract ROI relevant pointIds */ - //ToDo - if( true /*point in ROI*/) - { - PointsInROI = PointsOnPlane; - } + //ToDo - /*======STEP 3======= - * identify fiberIds for points in ROI */ - //prepare resulting vector - FibersInROI.reserve(PointsInROI.size()); + mitk::PlanarCircle::Pointer circleName = mitk::PlanarCircle::New(); + mitk::PlanarPolygon::Pointer polyName = mitk::PlanarPolygon::New(); + if (pf->GetNameOfClass() == circleName->GetNameOfClass() ) + { - vtkCellArray *clipperlines = clipperout->GetLines(); - clipperlines->InitTraversal(); - long numOfLineCells = clipperlines->GetNumberOfCells(); + if( true /*point in ROI*/) + { + PointsInROI = PointsOnPlane; + } + } - // go through resulting "sub"lines which are stored as cells, "i" corresponds to current line id. - for (int i=0, ic=0 ; iGetCell(ic, npts, pts); - // go through point ids in hosting subline, "j" corresponds to current pointindex in current line i. - for (long j=0; jGetLines(); + clipperlines->InitTraversal(); + long numOfLineCells = clipperlines->GetNumberOfCells(); - for (long k = 0; k < PointsInROI.size(); k++) - { // k corresponds to index in PointsInRoi vector - /* ==================== - * check if current point occurs in ROI - ======================*/ - if (pts[j] == PointsInROI[k]) { - //figure out which line does it belong to - if (clipperout->GetCellData()->HasArray("FB_IDs")) - { - int originalFibId = clipperout->GetCellData()->GetArray("FB_IDs")->GetTuple(i)[0]; - std::cout << "found pointid " << PointsInROI[k] << ": " << clipperout->GetPoint(PointsInROI[k])[0] << " | " << clipperout->GetPoint(PointsInROI[k])[1] << " | " << clipperout->GetPoint(PointsInROI[k])[2] << " in subline: " << i << " which belongs to fiber id: " << originalFibId << "\n" << endl; + // go through resulting "sub"lines which are stored as cells, "i" corresponds to current line id. + for (int i=0, ic=0 ; iGetCell(ic, npts, pts); + // go through point ids in hosting subline, "j" corresponds to current pointindex in current line i. + for (long j=0; jGetCellData()->HasArray("FB_IDs")) + { + int originalFibId = clipperout->GetCellData()->GetArray("FB_IDs")->GetTuple(i)[0]; + std::cout << "found pointid " << PointsInROI[k] << ": " << clipperout->GetPoint(PointsInROI[k])[0] << " | " << clipperout->GetPoint(PointsInROI[k])[1] << " | " << clipperout->GetPoint(PointsInROI[k])[2] << " in subline: " << i << " which belongs to fiber id: " << originalFibId << "\n" << endl; + + // do something to avoid duplicates + int oldFibInRoiSize = FibersInROI.size(); + if (oldFibInRoiSize != 0) { + + + for (int f=0; f::iterator finIt = FibersInROI.begin(); + while ( finIt != FibersInROI.end() ) { + std::cout << *finIt << endl; + ++finIt; + } + std::cout << "=====================\n"; - std::cout << "\n=====FINAL RESULT: fib_id ======\n"; - std::vector::iterator finIt = FibersInROI.begin(); - while ( finIt != FibersInROI.end() ) { - std::cout << *finIt << endl; - ++finIt; } - std::cout << "=====================\n"; - -} -void mitk::FiberBundleX::UpdateFiberGeometry() -{ + void mitk::FiberBundleX::UpdateFiberGeometry() + { - float min = itk::NumericTraits::min(); - float max = itk::NumericTraits::max(); - float b[] = {max, min, max, min, max, min}; + float min = itk::NumericTraits::min(); + float max = itk::NumericTraits::max(); + float b[] = {max, min, max, min, max, min}; - vtkCellArray* cells = m_FiberPolyData->GetLines(); - cells->InitTraversal(); - for (int i=0; iGetNumberOfCells(); i++) - { + vtkCellArray* cells = m_FiberPolyData->GetLines(); + cells->InitTraversal(); + for (int i=0; iGetNumberOfCells(); i++) + { - vtkCell* cell = m_FiberPolyData->GetCell(i); - int p = cell->GetNumberOfPoints(); - vtkPoints* points = cell->GetPoints(); - for (int j=0; jGetPoint(j, p); + vtkCell* cell = m_FiberPolyData->GetCell(i); + int p = cell->GetNumberOfPoints(); + vtkPoints* points = cell->GetPoints(); + for (int j=0; jGetPoint(j, p); - if (p[0]b[1]) - b[1]=p[0]; + if (p[0]b[1]) + b[1]=p[0]; - if (p[1]b[3]) - b[3]=p[1]; + if (p[1]b[3]) + b[3]=p[1]; - if (p[2]b[5]) - b[5]=p[2]; + if (p[2]b[5]) + b[5]=p[2]; - } - - } + } - // provide some buffer space at borders + } - for(int i=0; i<=4; i+=2){ - b[i] -=10; - } + // provide some buffer space at borders - for(int i=1; i<=5; i+=2){ - b[i] +=10; - } + for(int i=0; i<=4; i+=2){ + b[i] -=10; + } - mitk::Geometry3D::Pointer geometry = mitk::Geometry3D::New(); - geometry->SetImageGeometry(true); - geometry->SetFloatBounds(b); - this->SetGeometry(geometry); + for(int i=1; i<=5; i+=2){ + b[i] +=10; + } + mitk::Geometry3D::Pointer geometry = mitk::Geometry3D::New(); + geometry->SetImageGeometry(true); + geometry->SetFloatBounds(b); + this->SetGeometry(geometry); + } } /*============================== *++++ FIBER INFORMATION +++++++ ===============================*/ QStringList mitk::FiberBundleX::GetAvailableColorCodings() { QStringList availableColorCodings; int numColors = m_FiberPolyData->GetPointData()->GetNumberOfArrays(); for(int i=0; iGetPointData()->GetArrayName(i)); } //this controlstructure shall be implemented by the calling method if (availableColorCodings.isEmpty()) MITK_INFO << "no colorcodings available in fiberbundleX"; // for(int i=0; im_currentColorCoding; } void mitk::FiberBundleX::SetColorCoding(const char* requestedColorCoding) { // MITK_INFO << "FbX try to set colorCoding: " << requestedColorCoding << " compare with: " << COLORCODING_ORIENTATION_BASED; if(strcmp (COLORCODING_ORIENTATION_BASED,requestedColorCoding) == 0 ) { this->m_currentColorCoding = (char*) COLORCODING_ORIENTATION_BASED; this->m_isModified = true; } else if(strcmp (COLORCODING_FA_BASED,requestedColorCoding) == 0 ) { this->m_currentColorCoding = (char*) COLORCODING_FA_BASED; this->m_isModified = true; } else { MITK_INFO << "FIBERBUNDLE X: UNKNOWN COLORCODING in FIBERBUNDLEX Datastructure"; this->m_currentColorCoding = "---"; //will cause blank colorcoding of fibers this->m_isModified = true; } } bool mitk::FiberBundleX::isFiberBundleXModified() { - return m_isModified; + return m_isModified; } void mitk::FiberBundleX::setFBXModificationDone() { - m_isModified = false; + m_isModified = false; } // Resample fiber to get equidistant points void mitk::FiberBundleX::ResampleFibers(float len) { - vtkSmartPointer newPoly = vtkSmartPointer::New(); - vtkSmartPointer newCellArray = vtkSmartPointer::New(); - vtkSmartPointer newPoints = vtkSmartPointer::New(); + vtkSmartPointer newPoly = vtkSmartPointer::New(); + vtkSmartPointer newCellArray = vtkSmartPointer::New(); + vtkSmartPointer newPoints = vtkSmartPointer::New(); - vtkSmartPointer vLines = m_FiberPolyData->GetLines(); - vLines->InitTraversal(); - int numberOfLines = vLines->GetNumberOfCells(); + vtkSmartPointer vLines = m_FiberPolyData->GetLines(); + vLines->InitTraversal(); + int numberOfLines = vLines->GetNumberOfCells(); - for (int i=0; iGetNextCell ( numPoints, points ); + for (int i=0; iGetNextCell ( numPoints, points ); - vtkSmartPointer container = vtkSmartPointer::New(); + vtkSmartPointer container = vtkSmartPointer::New(); - double* point = m_FiberPolyData->GetPoint(points[0]); - vtkIdType pointId = newPoints->InsertNextPoint(point); - container->GetPointIds()->InsertNextId(pointId); + double* point = m_FiberPolyData->GetPoint(points[0]); + vtkIdType pointId = newPoints->InsertNextPoint(point); + container->GetPointIds()->InsertNextId(pointId); - float dtau = 0; - int cur_p = 1; - itk::Vector dR; - float normdR = 0; + float dtau = 0; + int cur_p = 1; + itk::Vector dR; + float normdR = 0; - for (;;) - { - while (dtau <= len && cur_p < numPoints) - { - itk::Vector v1; - point = m_FiberPolyData->GetPoint(points[cur_p-1]); - v1[0] = point[0]; - v1[1] = point[1]; - v1[2] = point[2]; - itk::Vector v2; - point = m_FiberPolyData->GetPoint(points[cur_p]); - v2[0] = point[0]; - v2[1] = point[1]; - v2[2] = point[2]; - - dR = v2 - v1; - normdR = std::sqrt(dR.GetSquaredNorm()); - dtau += normdR; - cur_p++; - } - - if (dtau >= len) - { - itk::Vector v1; - point = m_FiberPolyData->GetPoint(points[cur_p-1]); - v1[0] = point[0]; - v1[1] = point[1]; - v1[2] = point[2]; - - itk::Vector v2 = v1 - dR*( (dtau-len)/normdR ); - pointId = newPoints->InsertNextPoint(v2.GetDataPointer()); - container->GetPointIds()->InsertNextId(pointId); - } - else - { - point = m_FiberPolyData->GetPoint(points[numPoints-1]); - pointId = newPoints->InsertNextPoint(point); - container->GetPointIds()->InsertNextId(pointId); - break; - } - dtau = dtau-len; - } + for (;;) + { + while (dtau <= len && cur_p < numPoints) + { + itk::Vector v1; + point = m_FiberPolyData->GetPoint(points[cur_p-1]); + v1[0] = point[0]; + v1[1] = point[1]; + v1[2] = point[2]; + itk::Vector v2; + point = m_FiberPolyData->GetPoint(points[cur_p]); + v2[0] = point[0]; + v2[1] = point[1]; + v2[2] = point[2]; + + dR = v2 - v1; + normdR = std::sqrt(dR.GetSquaredNorm()); + dtau += normdR; + cur_p++; + } - newCellArray->InsertNextCell(container); - } + if (dtau >= len) + { + itk::Vector v1; + point = m_FiberPolyData->GetPoint(points[cur_p-1]); + v1[0] = point[0]; + v1[1] = point[1]; + v1[2] = point[2]; + + itk::Vector v2 = v1 - dR*( (dtau-len)/normdR ); + pointId = newPoints->InsertNextPoint(v2.GetDataPointer()); + container->GetPointIds()->InsertNextId(pointId); + } + else + { + point = m_FiberPolyData->GetPoint(points[numPoints-1]); + pointId = newPoints->InsertNextPoint(point); + container->GetPointIds()->InsertNextId(pointId); + break; + } + dtau = dtau-len; + } + + newCellArray->InsertNextCell(container); + } - newPoly->SetPoints(newPoints); - newPoly->SetLines(newCellArray); - m_FiberPolyData = newPoly; - UpdateFiberGeometry(); + newPoly->SetPoints(newPoints); + newPoly->SetLines(newCellArray); + m_FiberPolyData = newPoly; + UpdateFiberGeometry(); } /* ESSENTIAL IMPLEMENTATION OF SUPERCLASS METHODS */ void mitk::FiberBundleX::UpdateOutputInformation() { } void mitk::FiberBundleX::SetRequestedRegionToLargestPossibleRegion() { } bool mitk::FiberBundleX::RequestedRegionIsOutsideOfTheBufferedRegion() { - return false; + return false; } bool mitk::FiberBundleX::VerifyRequestedRegion() { - return true; + return true; } void mitk::FiberBundleX::SetRequestedRegion( itk::DataObject *data ) { }