diff --git a/Modules/DiffusionImaging/IODataStructures/FiberBundle/mitkFiberBundle.cpp b/Modules/DiffusionImaging/IODataStructures/FiberBundle/mitkFiberBundle.cpp index ab7e9e33bc..a8fb21dcc4 100644 --- a/Modules/DiffusionImaging/IODataStructures/FiberBundle/mitkFiberBundle.cpp +++ b/Modules/DiffusionImaging/IODataStructures/FiberBundle/mitkFiberBundle.cpp @@ -1,1665 +1,1863 @@ /*========================================================================= 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 "mitkFiberBundle.h" #include "mitkGeometry2D.h" #include "mitkVector.h" #include "mitkPlaneGeometry.h" #include #include "mitkPlanarFigure.h" #include "mitkPlanarCircle.h" #include "mitkPlanarRectangle.h" #include "mitkPlanarPolygon.h" #include "mitkPlanarFigureComposite.h" #include #include /* statics values to define the position of a fiberTractPoint * related to the plane of a ROI */ const int mitk::FiberBundle::TRACTPOINT_BACKFACE = 0; const int mitk::FiberBundle::TRACTPOINT_ON_PLANE = 1; const int mitk::FiberBundle::TRACTPOINT_FRNTFACE = 2; // implementation of all essential methods from superclass mitk::FiberBundle::FiberBundle() { m_GroupFiberBundle = FiberGroupType::New(); m_TractContainer = ContainerType::New(); //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); /* for debugging only */ m_debugITKContainer = itkStochTractContainerType::New(); } mitk::FiberBundle::~FiberBundle() { } void mitk::FiberBundle::SetBounds(float* b) { m_boundsFB[0] = b[0]; m_boundsFB[1] = b[1]; m_boundsFB[2] = b[2]; +} +void mitk::FiberBundle::SetBounds(double* b) +{ + m_boundsFB[0] = b[0]; + m_boundsFB[1] = b[1]; + m_boundsFB[2] = b[2]; } float* mitk::FiberBundle::GetBounds() { - return m_boundsFB; - } void mitk::FiberBundle::PushPoint(int fiberIndex, ContainerPointType point) { if( (unsigned)fiberIndex >= m_TractContainer->Size() ) { fiberIndex = m_TractContainer->Size(); ContainerTractType::Pointer tract = ContainerTractType::New(); tract->InsertElement(tract->Size(),point); m_TractContainer->InsertElement(fiberIndex, tract); } else if(fiberIndex>=0) { m_TractContainer->ElementAt(fiberIndex)->InsertElement(m_TractContainer->ElementAt(fiberIndex)->Size(), point); } } void mitk::FiberBundle::PushTract(ContainerTractType::Pointer tract) { m_TractContainer->InsertElement(m_TractContainer->Size(), tract); } mitk::FiberBundle::Pointer mitk::FiberBundle::JoinBundle(mitk::FiberBundle::Pointer bundle) { mitk::FiberBundle::Pointer retval = mitk::FiberBundle::New(); retval->SetGeometry(this->GetGeometry()); retval->SetBounds(this->m_boundsFB); retval->InsertBundle(this); retval->InsertBundle(bundle); return retval; } void mitk::FiberBundle::InsertBundle(mitk::FiberBundle::Pointer bundle) { // INCOMPLETE, SHOULD CHECK FOR DIFFERENT GEOMETRIES IN THIS+BUNDLE // DO INDEX1 -> WORLD -> INDEX2 TRANSFORMATION, IF THEY ARE DIFFERENT. int num = this->GetNumTracts(); FiberGroupType::Pointer groupFiberBundle = bundle->GetGroupFiberBundle(); ChildrenListType *fiberList = groupFiberBundle->GetChildren(); for(ChildrenListType::iterator itLst = fiberList->begin(); itLst != fiberList->end(); ++itLst) { itk::SpatialObject<3>::Pointer tmp_fbr; tmp_fbr = *itLst; mitk::FiberBundle::DTITubeType::Pointer dtiTract = dynamic_cast< mitk::FiberBundle::DTITubeType * > (tmp_fbr.GetPointer()); if (dtiTract.IsNull()) { MITK_INFO << "DTI Tract is NULL!!!!! omg"; continue; } dtiTract->SetId(num++); this->addSingleDTITract(dtiTract); } ContainerType::Pointer container = bundle->GetTractContainer(); for(int i=0; iSize();i++) { this->PushTract(container->ElementAt(i)); } } int mitk::FiberBundle::FindTractByEndpoints(mitk::FiberBundle::DTITubeType::Pointer searchTract) { int searchNrPnts = searchTract->GetNumberOfPoints(); mitk::FiberBundle::DTITubeType::PointListType searchPntList = searchTract->GetPoints(); typedef mitk::FiberBundle::DTITubeType::PointType PointType; DTITubePointType searchPointFirst = searchPntList.at(0); PointType searchPos1 = searchPointFirst.GetPosition(); DTITubePointType searchPointLast = searchPntList.at(searchNrPnts-1); PointType searchPos2 = searchPointLast.GetPosition(); FiberGroupType::Pointer groupFiberBundle = this->GetGroupFiberBundle(); ChildrenListType *fiberList = groupFiberBundle->GetChildren(); for(ChildrenListType::iterator itLst = fiberList->begin(); itLst != fiberList->end(); ++itLst) { itk::SpatialObject<3>::Pointer tmp_fbr; tmp_fbr = *itLst; mitk::FiberBundle::DTITubeType::Pointer dtiTract = dynamic_cast< mitk::FiberBundle::DTITubeType * > (tmp_fbr.GetPointer()); if (dtiTract.IsNull()) { MITK_INFO << "DTI Tract is NULL!!!!! omg"; continue; } mitk::FiberBundle::DTITubeType::PointListType dtiPntList = dtiTract->GetPoints(); int fibrNrPnts = dtiTract->GetNumberOfPoints(); DTITubePointType point_first = dtiPntList.at(0); PointType pos1 = point_first.GetPosition(); DTITubePointType point_last = dtiPntList.at(fibrNrPnts-1); PointType pos2 = point_last.GetPosition(); if( (pos1 == searchPos1 && pos2 == searchPos2) || (pos2 == searchPos1 && pos1 == searchPos2) ) { return dtiTract->GetId(); } } return -1; } mitk::FiberBundle::Pointer mitk::FiberBundle::SubstractBundle(mitk::FiberBundle::Pointer bundle) { mitk::FiberBundle::Pointer retval = mitk::FiberBundle::New(); retval->SetGeometry(this->GetGeometry()); mitk::FiberBundle::Pointer largeBundle = bundle; mitk::FiberBundle::Pointer smallBundle = this; MITK_INFO << "large children " << largeBundle->GetGroupFiberBundle()->GetNumberOfChildren() << "!="<GetNumTracts(); MITK_INFO << "small children " << smallBundle->GetGroupFiberBundle()->GetNumberOfChildren() << "!="<GetNumTracts(); if(this->GetGroupFiberBundle()->GetNumberOfChildren() > bundle->GetGroupFiberBundle()->GetNumberOfChildren()) { MITK_INFO << "this is large (" << this->GetNumTracts() << ">" << bundle->GetNumTracts() << ")"; largeBundle = this; smallBundle = bundle; } ContainerType::Pointer container = largeBundle->GetTractContainer(); int counter = 0; FiberGroupType::Pointer groupFiberBundle = largeBundle->GetGroupFiberBundle(); ChildrenListType *fiberList = groupFiberBundle->GetChildren(); MITK_INFO << "large number children " << groupFiberBundle->GetNumberOfChildren(); for(ChildrenListType::iterator itLst = fiberList->begin(); itLst != fiberList->end(); ++itLst) { itk::SpatialObject<3>::Pointer tmp_fbr; tmp_fbr = *itLst; mitk::FiberBundle::DTITubeType::Pointer dtiTract = dynamic_cast< mitk::FiberBundle::DTITubeType * > (tmp_fbr.GetPointer()); if (dtiTract.IsNull()) { MITK_INFO << "DTI Tract is NULL!!!!! omg"; continue; } int delId = smallBundle->FindTractByEndpoints(dtiTract); if( delId == -1 ) { retval->addSingleDTITract(dtiTract); retval->PushTract(container->ElementAt(counter)); } MITK_INFO << "Counter " << counter++; } return retval; } mitk::FiberBundle::ContainerPointType mitk::FiberBundle::GetPoint(int tractIndex, int pointIndex) { if (tractIndex>=0 && tractIndex=0 && pointIndexGetElement(tractIndex)->GetElement(pointIndex); } return NULL; } int mitk::FiberBundle::GetNumTracts() { return m_TractContainer->Size(); } int mitk::FiberBundle::GetNumPoints(int tractIndex) { if ((unsigned)tractIndex>=0 && (unsigned)tractIndexSize()) { return m_TractContainer->GetElement(tractIndex)->Size(); } else { //added by igi return NULL; } } mitk::FiberBundle::ContainerTractType::Pointer mitk::FiberBundle::GetTract(int tractIndex) { ContainerTractType::Pointer out; if ((unsigned)tractIndex>0 && (unsigned)tractIndexSize()) return m_TractContainer->GetElement(tractIndex); return out; } void mitk::FiberBundle::additkStochTractContainer(itkStochTractContainerType::Pointer itkStochCont) { //for debugging only m_debugITKContainer = itkStochCont; //******************** /* transform itkStochContainer to standardized TractContainer */ for (itkStochTractContainerType::ConstIterator itCont = itkStochCont->Begin(); itCont != itkStochCont->End(); ++itCont) { // get fiber of itkContainer itkStochTractType::Pointer tract = itCont->Value(); itkStochTractType::VertexListType::ConstPointer vertexlist = tract->GetVertexList(); //init a desired containerFiber ContainerTractType::Pointer contTract = ContainerTractType::New(); //get points of fiber for( int j=0; j<(int)vertexlist->Size(); ++j) { // put the point of vertex pointList in itkContainer itkStochTractType::VertexType vertex = vertexlist->GetElement(j); //prepare for dtiPoint ContainerPointType contPnt; contPnt[0] = (float) vertex[0]; contPnt[1] = (float) vertex[1]; contPnt[2] = (float) vertex[2]; contTract->InsertElement(contTract->Size(), contPnt); /* coordinate testing*/ /*if ((float)vertex[0] == contPnt[0]) { MITK_INFO << " [OK] ... X "; }else { MITK_INFO << "[FAIL] ... itkX: " << vertex[0] << " " << contPnt[0] << "\n" ; } if ((float)vertex[1] == contPnt[1]) { MITK_INFO << " [OK] ... Y "; }else { MITK_INFO << "[FAIL] ... itkY: " << vertex[1] << " " << contPnt[1] << "\n" ; } if ((float)vertex[2] == contPnt[2]) { MITK_INFO << " [OK] ... Z " << "\n" ; MITK_INFO << " Values X Y Z: " << contPnt[0] << " " << contPnt[1] << " " << contPnt[2] << "\n"; }else { MITK_INFO << "[FAIL] ... itkZ: " << vertex[2] << " " << contPnt[2] << "\n" ; } */ } // add filled fiber to container m_TractContainer->InsertElement(m_TractContainer->Size(), contTract); } } void mitk::FiberBundle::addTractContainer( ContainerType::Pointer tractContainer ) { m_TractContainer = tractContainer; } void mitk::FiberBundle::initFiberGroup() { /* iterate through the tractContainer and store fibers in DTISpatialObjects */ for (ContainerType::ConstIterator itCont = m_TractContainer->Begin(); itCont != m_TractContainer->End(); ++itCont) { // init new dtiTube and DTITubeType::Pointer dtiTube = DTITubeType::New(); DTITubeType::PointListType list; // get current tract of container ContainerTractType::Pointer contTract = itCont->Value(); // iterate through the number of points ... use iterator, no index-output is needed anyway for(ContainerTractType::Iterator itContTrct = contTract->Begin(); itContTrct != contTract->End(); ++itContTrct) { // init DTITube point DTITubePointType p; ContainerPointType cntp = itContTrct->Value(); p.SetPosition(cntp[0], cntp[1], cntp[2]); p.SetRadius(1); mitk::FiberBundle::fiberPostprocessing_setTensorMatrix( &p ); mitk::FiberBundle::fiberPostprocessing_FA( &p ); //mitk::FiberBundle::fiberPostprocessing_setTensorMatrix( &p ); p.AddField(DTITubePointType::GA, 3); p.SetColor(1,0,0,1); list.push_back(p); } // dtiTubes dtiTube->GetProperty()->SetName("dtiTube"); dtiTube->SetId(itCont->Index()); dtiTube->SetPoints(list); m_GroupFiberBundle->AddSpatialObject(dtiTube); } } void mitk::FiberBundle::fiberPostprocessing_setTensorMatrix(DTITubePointType *dtiP) { float tMatrix[6]; tMatrix[0]=0.0f; tMatrix[1]=1.0f; tMatrix[2]=2.0f; tMatrix[3]=3.0f; tMatrix[4]=4.0f; tMatrix[5]=5.0f; dtiP->SetTensorMatrix(tMatrix); } /* this method is a HowTo method, used for debugging only */ void mitk::FiberBundle::fiberPostprocessing_setPoint(DTITubePointType *dtiP, ContainerPointType vrtx) { /* get values of variable referenced by a ponter double vtxIdx1, vtxIdx2, vtxIdx3; vtxIdx1 = * (double*) &vrtx[0]; vtxIdx2 = * (double*) &vrtx[1]; vtxIdx3 = * (double*) &vrtx[2]; dtiP->SetPosition(vtxIdx1, vtxIdx2, vtxIdx3); */ dtiP->SetPosition(vrtx[0], vrtx[1], vrtx[2]); } void mitk::FiberBundle::fiberPostprocessing_FA(DTITubePointType *dtiP) { debug_PrototypeCounter ++; float valFA; if (debug_PrototypeCounter % 10 < 5) { valFA = 1.0; } else if (debug_PrototypeCounter % 10 == 7) { valFA = 0.3; } else if (debug_PrototypeCounter % 10 == 8) { valFA = 0; } else { valFA = 0.5; } dtiP->AddField(DTITubePointType::FA, valFA); } /* methods for high speed perfoermance dispay or live-monitoring of fiber results */ void mitk::FiberBundle::addContainer4speedDisplay(ContainerType::Pointer speedTractContainer) { } void mitk::FiberBundle::addSingleDTITract(mitk::FiberBundle::DTITubeType::Pointer dtiFbrTrct) { //MITK_INFO << " start addSingleDTITract(): " << m_GroupFiberBundle->GetNumberOfChildren(); m_GroupFiberBundle->AddSpatialObject(dtiFbrTrct); //MITK_INFO << "end addSingleDTITract(): " << m_GroupFiberBundle->GetNumberOfChildren(); } mitk::FiberBundle::FiberGroupType::Pointer mitk::FiberBundle::getGroupFiberBundle() { return m_GroupFiberBundle; } std::vector mitk::FiberBundle::getAllIDsInFiberBundle() { std::vector allFBIds; FiberGroupType::Pointer fiberGroup = this->getGroupFiberBundle(); ChildrenListType *FiberList; FiberList = fiberGroup->GetChildren(); for(ChildrenListType::iterator itLst = FiberList->begin(); itLst != FiberList->end(); ++itLst) { itk::SpatialObject<3>::Pointer tmp_fbr; tmp_fbr = *itLst; mitk::FiberBundle::DTITubeType::Pointer dtiTract = dynamic_cast< mitk::FiberBundle::DTITubeType * > (tmp_fbr.GetPointer()); if (dtiTract.IsNull()) { MITK_INFO << "DTI Tract is NULL!!!!! omg"; continue; } allFBIds.push_back(dtiTract->GetId()); } return allFBIds; } mitk::FiberBundle::Pointer mitk::FiberBundle::extractFibersById(std::vector idSet) { mitk::FiberBundle::Pointer resultingFibers = mitk::FiberBundle::New(); resultingFibers->SetGeometry(this->GetGeometry()); resultingFibers->SetBounds(this->GetBounds()); //get Fiber by ID //get childrenList //compare if current FiberID is in idSet FiberGroupType::Pointer fiberGroup = this->getGroupFiberBundle(); ChildrenListType *FiberList; FiberList = fiberGroup->GetChildren(); MITK_INFO << "writing fibers into datastructure:...."; for (int cg=0; cgPushTract( m_TractContainer->GetElement(trctId) ); } MITK_INFO << "init new fiberBundle..."; resultingFibers->initFiberGroup(); MITK_INFO << "init new fiberBundle [DONE]"; /* for(ChildrenListType::iterator itLst = FiberList->begin(); itLst != FiberList->end(); ++itLst) { itk::SpatialObject<3>::Pointer tmp_fbr; tmp_fbr = *itLst; mitk::FiberBundle::DTITubeType::Pointer dtiTract = dynamic_cast< mitk::FiberBundle::DTITubeType * > (tmp_fbr.GetPointer()); if (dtiTract.IsNull()) { MITK_INFO << "DTI Tract is NULL!!!!! omg"; continue; } // MITK_INFO << "current DTI tract id: " << dtiTract->GetId(); std::vector::iterator retFibers = find(idSet.begin(), idSet.end(), dtiTract->GetId()); if (retFibers != idSet.end()) { //MITK_INFO << "Fiber and ID equal: "; DTITubeType::Pointer copyDTITract = this->copySingleDTITract(dtiTract); MITK_INFO << "fibercontainer before adding new tract" << resultingFibers->GetNumTracts(); resultingFibers->addSingleDTITract(copyDTITract); MITK_INFO << "fibercontainer after adding new tract" << resultingFibers->GetNumTracts(); } //else { // MITK_INFO << "Fiber and ID not ident!"; //} //std::set::iterator retFibers //retFibers = idSet.find(dtiTract->GetId()); } */ return resultingFibers; } /* extract fibers using planar Figures */ //mitk::FiberBundle::Pointer mitk::FiberBundle::extractFibersPF(mitk::PlanarFigure::Pointer pf) std::vector mitk::FiberBundle::extractFibersByPF(mitk::PlanarFigure::Pointer pf, std::vector* smaller_set) { // if incoming pf is a pfc mitk::PlanarFigureComposite::Pointer pfcomp= dynamic_cast(pf.GetPointer()); if (!pfcomp.IsNull()) { //PFC switch (pfcomp->getOperationType()) { case 0: { //AND std::vector childResults = this->extractFibersByPF(pfcomp->getChildAt(0), smaller_set); std::vector tmpChild = childResults; for (int i=1; igetNumberOfChildren(); ++i) { tmpChild = extractFibersByPF(pfcomp->getChildAt(i),&tmpChild); } std::vector AND_Assamblage(tmpChild.begin(), tmpChild.end()); return AND_Assamblage; } case 1: { //OR std::vector childResults = this->extractFibersByPF(pfcomp->getChildAt(0), smaller_set); std::sort(childResults.begin(), childResults.end()); std::vector tmp_container(m_TractContainer->Size()); std::vector::iterator end; for (int i=1; igetNumberOfChildren(); ++i) { std::vector tmpChild = extractFibersByPF(pfcomp->getChildAt(i), smaller_set); sort(tmpChild.begin(), tmpChild.end()); end = std::set_union(childResults.begin(), childResults.end(), tmpChild.begin(), tmpChild.end(), tmp_container.begin() ); childResults.assign(tmp_container.begin(), end); } std::vector OR_Assamblage(childResults.begin(), childResults.end()); return OR_Assamblage; } case 2: { //NOT // FIRST AN AND OPERATION std::vector childResults = this->extractFibersByPF(pfcomp->getChildAt(0), smaller_set); std::sort(childResults.begin(), childResults.end()); std::vector tmpChild = childResults; for (int i=1; igetNumberOfChildren(); ++i) { tmpChild = extractFibersByPF(pfcomp->getChildAt(i),&tmpChild); } std::vector AND_Assamblage(tmpChild.begin(), tmpChild.end()); // get IDs of interesting fibers std::vector interesting_fibers; if(!smaller_set) interesting_fibers = this->getAllIDsInFiberBundle(); else interesting_fibers.assign(smaller_set->begin(), smaller_set->end()); std::sort(interesting_fibers.begin(), interesting_fibers.end()); // all interesting fibers that are not in the AND assemblage std::vector tmp_not(interesting_fibers.size()); std::vector::iterator end; end = std::set_difference(interesting_fibers.begin(), interesting_fibers.end(), AND_Assamblage.begin(), AND_Assamblage.end(), tmp_not.begin() ); std::vector NOT_Assamblage(tmp_not.begin(),end); return NOT_Assamblage; } default: MITK_INFO << "we have an UNDEFINED composition... ERROR" ; break; } } else { mitk::PlanarCircle::Pointer circleName = mitk::PlanarCircle::New(); mitk::PlanarRectangle::Pointer rectName = mitk::PlanarRectangle::New(); mitk::PlanarPolygon::Pointer polyName = mitk::PlanarPolygon::New(); if (pf->GetNameOfClass() == circleName->GetNameOfClass() ) { //MITK_INFO << "We have a circle :-) " ; int cntGaps = 0; //init output FiberBundle mitk::FiberBundle::Pointer FB_Clipped = mitk::FiberBundle::New(); FB_Clipped->SetGeometry(this->GetGeometry()); //get geometry containing the plane which we need to calculate the xrossingPoints mitk::Geometry2D::ConstPointer pfgeometry = pf->GetGeometry2D(); const mitk::PlaneGeometry* planeGeometry = dynamic_cast (pfgeometry.GetPointer()); std::vector XingPoints; std::vector fiberIDs; //################################################################# //############### Find Gap, FrontFace BackFace #################### //################################################################# //get fibercontainer and iterate through the fibers FiberGroupType::Pointer fiberGroup = this->getGroupFiberBundle(); //extract single fibers ChildrenListType *FiberList; FiberList = fiberGroup->GetChildren(); // iterate through each single tract //int cntFibId = -1; for(ChildrenListType::iterator itLst = FiberList->begin(); itLst != FiberList->end(); ++itLst) { //MITK_INFO << "***************** NEW FIBER *********************"; //cntFibId++; itk::SpatialObject<3>::Pointer tmp_fbr; tmp_fbr = *itLst; mitk::FiberBundle::DTITubeType::Pointer dtiTract = dynamic_cast< mitk::FiberBundle::DTITubeType * > (tmp_fbr.GetPointer()); if (dtiTract.IsNull()) { MITK_INFO << " could not cast groupFiberBundle child into dtiTract!... LEVEL 4 ERROR"; continue; } if (smaller_set && std::find(smaller_set->begin(), smaller_set->end(), dtiTract->GetId())==smaller_set->end()) continue; //get list of points int fibrNrPnts = dtiTract->GetNumberOfPoints(); mitk::FiberBundle::DTITubeType::PointListType dtiPntList = dtiTract->GetPoints(); // if one fiber is represented by just one point.... // check if this point is on the plane if (fibrNrPnts <= 0) { MITK_INFO << "HyperERROR in mitkFiberBundle.cpp, No point in fiber....check ur algorithm:"; continue; } /* for finding a gap we need to have knowledge of the previous normal * be aware that there can be more than 1 gaps! */ int prevPntFacing = -999999; int currPntFacing = -999999; //double prevFacing = -99999999099; mitk::Point3D prevFiberPntmm; for(int i=0; iGetGeometry()->IndexToWorld(tmpFiberVec, currentFiberPntmm); double faceing = pfgeometry->SignedDistance(currentFiberPntmm); //MITK_INFO << "FacingOutput: " << faceing; /////////////////////////////////////// if (faceing < 0) { //backface currPntFacing = TRACTPOINT_BACKFACE; //MITK_INFO << "is BACKFACE" << currentFiberPntmm ; } else if (faceing > 0) { //frontface currPntFacing = TRACTPOINT_FRNTFACE; // MITK_INFO << "is FRONTFACE" << currentFiberPntmm ; } else if (faceing == 0) { //onplane currPntFacing = TRACTPOINT_ON_PLANE; //MITK_INFO << "is on PLANE" << currentFiberPntmm ; } //////////////////////////////////////// if (currPntFacing == TRACTPOINT_ON_PLANE) { //strike, //calculate distance //TODO SOURCE THIS CONTROLSTRUCTURE OUT if(isPointInSelection(tmpFiberVec,pf)) { DTITubeType::Pointer copyDTITract = copySingleDTITract(dtiTract); //MITK_INFO << "GroupFB extract after copy of Children: " << fiberGroup->GetNumberOfChildren(); FB_Clipped->addSingleDTITract(copyDTITract); } } else { // Point is BACKFACE or FRONTFACE if (i > 0) { //check if there is a gap between previous and current bool isGap = checkForGap(currPntFacing, prevPntFacing); if (isGap == true) { ++cntGaps; // mitk::Vector3D LineDirection; LineDirection[0] = currentFiberPntmm[0] - prevFiberPntmm[0]; LineDirection[1] = currentFiberPntmm[1] - prevFiberPntmm[1]; LineDirection[2] = currentFiberPntmm[2] - prevFiberPntmm[2]; mitk::Line3D Xingline( prevFiberPntmm, LineDirection ); mitk::Point3D intersectionPoint; Vector3D planeNormal = planeGeometry->GetNormal(); planeNormal.Normalize(); Vector3D lineDirection = Xingline.GetDirection(); lineDirection.Normalize(); double t = planeNormal * lineDirection; if ( fabs( t ) < eps ) { } Vector3D diff; diff = planeGeometry->GetOrigin() - Xingline.GetPoint(); t = ( planeNormal * diff ) / t; intersectionPoint = Xingline.GetPoint() + lineDirection * t; // bool successXing = planeGeometry->IntersectionPoint( Xingline, intersectionPoint ); //mitk::Point3D intersectionPointmm; //planeGeometry->IndexToWorld(intersectionPoint,intersectionPointmm ); // MITK_INFO << "PlaneIntersectionPoint: " << intersectionPoint; if (false) { MITK_INFO << " ERROR CALCULATING INTERSECTION POINT.....should not happen!! "; } //TODO more nice if this if is outside... bool pntInROI = isPointInSelection(intersectionPoint,pf); if(pntInROI) { // MITK_INFO << "POINT ALSO in ROI"; // MITK_INFO << "GroupFB extract before copy new object. of Children: " << fiberGroup->GetNumberOfChildren(); /* dtiTubeSpatial::Pointer can not occur in 2 GroupSpatialObjects, therefore we have to copy the whole dtiTract of current List and add the copy to the desired FiberBundle */ // DTITubeType::Pointer copyDTITract = copySingleDTITract(dtiTract); // MITK_INFO << "GroupFB extract after copy of Children: " << fiberGroup->GetNumberOfChildren(); //FB_Clipped->addSingleDTITract(copyDTITract); //MITK_INFO << "GroupFB extract after adding dtiTract to now FB NR. of Children: " << fiberGroup->GetNumberOfChildren(); //MITK_INFO << "DTI Tract ID: " << dtiTract->GetId(); // MITK_INFO << "size of Vector before pushing: " << fiberIDs.size(); fiberIDs.push_back(dtiTract->GetId()); // MITK_INFO << "size of Vector after pushing: " << fiberIDs.size(); //MITK_INFO << "GroupFB extract after adding dtiTract to now FB NR. of Children: " << fiberGroup->GetNumberOfChildren(); break; } } // MITK_INFO << "---no gap---"; } //endif i>0 } //endif Facing // MITK_INFO << "GroupFB extract end Facing, NR. of Children: " << fiberGroup->GetNumberOfChildren(); //update point flag prevPntFacing = currPntFacing; prevFiberPntmm = currentFiberPntmm; } //end for fiberPoints //MITK_INFO ;<< "GroupFB extract end of single tract, NR. of Children: " << fiberGroup->GetNumberOfChildren(); } //end for fiberTracts // MITK_INFO << "GroupFB extract end of iterating through fiberBundle, NR. of Children: " << fiberGroup->GetNumberOfChildren(); // MITK_INFO << "selected " << fiberIDs.size() << " fibers " << " | counted gaps: " << cntGaps; return fiberIDs; } else if (pf->GetNameOfClass() == rectName->GetNameOfClass() ){ MITK_INFO << "We have a rectangle :-) " ; } else if (pf->GetNameOfClass() == polyName->GetNameOfClass() ) { //MITK_INFO << "We have a polygon :-) " ; int cntGaps = 0; //init output FiberBundle mitk::FiberBundle::Pointer FB_Clipped = mitk::FiberBundle::New(); FB_Clipped->SetGeometry(this->GetGeometry()); //get geometry containing the plane which we need to calculate the xrossingPoints mitk::Geometry2D::ConstPointer pfgeometry = pf->GetGeometry2D(); const mitk::PlaneGeometry* planeGeometry = dynamic_cast (pfgeometry.GetPointer()); std::vector XingPoints; std::vector fiberIDs; //################################################################# //############### Find Gap, FrontFace BackFace #################### //################################################################# //get fibercontainer and iterate through the fibers FiberGroupType::Pointer fiberGroup = this->getGroupFiberBundle(); //extract single fibers ChildrenListType *FiberList; FiberList = fiberGroup->GetChildren(); int nrFibrs = fiberGroup->GetNumberOfChildren(); // iterate through each single tract int cntFib = 1; for(ChildrenListType::iterator itLst = FiberList->begin(); itLst != FiberList->end(); ++itLst) { if (cntFib % 500 == 0) { MITK_INFO << "================\n prosessed fibers: " << cntFib << " of " << nrFibrs;; } ++cntFib; //MITK_INFO << "***************** NEW FIBER *********************"; //cntFibId++; itk::SpatialObject<3>::Pointer tmp_fbr; tmp_fbr = *itLst; mitk::FiberBundle::DTITubeType::Pointer dtiTract = dynamic_cast< mitk::FiberBundle::DTITubeType * > (tmp_fbr.GetPointer()); if (dtiTract.IsNull()) { MITK_INFO << " could not cast groupFiberBundle child into dtiTract!... LEVEL 4 ERROR"; continue; } if (smaller_set && std::find(smaller_set->begin(), smaller_set->end(), dtiTract->GetId())==smaller_set->end()) continue; //get list of points int fibrNrPnts = dtiTract->GetNumberOfPoints(); mitk::FiberBundle::DTITubeType::PointListType dtiPntList = dtiTract->GetPoints(); // if one fiber is represented by just one point.... // check if this point is on the plane if (fibrNrPnts <= 0) { MITK_INFO << "HyperERROR in mitkFiberBundle.cpp, No point in fiber....check ur algorithm:"; continue; } /* for finding a gap we need to have knowledge of the previous normal * be aware that there can be more than 1 gaps! */ int prevPntFacing = -999999; int currPntFacing = -999999; //double prevFacing = -99999999099; mitk::Point3D prevFiberPntmm; for(int i=0; iGetGeometry()->IndexToWorld(tmpFiberVec, currentFiberPntmm); double faceing = pfgeometry->SignedDistance(currentFiberPntmm); //MITK_INFO << "FacingOutput: " << faceing; /////////////////////////////////////// if (faceing < 0) { //backface currPntFacing = TRACTPOINT_BACKFACE; //MITK_INFO << "is BACKFACE" << currentFiberPntmm ; } else if (faceing > 0) { //frontface currPntFacing = TRACTPOINT_FRNTFACE; // MITK_INFO << "is FRONTFACE" << currentFiberPntmm ; } else if (faceing == 0) { //onplane currPntFacing = TRACTPOINT_ON_PLANE; //MITK_INFO << "is on PLANE" << currentFiberPntmm ; } //////////////////////////////////////// if (currPntFacing == TRACTPOINT_ON_PLANE) { //strike, //calculate distance //TODO SOURCE THIS CONTROLSTRUCTURE OUT if(isPointInSelection(tmpFiberVec,pf)) { DTITubeType::Pointer copyDTITract = copySingleDTITract(dtiTract); //MITK_INFO << "GroupFB extract after copy of Children: " << fiberGroup->GetNumberOfChildren(); FB_Clipped->addSingleDTITract(copyDTITract); } } else { // Point is BACKFACE or FRONTFACE if (i > 0) { //check if there is a gap between previous and current bool isGap = checkForGap(currPntFacing, prevPntFacing); if (isGap == true) { ++cntGaps; // mitk::Vector3D LineDirection; LineDirection[0] = currentFiberPntmm[0] - prevFiberPntmm[0]; LineDirection[1] = currentFiberPntmm[1] - prevFiberPntmm[1]; LineDirection[2] = currentFiberPntmm[2] - prevFiberPntmm[2]; mitk::Line3D Xingline( prevFiberPntmm, LineDirection ); mitk::Point3D intersectionPoint; Vector3D planeNormal = planeGeometry->GetNormal(); planeNormal.Normalize(); Vector3D lineDirection = Xingline.GetDirection(); lineDirection.Normalize(); double t = planeNormal * lineDirection; if ( fabs( t ) < eps ) { } Vector3D diff; diff = planeGeometry->GetOrigin() - Xingline.GetPoint(); t = ( planeNormal * diff ) / t; intersectionPoint = Xingline.GetPoint() + lineDirection * t; // bool successXing = planeGeometry->IntersectionPoint( Xingline, intersectionPoint ); //mitk::Point3D intersectionPointmm; //planeGeometry->IndexToWorld(intersectionPoint,intersectionPointmm ); // MITK_INFO << "PlaneIntersectionPoint: " << intersectionPoint; if (false) { MITK_INFO << " ERROR CALCULATING INTERSECTION POINT.....should not happen!! "; } //TODO more nice if this if is outside... bool pntInROI = isPointInSelection(intersectionPoint,pf); if(pntInROI) { // MITK_INFO << "POINT ALSO in ROI"; // MITK_INFO << "GroupFB extract before copy new object. of Children: " << fiberGroup->GetNumberOfChildren(); /* dtiTubeSpatial::Pointer can not occur in 2 GroupSpatialObjects, therefore we have to copy the whole dtiTract of current List and add the copy to the desired FiberBundle */ // DTITubeType::Pointer copyDTITract = copySingleDTITract(dtiTract); // MITK_INFO << "GroupFB extract after copy of Children: " << fiberGroup->GetNumberOfChildren(); //FB_Clipped->addSingleDTITract(copyDTITract); //MITK_INFO << "GroupFB extract after adding dtiTract to now FB NR. of Children: " << fiberGroup->GetNumberOfChildren(); //MITK_INFO << "DTI Tract ID: " << dtiTract->GetId(); // MITK_INFO << "size of Vector before pushing: " << fiberIDs.size(); fiberIDs.push_back(dtiTract->GetId()); // MITK_INFO << "size of Vector after pushing: " << fiberIDs.size(); //MITK_INFO << "GroupFB extract after adding dtiTract to now FB NR. of Children: " << fiberGroup->GetNumberOfChildren(); break; } } // MITK_INFO << "---no gap---"; } //endif i>0 } //endif Facing // MITK_INFO << "GroupFB extract end Facing, NR. of Children: " << fiberGroup->GetNumberOfChildren(); //update point flag prevPntFacing = currPntFacing; prevFiberPntmm = currentFiberPntmm; } //end for fiberPoints //MITK_INFO ;<< "GroupFB extract end of single tract, NR. of Children: " << fiberGroup->GetNumberOfChildren(); } //end for fiberTracts // MITK_INFO << "GroupFB extract end of iterating through fiberBundle, NR. of Children: " << fiberGroup->GetNumberOfChildren(); // MITK_INFO << "selected " << fiberIDs.size() << " fibers " << " | counted gaps: " << cntGaps; return fiberIDs; } else { MITK_INFO << "[ERROR] unhandled PlanarFigureType found!"; } } } mitk::FiberBundle::DTITubeType::Pointer mitk::FiberBundle::copySingleDTITract(mitk::FiberBundle::DTITubeType::Pointer currentDtiFiber) { DTITubeType::Pointer newCopyDtiFiber = DTITubeType::New(); //*** get ID newCopyDtiFiber->SetId( currentDtiFiber->GetId() ); //*** get points DTITubeType::PointListType list; //get list of dtiPoints int fibrNrPnts = currentDtiFiber->GetNumberOfPoints(); mitk::FiberBundle::DTITubeType::PointListType dtiPntList = currentDtiFiber->GetPoints(); for(int i=0; iSetPoints(list); std::string dtiname = currentDtiFiber->GetProperty()->GetName(); newCopyDtiFiber->GetProperty()->SetName(dtiname.c_str()); return newCopyDtiFiber; } /* This Method checks * To recognize a gap between the 2 points, the previous must differ from the current * but if the previous is on the plane and the current one not, then mark this situation as no gap * if both, previous and current are on plane, you'll never jump into this Method */ bool mitk::FiberBundle::checkForGap(int crntPntFacing, int prevPntFacing) { bool isGap = false; if (prevPntFacing != TRACTPOINT_ON_PLANE && crntPntFacing != prevPntFacing) { isGap = true; } else if (prevPntFacing == TRACTPOINT_ON_PLANE && crntPntFacing == TRACTPOINT_ON_PLANE) { MITK_INFO << "###########################################"; MITK_INFO << "$$$ HYPER ERROR, LOGIC MALFUNCTION!! previous point and current point in a fiber are recognized as a potential GAP! THIS IS NOT ALLOWED $$$"; MITK_INFO << "###########################################"; } return isGap; } mitk::Point3D mitk::FiberBundle::calculateCrossingPoint(mitk::Point3D pntFrnt, mitk::Point3D pntbck, mitk::PlanarFigure::Pointer pf) { mitk::Point3D pntXing; //################################################################# //######### Calculate intersection of plane and fiber ############# //################################################################# // transform in space :-) // y = k*x +d // k = (y1 - y0)/(x1 - x0) // d = ok // z adoption, take xy ratio to plane intersection and adopt it to z coordinate // z_intersx = (x1 - intersX)/(x1 - x0) * (z1 - z0) + z1 double y; double k; //slope double d; double x0 = pntFrnt[0]; double y0 = pntFrnt[1]; double z0 = pntFrnt[2]; double x1 = pntbck[0]; double y1 = pntbck[1]; double z1 = pntbck[2]; k = (y1 - y0) / (x1 - x0); // if slope == 0 then leave y as it is, change x // if slope == 1 then leave x as it is, change y // if z of p0 and p1 is the same, just take z /* mitk::PlanarCircle::Pointer circleName = mitk::PlanarCircle::New(); mitk::PlanarRectangle::Pointer rectName = mitk::PlanarRectangle::New(); mitk::PlanarPolygon::Pointer polyName = mitk::PlanarPolygon::New(); if (pf->GetNameOfClass() == circleName->GetNameOfClass() ) { MITK_INFO << "We have a circle :-) " ; //controlpoint 1 is middlepoint //controlpoint 2 is radiuspoint mitk::Vector3D V1w = pf->GetWorldControlPoint(0); //centerPoint mitk::Vector3D V2w = pf->GetWorldControlPoint(1); //radiusPoint mitk::Vector3D V1; mitk::Vector3D V2; this->GetGeometry()->WorldToIndex(V1w, V1); this->GetGeometry()->WorldToIndex(V2w, V2); //calculate distance between those 2 and mitk::Point3D distV; distV = V2 - V1; distV[0] = sqrt( pow(distV[0], 2.0) ); distV[1] = sqrt( pow(distV[1], 2.0) ); distV[2] = sqrt( pow(distV[2], 2.0) ); mitk::Point3D distPnt; distPnt = pnt3D - V1; distPnt[0] = sqrt( pow(distPnt[0], 2.0) ); distPnt[1] = sqrt( pow(distPnt[1], 2.0) ); distPnt[2] = sqrt( pow(distPnt[2], 2.0) ); if ( (distPnt <= distV) ) { pntIsInside = true; } return pntIsInside; //compare the result to the distance of all points an a fiber } else if (pf->GetNameOfClass() == rectName->GetNameOfClass() ){ MITK_INFO << "We have a rectangle :-) " ; } else if (pf->GetNameOfClass() == polyName->GetNameOfClass() ) { MITK_INFO << "We have a polygon :-) " ; } */ return pntXing; } bool mitk::FiberBundle::isPointInSelection(mitk::Point3D pnt3D, mitk::PlanarFigure::Pointer pf) { /* TODO needs to be redesigned.... each time because in planarPolygonsection VTK object will be initialized for each point!...PERFORMANCE LACK!!!!!!! */ //calculate distances mitk::PlanarCircle::Pointer circleName = mitk::PlanarCircle::New(); mitk::PlanarRectangle::Pointer rectName = mitk::PlanarRectangle::New(); mitk::PlanarPolygon::Pointer polyName = mitk::PlanarPolygon::New(); if (pf->GetNameOfClass() == circleName->GetNameOfClass() ) { //MITK_INFO << "We have a circle :-) " ; //controlpoint 1 is middlepoint //controlpoint 2 is radiuspoint mitk::Point3D V1w = pf->GetWorldControlPoint(0); //centerPoint mitk::Point3D V2w = pf->GetWorldControlPoint(1); //radiusPoint mitk::Vector3D V1; mitk::Vector3D V2; // this->GetGeometry()->WorldToIndex(V1w, V1); // this->GetGeometry()->WorldToIndex(V2w, V2); //calculate distance between those 2 and double distPF; distPF = sqrt((double) (V2w[0] - V1w[0]) * (V2w[0] - V1w[0]) + (V2w[1] - V1w[1]) * (V2w[1] - V1w[1]) + (V2w[2] - V1w[2]) * (V2w[2] - V1w[2])); double XdistPnt = sqrt((double) (pnt3D[0] - V1w[0]) * (pnt3D[0] - V1w[0]) + (pnt3D[1] - V1w[1]) * (pnt3D[1] - V1w[1]) + (pnt3D[2] - V1w[2]) * (pnt3D[2] - V1w[2])) ; if ( (distPF > XdistPnt) ) { return true; } return false; //compare the result to the distance of all points an a fiber } else if (pf->GetNameOfClass() == rectName->GetNameOfClass() ){ MITK_INFO << "We have a rectangle :-) " ; } else if (pf->GetNameOfClass() == polyName->GetNameOfClass() ) { //create vtkPolygon using controlpoints from planarFigure polygon vtkPolygon* polygonVtk = vtkPolygon::New(); //get the control points from pf and insert them to vtkPolygon unsigned int nrCtrlPnts = pf->GetNumberOfControlPoints(); // MITK_INFO << "We have a polygon with " << nrCtrlPnts << " controlpoints: " ; for (int i=0; iGetPoints()->InsertNextPoint((double)pf->GetWorldControlPoint(i)[0], (double)pf->GetWorldControlPoint(i)[1], (double)pf->GetWorldControlPoint(i)[2] ); } //prepare everything for using pointInPolygon function double n[3]; polygonVtk->ComputeNormal(polygonVtk->GetPoints()->GetNumberOfPoints(), static_cast(polygonVtk->GetPoints()->GetData()->GetVoidPointer(0)), n); double bounds[6]; polygonVtk->GetPoints()->GetBounds(bounds); double checkIn[3] = {pnt3D[0], pnt3D[1], pnt3D[2]}; int isInPolygon = polygonVtk->PointInPolygon(checkIn, polygonVtk->GetPoints()->GetNumberOfPoints() , static_cast(polygonVtk->GetPoints()->GetData()->GetVoidPointer(0)), bounds, n); // MITK_INFO << "======IsPointOnPolygon:========\n" << isInPolygon << "\n ======================== "; polygonVtk->Delete(); if (isInPolygon == 1) { // MITK_INFO << "return true"; return true; } else if (isInPolygon == 0) { // MITK_INFO << "return false"; return false; } else { MITK_INFO << "&*&*&*&*&*&*&*&*&*&*&*&*&*&*&*&*&*& \n YOUR DRAWN POLYGON DOES IS DEGENERATED AND NOT ACCEPTED \n DRAW A NEW ONE!! HAI CAPITO \n &*&*&*&*&*&*&*&*&*&*&*&*&*&*&*&*&*&"; } } } void mitk::FiberBundle::debug_members() { /* Debug Workflow description * Test1: check if both, groupSpatialObject and Tract container have the same amount of fiberTracts * Test2: check if points in tracts contain the same coordinates * next... to be continued */ /* ######### TEST 1 START ######### */ //************************************* MITK_INFO << " ############### \n *** TEST Equal Amount of Fibers *** \n "; unsigned int groupEls = m_GroupFiberBundle->GetNumberOfChildren(); unsigned int contEls = m_TractContainer->Size(); unsigned int itkcontEls = m_debugITKContainer->Size(); if (groupEls == contEls && contEls == itkcontEls) { MITK_INFO << "[OK] .... Test1 passed. # of Fibers: " << groupEls << " \n ******************** "; } else { MITK_INFO << "[FAIL]: Container and FiberGroup do not contain same amount of fibers! \n "; // MITK_INFO << " Container # of Fibers: " << contEls << " | FiberBundle # of Fibers: " << groupEls << "\n"; MITK_INFO << " # of Fibers m_Cont: " << contEls << " | GroupFibers: " << groupEls << " | ITKCont: " << itkcontEls << "\n"; } /* ######### TEST 1 END ######### */ //*********************************** /* ######### TEST 2 START ######### */ //************************************* /* iterate through itkcontainer*/ itkStochTractContainerType::ConstIterator itITKCnt; itITKCnt = m_debugITKContainer->Begin(); /* extract DTIFiberTracts of the GroupFiberBundle Object */ // all smartPointers to fibers stored in in a ChildrenList ChildrenListType * FiberList; FiberList = m_GroupFiberBundle->GetChildren(); /* iterate through container, itkcontainer groupFiberBundle in one iteration step */ ChildrenListType::iterator itLst; //STL "list" itself provides no index output of current iteration step. itLst = FiberList->begin(); ContainerType::ConstIterator vecIter; for ( vecIter = m_TractContainer->Begin(); vecIter != m_TractContainer->End(); vecIter++ ) { unsigned int itIdx = vecIter->Index(); MITK_INFO << "FiberIteration: " << itIdx << "\n" ; //get single tract of container ContainerTractType::Pointer contTract = vecIter->Value(); int contNrPnts = contTract->Size(); //get singel tract of itkContainer itkStochTractType::Pointer itkcontTract = itITKCnt->Value(); itkStochTractType::VertexListType::ConstPointer itkcontVrtx = itkcontTract->GetVertexList(); int itkcontNrPnts = itkcontVrtx->Size(); /* lists output is SpatialObject, we know we have DTITubeSpacialObjects dynamic cast only likes pointers, no smartpointers, so each dsmartpointer has membermethod .GetPointer() */ itk::SpatialObject<3>::Pointer tmp_fbr; tmp_fbr = *itLst; DTITubeType::Pointer dtiTract = dynamic_cast (tmp_fbr.GetPointer()); if (dtiTract.IsNull()) { MITK_INFO << " ############### *** ERRROR *** ############### \n ############### *** ERRROR *** ############### \n ############### *** ERRROR *** ############### \n "; return; } //get points of tract int fibrNrPnts = dtiTract->GetNumberOfPoints(); DTITubeType::PointListType dtiPntList = dtiTract->GetPoints(); MITK_INFO << " ############### \n *** TEST Equal Amount of Points in Tract *** \n "; if (contNrPnts == itkcontNrPnts && itkcontNrPnts == fibrNrPnts) { MITK_INFO << "[OK] .... Test2 passed. # of Points in fiber: " << fibrNrPnts << " \n ******************** "; } else { MITK_INFO << "[FAIL]: Tracts do not contain same amount of points! \n "; MITK_INFO << " # of Points m_Cont: " << contNrPnts << " | GroupFibers: " << fibrNrPnts << " | ITKCont: " << itkcontNrPnts << "\n"; } //use for()loop with index instead of iterator cuz of accessing more elements, std vectors provide no index output for(int ip=0; ipGetElement(ip); //get point from itkStochContainer itkStochTractType::VertexType itkPnt = itkcontVrtx->GetElement(ip); //get point from dtiGroup DTITubePointType tmpDtiPnt = dtiPntList.at(ip); DTITubePointType::PointType dtiPoint = tmpDtiPnt.GetPosition(); if (tmpcontPnt[0] == (float)itkPnt[0] && (float)itkPnt[0] == (float)dtiPoint[0]) { MITK_INFO << "TractCont | ITKCont | DTIGroup X: " << tmpcontPnt[0] << "...TEST [OK] " << "\n"; }else{ MITK_INFO << "TractCont | ITKCont | DTIGroup X: " << tmpcontPnt[0] << " " << itkPnt[0] << " " << dtiPoint[0] << "...TEST ##### [FAIL] \n"; } if (tmpcontPnt[1] == (float)itkPnt[1] && (float)itkPnt[1] == (float)dtiPoint[1]) { MITK_INFO << "TractCont | ITKCont | DTIGroup Y: " << tmpcontPnt[1] << "...TEST [OK] " << "\n"; }else{ MITK_INFO << "TractCont | ITKCont | DTIGroup Y: " << tmpcontPnt[1] << " " << itkPnt[1] << " " << dtiPoint[1] << "\n"; } if (tmpcontPnt[2] == (float)itkPnt[2] && (float)itkPnt[2] == (float)dtiPoint[2]) { MITK_INFO << "TractCont | ITKCont | DTIGroup Z: " << tmpcontPnt[2] << "...TEST [OK] " << "\n"; }else{ MITK_INFO << "TractCont | ITKCont | DTIGroup Z: " << tmpcontPnt[2] << " " << itkPnt[2] << " " << dtiPoint[2] << "\n"; } } ++itITKCnt; ++itLst; } } +vtkPolyData* mitk::FiberBundle::GeneratePolydata() +{ + MITK_INFO << "writing polydata"; + //extractn single fibers + //in the groupFiberBundle all smartPointers to single fibers are stored in in a ChildrenList + mitk::FiberBundle::ChildrenListType * FiberList; + FiberList = this->m_GroupFiberBundle->GetChildren(); + + /* ######## FIBER PREPARATION END ######### */ + + /* ######## VTK FIBER REPRESENTATION ######## */ + //create a vtkPoints object and store the all the brainFiber points in it + vtkPoints *vtkpoints = vtkPoints::New(); + + //in vtkcells all polylines are stored, actually all id's of them are stored + vtkCellArray *vtkcells = vtkCellArray::New(); + + //in some cases a fiber includes just 1 point, so put it in here + vtkCellArray *vtkVrtxs = vtkCellArray::New(); + + //colors and alpha value for each single point, RGBA = 4 components + vtkUnsignedCharArray *colorsT = vtkUnsignedCharArray::New(); + colorsT->SetNumberOfComponents(4); + colorsT->SetName("ColorValues"); + + vtkDoubleArray *faColors = vtkDoubleArray::New(); + faColors->SetName("FaColors"); + + //vtkDoubleArray *tubeRadius = vtkDoubleArray::New(); + //tubeRadius->SetName("TubeRadius"); + + + // iterate through FiberList + for(mitk::FiberBundle::ChildrenListType::iterator itLst = FiberList->begin(); + itLst != FiberList->end(); + ++itLst) + { + //all points are stored in one vtkpoints list, soooooooo that the lines find their point id to start and end we need some kind of helper index who monitors the current ids for a polyline + unsigned long pntIdxHelper = vtkpoints->GetNumberOfPoints(); + + // lists output is SpatialObject, we know we have DTITubeSpacialObjects + // dynamic cast only likes pointers, no smartpointers, so each dsmartpointer has membermethod .GetPointer() + itk::SpatialObject<3>::Pointer tmp_fbr; + tmp_fbr = *itLst; + mitk::FiberBundle::DTITubeType::Pointer dtiTract = dynamic_cast< mitk::FiberBundle::DTITubeType * > (tmp_fbr.GetPointer()); + if (dtiTract.IsNull()) { + return NULL; } + + //get list of points + int fibrNrPnts = dtiTract->GetNumberOfPoints(); + mitk::FiberBundle::DTITubeType::PointListType dtiPntList = dtiTract->GetPoints(); + + //create a new polyline for a dtiTract + //smartpointer + vtkPolyLine *polyLine = vtkPolyLine::New(); + polyLine->GetPointIds()->SetNumberOfIds(fibrNrPnts); + unsigned char rgba[4] = {255,255,255,255}; + + //tubeRadius->SetNumberOfTuples(fibrNrPnts); + //double tbradius = 1;//default value for radius + + if (fibrNrPnts <= 0) { //this should never occour! but who knows + MITK_INFO << "HyperERROR in fiberBundleMapper3D.cpp ...no point in fiberBundle!!! .. check ur trackingAlgorithm"; + continue; + } + + + for (int i=0; iGetGeometry()->IndexToWorld(indexPnt, worldPnt); + double worldFbrPnt[3] = {worldPnt[0], worldPnt[1], worldPnt[2]}; + vtkpoints->InsertNextPoint(worldFbrPnt); + + // tubeRadius->SetTuple1(i,tbradius); //tuple with 1 argument + + + if (fibrNrPnts == 1) { + // if there ist just 1 point in a fiber...wtf, but however represent it as a point + vtkVertex *vrtx = vtkVertex::New(); + vrtx->GetPointIds()->SetNumberOfIds(1); + vrtx->GetPointIds()->SetId(i,i+pntIdxHelper); + colorsT->InsertNextTupleValue(rgba); + vtkVrtxs->InsertNextCell(vrtx); + + } else { + + polyLine->GetPointIds()->SetId(i,i+pntIdxHelper); + + //colorcoding orientation based + if (i0) + { + //nimm nur diff1 + mitk::FiberBundle::DTITubePointType nxttmpFiberPntLst = dtiPntList.at(i+1); + mitk::FiberBundle::DTITubePointType::PointType nxttmpFiberPnt = nxttmpFiberPntLst.GetPosition(); + //double nxttmpvtkPnt[3] = {nxttmpFiberPnt[0], nxttmpFiberPnt[1], nxttmpFiberPnt[2]}; + + vnl_vector_fixed< double, 3 > tmpPntvtk((double)tmpvtkPnt[0], (double)tmpvtkPnt[1],(double)tmpvtkPnt[2]); + vnl_vector_fixed< double, 3 > nxttmpPntvtk(nxttmpFiberPnt[0], nxttmpFiberPnt[1], nxttmpFiberPnt[2]); + + vnl_vector_fixed< double, 3 > diff; + diff = tmpPntvtk - nxttmpPntvtk; + 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); + + + + } else if(i==0) { + //explicit handling of startpoint of line + + //nimm nur diff1 + mitk::FiberBundle::DTITubePointType nxttmpFiberPntLst = dtiPntList.at(i+1); + mitk::FiberBundle::DTITubePointType::PointType nxttmpFiberPnt = nxttmpFiberPntLst.GetPosition(); + //double nxttmpvtkPnt[3] = {nxttmpFiberPnt[0], nxttmpFiberPnt[1], nxttmpFiberPnt[2]}; + + vnl_vector_fixed< double, 3 > tmpPntvtk((double)tmpvtkPnt[0], (double)tmpvtkPnt[1],(double)tmpvtkPnt[2]); + vnl_vector_fixed< double, 3 > nxttmpPntvtk(nxttmpFiberPnt[0], nxttmpFiberPnt[1], nxttmpFiberPnt[2]); + + vnl_vector_fixed< double, 3 > diff; + diff = tmpPntvtk - nxttmpPntvtk; + 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); + + + + + } else if(i==fibrNrPnts) { + // nimm nur diff2 + mitk::FiberBundle::DTITubePointType nxttmpFiberPntLst = dtiPntList.at(i-1); + mitk::FiberBundle::DTITubePointType::PointType nxttmpFiberPnt = nxttmpFiberPntLst.GetPosition(); + + vnl_vector_fixed< double, 3 > tmpPntvtk((double)tmpvtkPnt[0], (double)tmpvtkPnt[1],(double)tmpvtkPnt[2]); + vnl_vector_fixed< double, 3 > nxttmpPntvtk(nxttmpFiberPnt[0], nxttmpFiberPnt[1], nxttmpFiberPnt[2]); + + vnl_vector_fixed< double, 3 > diff; + diff = tmpPntvtk - nxttmpPntvtk; + 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); + + + + + } + + colorsT->InsertNextTupleValue(rgba); + + //get FA value + float faVal = tmpFiberPntLst.GetField(mitk::FiberBundle::DTITubePointType::FA); + //use insertNextValue cuz FA Values are reperesented as a single number (1 Tuple containing 1 parameter) + faColors->InsertNextValue((double) faVal); + + + } + } + vtkcells->InsertNextCell(polyLine); + + } + + //vtkcells->InitTraversal(); + + // Put points and lines together in one polyData structure + m_PolyData = vtkPolyData::New(); + m_PolyData->SetPoints(vtkpoints); + m_PolyData->SetLines(vtkcells); + if (vtkVrtxs->GetSize() > 0) { + m_PolyData->SetVerts(vtkVrtxs); + } + m_PolyData->GetPointData()->AddArray(colorsT); + m_PolyData->GetPointData()->AddArray(faColors); + return m_PolyData; +} + /* NECESSARY IMPLEMENTATION OF SUPERCLASS METHODS */ void mitk::FiberBundle::UpdateOutputInformation() { } void mitk::FiberBundle::SetRequestedRegionToLargestPossibleRegion() { } bool mitk::FiberBundle::RequestedRegionIsOutsideOfTheBufferedRegion() { return false; } bool mitk::FiberBundle::VerifyRequestedRegion() { return true; } void mitk::FiberBundle::SetRequestedRegion( itk::DataObject *data ) { } /* TUTORIAL INSERT POINTS / FIBERS to TRACTCONTAINER */ // points and vectors do not need to be initiated but itkVectorContainer /*ContainerPointType pnt1; pnt1[0] = 1.0; pnt1[1] = 2.0; pnt1[2] = 3.0; ContainerPointType pnt2; pnt2[0] = 4.0; pnt2[1] = 5.0; pnt2[2] = 6.0; ContainerTractType tract1; tract1.push_back(pnt1); tract1.push_back(pnt2); ContainerType::Pointer testContainer = ContainerType::New(); unsigned int freeIdx = testContainer->Size(); MITK_INFO << freeIdx << "\n"; testContainer->InsertElement(freeIdx, tract1); //iterate through all fibers stored in container for(ContainerType::ConstIterator itCont = testContainer->Begin(); itCont != testContainer->End(); itCont++) { //get single tract ContainerTractType tmp_fiber = itCont->Value(); // MITK_INFO << tmp_fiber << "\n"; //iterate through all points within a fibertract for(ContainerTractType::iterator itPnt = tmp_fiber.begin(); itPnt != tmp_fiber.end(); ++itPnt) { // get single point with its coordinates ContainerPointType tmp_pntEx = *itPnt; MITK_INFO << tmp_pntEx[0] << "\n"; MITK_INFO << tmp_pntEx[1] << "\n"; MITK_INFO << tmp_pntEx[2] << "\n"; } } ################### DTI FIBERs TUTORIAL ########################### TUTORIAL HOW TO READ POINTS / FIBERS from DTIGroupSpatialObjectContainer assume our dti fibers are stored in m_GroupFiberBundle // all smartPointers to fibers stored in in a ChildrenList ChildrenListType * FiberList; FiberList = m_GroupFiberBundle->GetChildren(); // iterate through container, itkcontainer groupFiberBundle in one iteration step for(ChildrenListType::iterator itLst = FiberList->begin(); itLst != FiberList->end(); ++FiberList) { // lists output is SpatialObject, we know we have DTITubeSpacialObjects // dynamic cast only likes pointers, no smartpointers, so each dsmartpointer has membermethod .GetPointer() itk::SpatialObject<3>::Pointer tmp_fbr; tmp_fbr = *itLst; DTITubeType::Pointer dtiTract = dynamic_cast (tmp_fbr.GetPointer()); if (dtiTract.IsNull()) { return; } //get list of points int fibrNrPnts = dtiTract->GetNumberOfPoints(); DTITubeType::PointListType dtiPntList = dtiTract->GetPoints(); } */ diff --git a/Modules/DiffusionImaging/IODataStructures/FiberBundle/mitkFiberBundle.h b/Modules/DiffusionImaging/IODataStructures/FiberBundle/mitkFiberBundle.h index 36f65eb3de..865da20633 100644 --- a/Modules/DiffusionImaging/IODataStructures/FiberBundle/mitkFiberBundle.h +++ b/Modules/DiffusionImaging/IODataStructures/FiberBundle/mitkFiberBundle.h @@ -1,162 +1,172 @@ /*========================================================================= - + Program: Medical Imaging & Interaction Toolkit Module: $RCSfile$ Language: C++ Date: $Date$ Version: $Revision: 11989 $ - + 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 _MITK_FiberBundle_H #define _MITK_FiberBundle_H #include "mitkBaseData.h" #include "MitkDiffusionImagingExports.h" #include "mitkPlanarFigure.h" -/* This Class represents a bunch of FiberTracts as a Bundle. +/* This Class represents a bunch of FiberTracts as a Bundle. A Bundle is represented by a GroupSpatialObject */ #include "itkDTITubeSpatialObject.h" #include "itkDTITubeSpatialObjectPoint.h" #include "itkGroupSpatialObject.h" #include "itkPolyLineParametricPath.h" #include "itkSlowPolyLineParametricPath.h" #include "itkVectorContainer.h" #include "itkPointSet.h" #include "itkVector.h" +#include +#include +#include +#include +#include +#include +#include +#include namespace mitk { - + /** * \brief Base Class for Fiber Bundles; */ class MitkDiffusionImaging_EXPORT FiberBundle : public BaseData { - - /* friend classes wanna access typedefs + + /* friend classes wanna access typedefs ContainerPointType, ContainerTractType, ContainerType */ friend class FiberBundleWriter; friend class FiberBundleReader; // friend class itkTractsToDWIImageFilter; - + /** Types for the standardized TractContainer **/ typedef itk::Point ContainerPointType; //no need to init, is no smartpointer typedef itk::VectorContainer ContainerTractType; - typedef itk::VectorContainer< unsigned int, ContainerTractType::Pointer > ContainerType; //init via smartpointer - - - + typedef itk::VectorContainer< unsigned int, ContainerTractType::Pointer > ContainerType; //init via smartpointer + + + /** Types for the ITK Stochastic TractContainer **/ typedef itk::SlowPolyLineParametricPath< 3 > itkStochTractType; typedef itk::VectorContainer< unsigned int, itkStochTractType::Pointer > itkStochTractContainerType; // virtual methods that need to be implemented virtual void UpdateOutputInformation(); virtual void SetRequestedRegionToLargestPossibleRegion(); virtual bool RequestedRegionIsOutsideOfTheBufferedRegion(); virtual bool VerifyRequestedRegion(); virtual void SetRequestedRegion( itk::DataObject *data ); - - + + public: - + static const int TRACTPOINT_BACKFACE; static const int TRACTPOINT_ON_PLANE; static const int TRACTPOINT_FRNTFACE; - + /* DTITubeSpatialObject Definitions */ typedef itk::GroupSpatialObject<3> FiberGroupType; typedef FiberGroupType::ChildrenListType ChildrenListType; - + typedef itk::DTITubeSpatialObject<3> DTITubeType; typedef itk::DTITubeSpatialObjectPoint<3> DTITubePointType; - + mitkClassMacro( FiberBundle, BaseData ); itkNewMacro( Self ); - + /* Handle Output Type of ITK Stochastic Tractography Fiber Tracking */ void addTractContainer( ContainerType::Pointer ); void additkStochTractContainer(itkStochTractContainerType::Pointer); void initFiberGroup(); void addSingleDTITract(mitk::FiberBundle::DTITubeType::Pointer); DTITubeType::Pointer copySingleDTITract(DTITubeType::Pointer); /* Methods for PlanarFigure ROIs */ //mitk::FiberBundle::Pointer extractFibersPF(mitk::PlanarFigure::Pointer); std::vector extractFibersByPF(mitk::PlanarFigure::Pointer, std::vector* set=0); mitk::FiberBundle::Pointer extractFibersById(std::vector ); std::vector getAllIDsInFiberBundle(); - + mitk::Point3D calculateCrossingPoint(mitk::Point3D , mitk::Point3D , mitk::PlanarFigure::Pointer ); //depricated bool checkForGap(int, int); //depricated /*********************************/ - - + + void debug_members(); - + void SetBounds(float* b); + void SetBounds(double* b); float* GetBounds(); - - + + //**** REALTIME MONITOR CONTAINER METHOD ****// //flag overwrite existing bundle void addContainer4speedDisplay( ContainerType::Pointer ); itkGetMacro(GroupFiberBundle, FiberGroupType::Pointer); itkGetMacro(TractContainer, ContainerType::Pointer); //** explicit handling of FiberBundleDataStructure contents *// void PushPoint(int fiberIndex, ContainerPointType point); void PushTract(ContainerTractType::Pointer tract); ContainerPointType GetPoint(int tractIndex, int pointIndex); ContainerTractType::Pointer GetTract(int tractIndex); int GetNumTracts(); int GetNumPoints(int tractIndex); FiberGroupType::Pointer getGroupFiberBundle(); mitk::FiberBundle::Pointer JoinBundle(mitk::FiberBundle::Pointer bundle); int FindTractByEndpoints(mitk::FiberBundle::DTITubeType::Pointer searchTract); mitk::FiberBundle::Pointer SubstractBundle(mitk::FiberBundle::Pointer bundle); void InsertBundle(mitk::FiberBundle::Pointer bundle); + vtkPolyData* GeneratePolydata(); protected: FiberBundle(); virtual ~FiberBundle(); - + private: FiberGroupType::Pointer m_GroupFiberBundle; ContainerType::Pointer m_TractContainer; itkStochTractContainerType::Pointer m_debugITKContainer; - - void fiberPostprocessing_FA( DTITubePointType* ); + + void fiberPostprocessing_FA( DTITubePointType* ); void fiberPostprocessing_setPoint(DTITubePointType* , ContainerPointType ); void fiberPostprocessing_setTensorMatrix(DTITubePointType*); - + int debug_PrototypeCounter; float m_boundsFB[3]; - + /* Methods for PlanarFigure ROIs */ bool isPointInSelection(mitk::Point3D, mitk::PlanarFigure::Pointer); - - + vtkPolyData* m_PolyData; + }; - + } // namespace mitk #endif /* _MITK_FiberBundle_H */ diff --git a/Modules/DiffusionImaging/IODataStructures/FiberBundle/mitkFiberBundleReader.cpp b/Modules/DiffusionImaging/IODataStructures/FiberBundle/mitkFiberBundleReader.cpp index c9825a5478..0f807829e6 100644 --- a/Modules/DiffusionImaging/IODataStructures/FiberBundle/mitkFiberBundleReader.cpp +++ b/Modules/DiffusionImaging/IODataStructures/FiberBundle/mitkFiberBundleReader.cpp @@ -1,314 +1,389 @@ /*========================================================================= Program: Medical Imaging & Interaction Toolkit Language: C++ Date: $Date: 2009-07-14 19:11:20 +0200 (Tue, 14 Jul 2009) $ Version: $Revision: 18127 $ 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 "mitkFiberBundleReader.h" -#include "itkMetaDataObject.h" +#include #include #include -#include "itkAffineGeometryFrame.h" -#include "mitkSlicedGeometry3D.h" -#include "mitkPlaneGeometry.h" -#include "mitkGeometry2D.h" +#include +#include +#include +#include +#include +#include +#include +#include +#include const char* mitk::FiberBundleReader::XML_GEOMETRY = "geometry"; const char* mitk::FiberBundleReader::XML_MATRIX_XX = "xx"; const char* mitk::FiberBundleReader::XML_MATRIX_XY = "xy"; const char* mitk::FiberBundleReader::XML_MATRIX_XZ = "xz"; const char* mitk::FiberBundleReader::XML_MATRIX_YX = "yx"; const char* mitk::FiberBundleReader::XML_MATRIX_YY = "yy"; const char* mitk::FiberBundleReader::XML_MATRIX_YZ = "yz"; const char* mitk::FiberBundleReader::XML_MATRIX_ZX = "zx"; const char* mitk::FiberBundleReader::XML_MATRIX_ZY = "zy"; const char* mitk::FiberBundleReader::XML_MATRIX_ZZ = "zz"; const char* mitk::FiberBundleReader::XML_ORIGIN_X = "origin_x"; const char* mitk::FiberBundleReader::XML_ORIGIN_Y = "origin_y"; const char* mitk::FiberBundleReader::XML_ORIGIN_Z = "origin_z"; const char* mitk::FiberBundleReader::XML_SPACING_X = "spacing_x"; const char* mitk::FiberBundleReader::XML_SPACING_Y = "spacing_y"; const char* mitk::FiberBundleReader::XML_SPACING_Z = "spacing_z"; const char* mitk::FiberBundleReader::XML_SIZE_X = "size_x"; const char* mitk::FiberBundleReader::XML_SIZE_Y = "size_y"; const char* mitk::FiberBundleReader::XML_SIZE_Z = "size_z"; const char* mitk::FiberBundleReader::XML_FIBER_BUNDLE = "fiber_bundle"; const char* mitk::FiberBundleReader::XML_FIBER = "fiber"; const char* mitk::FiberBundleReader::XML_PARTICLE = "particle"; const char* mitk::FiberBundleReader::XML_ID = "id"; const char* mitk::FiberBundleReader::XML_POS_X = "pos_x"; const char* mitk::FiberBundleReader::XML_POS_Y = "pos_y"; const char* mitk::FiberBundleReader::XML_POS_Z = "pos_z"; const char* mitk::FiberBundleReader::XML_NUM_FIBERS = "num_fibers"; const char* mitk::FiberBundleReader::XML_NUM_PARTICLES = "num_particles"; const char* mitk::FiberBundleReader::XML_FIBER_BUNDLE_FILE = "fiber_bundle_file" ; const char* mitk::FiberBundleReader::XML_FILE_VERSION = "file_version" ; const char* mitk::FiberBundleReader::VERSION_STRING = "0.1" ; namespace mitk { void FiberBundleReader ::GenerateData() - { + { MITK_INFO << "Reading fiber bundle"; if ( ( ! m_OutputCache ) ) { Superclass::SetNumberOfRequiredOutputs(0); this->GenerateOutputInformation(); } if (!m_OutputCache) { itkWarningMacro("Tree cache is empty!"); } Superclass::SetNumberOfRequiredOutputs(1); Superclass::SetNthOutput(0, m_OutputCache.GetPointer()); } void FiberBundleReader::GenerateOutputInformation() - { + { m_OutputCache = OutputType::New(); + std::string ext = itksys::SystemTools::GetFilenameLastExtension(m_FileName); + ext = itksys::SystemTools::LowerCase(ext); + if ( m_FileName == "") { } - else + else if (ext == ".fib") { try { TiXmlDocument doc( m_FileName ); doc.LoadFile(); TiXmlHandle hDoc(&doc); TiXmlElement* pElem; TiXmlHandle hRoot(0); pElem = hDoc.FirstChildElement().Element(); // save this for later hRoot = TiXmlHandle(pElem); pElem = hRoot.FirstChildElement(FiberBundleReader::XML_GEOMETRY).Element(); // read geometry mitk::Geometry3D::Pointer geometry = mitk::Geometry3D::New(); // read origin mitk::Point3D origin; double temp = 0; pElem->Attribute(FiberBundleReader::XML_ORIGIN_X, &temp); origin[0] = temp; pElem->Attribute(FiberBundleReader::XML_ORIGIN_Y, &temp); origin[1] = temp; pElem->Attribute(FiberBundleReader::XML_ORIGIN_Z, &temp); origin[2] = temp; geometry->SetOrigin(origin); // read spacing float spacing[3]; pElem->Attribute(FiberBundleReader::XML_SPACING_X, &temp); spacing[0] = temp; pElem->Attribute(FiberBundleReader::XML_SPACING_Y, &temp); spacing[1] = temp; pElem->Attribute(FiberBundleReader::XML_SPACING_Z, &temp); spacing[2] = temp; geometry->SetSpacing(spacing); // read transform vtkMatrix4x4* m = vtkMatrix4x4::New(); pElem->Attribute(FiberBundleReader::XML_MATRIX_XX, &temp); m->SetElement(0,0,temp); pElem->Attribute(FiberBundleReader::XML_MATRIX_XY, &temp); m->SetElement(1,0,temp); pElem->Attribute(FiberBundleReader::XML_MATRIX_XZ, &temp); m->SetElement(2,0,temp); pElem->Attribute(FiberBundleReader::XML_MATRIX_YX, &temp); m->SetElement(0,1,temp); pElem->Attribute(FiberBundleReader::XML_MATRIX_YY, &temp); m->SetElement(1,1,temp); pElem->Attribute(FiberBundleReader::XML_MATRIX_YZ, &temp); m->SetElement(2,1,temp); pElem->Attribute(FiberBundleReader::XML_MATRIX_ZX, &temp); m->SetElement(0,2,temp); pElem->Attribute(FiberBundleReader::XML_MATRIX_ZY, &temp); m->SetElement(1,2,temp); pElem->Attribute(FiberBundleReader::XML_MATRIX_ZZ, &temp); m->SetElement(2,2,temp); m->SetElement(0,3,origin[0]); m->SetElement(1,3,origin[1]); m->SetElement(2,3,origin[2]); m->SetElement(3,3,1); geometry->SetIndexToWorldTransformByVtkMatrix(m); // read bounds float bounds[] = {0, 0, 0, 0, 0, 0}; pElem->Attribute(FiberBundleReader::XML_SIZE_X, &temp); bounds[1] = temp; pElem->Attribute(FiberBundleReader::XML_SIZE_Y, &temp); bounds[3] = temp; pElem->Attribute(FiberBundleReader::XML_SIZE_Z, &temp); bounds[5] = temp; geometry->SetFloatBounds(bounds); // read bounds float bounds2[] = {0, 0, 0}; bounds2[0] = bounds[1]; bounds2[1] = bounds[3]; bounds2[2] = bounds[5]; m_OutputCache->SetBounds(bounds2); geometry->SetImageGeometry(true); m_OutputCache->SetGeometry(geometry); // generate tract container ContainerType::Pointer tractContainer = ContainerType::New(); - + int fiberID = 0; pElem = hRoot.FirstChildElement(FiberBundleReader::XML_FIBER_BUNDLE).FirstChild().Element(); for( pElem; pElem; pElem=pElem->NextSiblingElement()) { TiXmlElement* pElem2 = pElem->FirstChildElement(); ContainerTractType::Pointer tract = ContainerTractType::New(); for( pElem2; pElem2; pElem2=pElem2->NextSiblingElement()) { ContainerPointType point; pElem2->Attribute(FiberBundleReader::XML_POS_X, &temp); point[0] = temp; pElem2->Attribute(FiberBundleReader::XML_POS_Y, &temp); point[1] = temp; pElem2->Attribute(FiberBundleReader::XML_POS_Z, &temp); point[2] = temp; tract->InsertElement(tract->Size(), point); } pElem->Attribute(FiberBundleReader::XML_ID, &fiberID); tractContainer->CreateIndex(fiberID); tractContainer->SetElement(fiberID, tract); } m_OutputCache->addTractContainer(tractContainer); m_OutputCache->initFiberGroup(); MITK_INFO << "Fiber bundle read"; } catch(...) { MITK_INFO << "Could not read file "; } } + else if (ext == ".afib") + { + // generate tract container + ContainerType::Pointer tractContainer = ContainerType::New(); + mitk::Geometry3D::Pointer geometry = mitk::Geometry3D::New(); + + ///We create a Generic Reader to test de .vtk/ + vtkDataReader *chooser=vtkDataReader::New(); + chooser->SetFileName(m_FileName.c_str() ); + if( chooser->IsFilePolyData()) + { + vtkPolyDataReader *reader = vtkPolyDataReader::New(); + reader->SetFileName( m_FileName.c_str() ); + reader->Update(); + + if ( reader->GetOutput() != NULL ) + { + vtkPolyData* output = reader->GetOutput(); + output->ComputeBounds(); + double bounds[3]; + output->GetBounds(bounds); + double center[3]; + output->GetCenter(center); + Point3D origin; + origin.SetElement(0, -center[0]); + origin.SetElement(1, -center[1]); + origin.SetElement(2, -center[2]); + MITK_INFO << origin; + + mitk::Surface::Pointer surf = mitk::Surface::New(); + surf->SetVtkPolyData(output); + mitk::Geometry3D* geom = surf->GetGeometry(); + //geom->SetOrigin(origin); + geom->SetImageGeometry(true); + m_OutputCache->SetBounds(bounds); + m_OutputCache->SetGeometry(geom); + vtkCellArray* cells = output->GetLines(); + + cells->InitTraversal(); + + for (int i=0; iGetNumberOfCells(); i++) + { + ContainerTractType::Pointer tract = ContainerTractType::New(); + vtkCell* cell = output->GetCell(i); + int p = cell->GetNumberOfPoints(); + vtkPoints* points = cell->GetPoints(); + for (int j=0; jGetPoint(j, p); + ContainerPointType point; + point[0] = p[0]; + point[1] = p[1]; + point[2] = p[2]; + tract->InsertElement(tract->Size(), point); + } + tractContainer->InsertElement(i, tract); + } + } + reader->Delete(); + } + chooser->Delete(); + + m_OutputCache->addTractContainer(tractContainer); + m_OutputCache->initFiberGroup(); + MITK_INFO << "Fiber bundle read"; + } } void FiberBundleReader::Update() { this->GenerateData(); } - + const char* FiberBundleReader ::GetFileName() const { return m_FileName.c_str(); } - + void FiberBundleReader ::SetFileName(const char* aFileName) { m_FileName = aFileName; } - + const char* FiberBundleReader ::GetFilePrefix() const { return m_FilePrefix.c_str(); } - + void FiberBundleReader ::SetFilePrefix(const char* aFilePrefix) { m_FilePrefix = aFilePrefix; } - + const char* FiberBundleReader ::GetFilePattern() const { return m_FilePattern.c_str(); } - + void FiberBundleReader ::SetFilePattern(const char* aFilePattern) { m_FilePattern = aFilePattern; } - + bool FiberBundleReader - ::CanReadFile(const std::string filename, const std::string /*filePrefix*/, const std::string /*filePattern*/) + ::CanReadFile(const std::string filename, const std::string /*filePrefix*/, const std::string /*filePattern*/) { // First check the extension if( filename == "" ) { return false; } std::string ext = itksys::SystemTools::GetFilenameLastExtension(filename); ext = itksys::SystemTools::LowerCase(ext); - if (ext == ".fib" ) + if (ext == ".fib" || ext == ".afib") { return true; } return false; } } //namespace MITK diff --git a/Modules/DiffusionImaging/IODataStructures/FiberBundle/mitkFiberBundleWriter.cpp b/Modules/DiffusionImaging/IODataStructures/FiberBundle/mitkFiberBundleWriter.cpp index 773462ae1d..d0316eab70 100644 --- a/Modules/DiffusionImaging/IODataStructures/FiberBundle/mitkFiberBundleWriter.cpp +++ b/Modules/DiffusionImaging/IODataStructures/FiberBundle/mitkFiberBundleWriter.cpp @@ -1,214 +1,231 @@ /*========================================================================= - + Program: Medical Imaging & Interaction Toolkit Language: C++ Date: $Date: 2008-12-10 18:05:13 +0100 (Mi, 10 Dez 2008) $ Version: $Revision: 15922 $ - + 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 "mitkFiberBundleWriter.h" - #include const char* mitk::FiberBundleWriter::XML_GEOMETRY = "geometry"; const char* mitk::FiberBundleWriter::XML_MATRIX_XX = "xx"; const char* mitk::FiberBundleWriter::XML_MATRIX_XY = "xy"; const char* mitk::FiberBundleWriter::XML_MATRIX_XZ = "xz"; const char* mitk::FiberBundleWriter::XML_MATRIX_YX = "yx"; const char* mitk::FiberBundleWriter::XML_MATRIX_YY = "yy"; const char* mitk::FiberBundleWriter::XML_MATRIX_YZ = "yz"; const char* mitk::FiberBundleWriter::XML_MATRIX_ZX = "zx"; const char* mitk::FiberBundleWriter::XML_MATRIX_ZY = "zy"; const char* mitk::FiberBundleWriter::XML_MATRIX_ZZ = "zz"; const char* mitk::FiberBundleWriter::XML_ORIGIN_X = "origin_x"; const char* mitk::FiberBundleWriter::XML_ORIGIN_Y = "origin_y"; const char* mitk::FiberBundleWriter::XML_ORIGIN_Z = "origin_z"; const char* mitk::FiberBundleWriter::XML_SPACING_X = "spacing_x"; const char* mitk::FiberBundleWriter::XML_SPACING_Y = "spacing_y"; const char* mitk::FiberBundleWriter::XML_SPACING_Z = "spacing_z"; const char* mitk::FiberBundleWriter::XML_SIZE_X = "size_x"; const char* mitk::FiberBundleWriter::XML_SIZE_Y = "size_y"; const char* mitk::FiberBundleWriter::XML_SIZE_Z = "size_z"; const char* mitk::FiberBundleWriter::XML_FIBER_BUNDLE = "fiber_bundle"; const char* mitk::FiberBundleWriter::XML_FIBER = "fiber"; const char* mitk::FiberBundleWriter::XML_PARTICLE = "particle"; const char* mitk::FiberBundleWriter::XML_ID = "id"; const char* mitk::FiberBundleWriter::XML_POS_X = "pos_x"; const char* mitk::FiberBundleWriter::XML_POS_Y = "pos_y"; const char* mitk::FiberBundleWriter::XML_POS_Z = "pos_z"; const char* mitk::FiberBundleWriter::XML_NUM_FIBERS = "num_fibers"; const char* mitk::FiberBundleWriter::XML_NUM_PARTICLES = "num_particles"; const char* mitk::FiberBundleWriter::XML_FIBER_BUNDLE_FILE = "fiber_bundle_file" ; const char* mitk::FiberBundleWriter::XML_FILE_VERSION = "file_version" ; const char* mitk::FiberBundleWriter::VERSION_STRING = "0.1" ; +const char* mitk::FiberBundleWriter::ASCII_FILE = "ascii_file" ; + +const char* mitk::FiberBundleWriter::FILE_NAME = "file_name" ; + mitk::FiberBundleWriter::FiberBundleWriter() : m_FileName(""), m_FilePrefix(""), m_FilePattern(""), m_Success(false) { this->SetNumberOfRequiredInputs( 1 ); } mitk::FiberBundleWriter::~FiberBundleWriter() {} void mitk::FiberBundleWriter::GenerateData() { MITK_INFO << "Writing fiber bundle"; - m_Success = false; - InputType* input = this->GetInput(); - if (input == NULL) - { - itkWarningMacro(<<"Sorry, input to FiberBundleWriter is NULL!"); - return; - } - if ( m_FileName == "" ) - { - itkWarningMacro( << "Sorry, filename has not been set!" ); - return ; - } -// const char* name = m_FileName.c_str(); -/* might be more helpful to use the typdefs directly of mitk::FiberBundle instead of copy paste - typedef itk::Point ContainerPointType; //no need to init - typedef std::vector ContainerTractType; //no need to init, NOTE provides NO index-output while iterating - typedef itk::VectorContainer< unsigned int, ContainerTractType::Pointer > ContainerType; //init via smartpointer -*/ - - /* direct linked includes of mitkFiberBundle DataStructure */ - typedef mitk::FiberBundle::ContainerPointType ContainerPointType; - typedef mitk::FiberBundle::ContainerTractType ContainerTractType; - typedef mitk::FiberBundle::ContainerType ContainerType; - - - ContainerType::Pointer tractContainer = input->GetTractContainer(); + m_Success = false; + InputType* input = this->GetInput(); + if (input == NULL) + { + itkWarningMacro(<<"Sorry, input to FiberBundleWriter is NULL!"); + return; + } + if ( m_FileName == "" ) + { + itkWarningMacro( << "Sorry, filename has not been set!" ); + return ; + } + + std::string ext = itksys::SystemTools::GetFilenameLastExtension(m_FileName); + ext = itksys::SystemTools::LowerCase(ext); + + if (ext == ".fib") + { + /* direct linked includes of mitkFiberBundle DataStructure */ + typedef mitk::FiberBundle::ContainerPointType ContainerPointType; + typedef mitk::FiberBundle::ContainerTractType ContainerTractType; + typedef mitk::FiberBundle::ContainerType ContainerType; + + ContainerType::Pointer tractContainer = input->GetTractContainer(); mitk::Geometry3D* geometry = input->GetGeometry(); TiXmlDocument documentXML; TiXmlDeclaration* declXML = new TiXmlDeclaration( "1.0", "", "" ); // TODO what to write here? encoding? etc.... documentXML.LinkEndChild( declXML ); TiXmlElement* mainXML = new TiXmlElement(mitk::FiberBundleWriter::XML_FIBER_BUNDLE_FILE); mainXML->SetAttribute(mitk::FiberBundleWriter::XML_FILE_VERSION, mitk::FiberBundleWriter::VERSION_STRING); documentXML.LinkEndChild(mainXML); TiXmlElement* geometryXML = new TiXmlElement(mitk::FiberBundleWriter::XML_GEOMETRY); geometryXML->SetDoubleAttribute(mitk::FiberBundleWriter::XML_MATRIX_XX, geometry->GetMatrixColumn(0)[0]); geometryXML->SetDoubleAttribute(mitk::FiberBundleWriter::XML_MATRIX_XY, geometry->GetMatrixColumn(0)[1]); geometryXML->SetDoubleAttribute(mitk::FiberBundleWriter::XML_MATRIX_XZ, geometry->GetMatrixColumn(0)[2]); geometryXML->SetDoubleAttribute(mitk::FiberBundleWriter::XML_MATRIX_YX, geometry->GetMatrixColumn(1)[0]); geometryXML->SetDoubleAttribute(mitk::FiberBundleWriter::XML_MATRIX_YY, geometry->GetMatrixColumn(1)[1]); geometryXML->SetDoubleAttribute(mitk::FiberBundleWriter::XML_MATRIX_YZ, geometry->GetMatrixColumn(1)[2]); geometryXML->SetDoubleAttribute(mitk::FiberBundleWriter::XML_MATRIX_ZX, geometry->GetMatrixColumn(2)[0]); geometryXML->SetDoubleAttribute(mitk::FiberBundleWriter::XML_MATRIX_ZY, geometry->GetMatrixColumn(2)[1]); geometryXML->SetDoubleAttribute(mitk::FiberBundleWriter::XML_MATRIX_ZZ, geometry->GetMatrixColumn(2)[2]); geometryXML->SetDoubleAttribute(mitk::FiberBundleWriter::XML_ORIGIN_X, geometry->GetOrigin()[0]); geometryXML->SetDoubleAttribute(mitk::FiberBundleWriter::XML_ORIGIN_Y, geometry->GetOrigin()[1]); geometryXML->SetDoubleAttribute(mitk::FiberBundleWriter::XML_ORIGIN_Z, geometry->GetOrigin()[2]); geometryXML->SetDoubleAttribute(mitk::FiberBundleWriter::XML_SPACING_X, geometry->GetSpacing()[0]); geometryXML->SetDoubleAttribute(mitk::FiberBundleWriter::XML_SPACING_Y, geometry->GetSpacing()[1]); geometryXML->SetDoubleAttribute(mitk::FiberBundleWriter::XML_SPACING_Z, geometry->GetSpacing()[2]); geometryXML->SetDoubleAttribute(mitk::FiberBundleWriter::XML_SIZE_X, input->GetBounds()[0]); geometryXML->SetDoubleAttribute(mitk::FiberBundleWriter::XML_SIZE_Y, input->GetBounds()[1]); geometryXML->SetDoubleAttribute(mitk::FiberBundleWriter::XML_SIZE_Z, input->GetBounds()[2]); - + mainXML->LinkEndChild(geometryXML); TiXmlElement* fiberBundleXML = new TiXmlElement(mitk::FiberBundleWriter::XML_FIBER_BUNDLE); fiberBundleXML->SetAttribute(mitk::FiberBundleWriter::XML_NUM_FIBERS, tractContainer->size()); int numParticles = 0; for (int i=0; iSize(); i++) { ContainerTractType::Pointer tract = tractContainer->GetElement(i); TiXmlElement* fiberXML = new TiXmlElement(mitk::FiberBundleWriter::XML_FIBER); fiberXML->SetAttribute(mitk::FiberBundleWriter::XML_ID, i); fiberXML->SetAttribute(mitk::FiberBundleWriter::XML_NUM_PARTICLES, tract->Size()); numParticles += tract->Size(); for (int j=0; jSize(); j++) { TiXmlElement* particleXML = new TiXmlElement(mitk::FiberBundleWriter::XML_PARTICLE); ContainerPointType p = tract->GetElement(j); particleXML->SetAttribute(mitk::FiberBundleWriter::XML_ID, j); particleXML->SetDoubleAttribute(mitk::FiberBundleWriter::XML_POS_X, p[0]); particleXML->SetDoubleAttribute(mitk::FiberBundleWriter::XML_POS_Y, p[1]); particleXML->SetDoubleAttribute(mitk::FiberBundleWriter::XML_POS_Z, p[2]); fiberXML->LinkEndChild(particleXML); } fiberBundleXML->LinkEndChild(fiberXML); } fiberBundleXML->SetAttribute(mitk::FiberBundleWriter::XML_NUM_PARTICLES, numParticles); mainXML->LinkEndChild(fiberBundleXML); documentXML.SaveFile( m_FileName ); + m_Success = true; + MITK_INFO << "Fiber bundle written"; + + }else if (ext == ".afib" || ext == ".vtk") { + vtkPolyDataWriter* writer = vtkPolyDataWriter::New(); + writer->SetInput(input->GeneratePolydata()); + writer->SetFileName(m_FileName.c_str()); + writer->SetFileTypeToASCII(); + writer->Write(); + + m_Success = true; + MITK_INFO << "Fiber bundle written as polydata"; + } + } void mitk::FiberBundleWriter::SetInput( InputType* diffVolumes ) { this->ProcessObject::SetNthInput( 0, diffVolumes ); } mitk::FiberBundle* mitk::FiberBundleWriter::GetInput() { if ( this->GetNumberOfInputs() < 1 ) { return NULL; } else { return dynamic_cast ( this->ProcessObject::GetInput( 0 ) ); } } std::vector mitk::FiberBundleWriter::GetPossibleFileExtensions() { std::vector possibleFileExtensions; possibleFileExtensions.push_back(".fib"); + possibleFileExtensions.push_back(".afib"); + possibleFileExtensions.push_back(".vtk"); return possibleFileExtensions; } diff --git a/Modules/DiffusionImaging/IODataStructures/FiberBundle/mitkFiberBundleWriter.h b/Modules/DiffusionImaging/IODataStructures/FiberBundle/mitkFiberBundleWriter.h index 4e684751a5..9738c30c90 100644 --- a/Modules/DiffusionImaging/IODataStructures/FiberBundle/mitkFiberBundleWriter.h +++ b/Modules/DiffusionImaging/IODataStructures/FiberBundle/mitkFiberBundleWriter.h @@ -1,211 +1,216 @@ /*========================================================================= - + Program: Medical Imaging & Interaction Toolkit Language: C++ Date: $Date: 2008-08-27 17:18:46 +0200 (Mi, 27 Aug 2008) $ Version: $Revision: 15096 $ - + 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 __mitkFiberBundleWriter_h #define __mitkFiberBundleWriter_h #include #include #include "mitkFiberBundle.h" +#include namespace mitk { /** * Writes fiber bundles to a file * @ingroup Process */ class FiberBundleWriter : public mitk::FileWriterWithInformation { public: mitkClassMacro( FiberBundleWriter, mitk::FileWriterWithInformation ); //mitkWriterMacro; virtual void Write() { if ( this->GetInput() == NULL ) { itkExceptionMacro(<<"Write:Please specify an input!"); return; } /* Fill in image information.*/ this->UpdateOutputInformation(); (*(this->GetInputs().begin()))->SetRequestedRegionToLargestPossibleRegion(); this->PropagateRequestedRegion(NULL); this->UpdateOutputData(NULL); } virtual void Update() { Write(); } itkNewMacro( Self ); - + typedef mitk::FiberBundle InputType; - + /** * Sets the filename of the file to write. * @param FileName the name of the file to write. */ itkSetStringMacro( FileName ); /** * @returns the name of the file to be written to disk. */ itkGetStringMacro( FileName ); /** * @warning multiple write not (yet) supported */ itkSetStringMacro( FilePrefix ); /** * @warning multiple write not (yet) supported */ itkGetStringMacro( FilePrefix ); /** * @warning multiple write not (yet) supported */ itkSetStringMacro( FilePattern ); /** * @warning multiple write not (yet) supported */ itkGetStringMacro( FilePattern ); /** * Sets the input object for the filter. * @param input the diffusion volumes to write to file. */ void SetInput( InputType* input ); /** * @returns the 0'th input object of the filter. */ InputType* GetInput(); /** * Returns false if an error happened during writing */ itkGetMacro( Success, bool ); - + /** * @return possible file extensions for the data type associated with the writer */ virtual std::vector GetPossibleFileExtensions(); // FileWriterWithInformation methods virtual const char * GetDefaultFilename() { return "FiberBundle.fib"; } - virtual const char * GetFileDialogPattern() { return "Fiber Bundle (*.fib"; } + virtual const char * GetFileDialogPattern() { return "Fiber Bundle (*.fib *.afib *.vtk)"; } virtual const char * GetDefaultExtension() { return ".fib"; } virtual bool CanWriteDataType(BaseData::Pointer data) { return (dynamic_cast(data.GetPointer()) != NULL); }; - virtual void DoWrite(BaseData::Pointer data) { + virtual void DoWrite(BaseData::Pointer data) { if (CanWriteDataType(data)) { this->SetInput(dynamic_cast(data.GetPointer())); - this->Update(); + this->Update(); } }; static const char* XML_GEOMETRY; static const char* XML_MATRIX_XX; static const char* XML_MATRIX_XY; static const char* XML_MATRIX_XZ; static const char* XML_MATRIX_YX; static const char* XML_MATRIX_YY; static const char* XML_MATRIX_YZ; static const char* XML_MATRIX_ZX; static const char* XML_MATRIX_ZY; static const char* XML_MATRIX_ZZ; static const char* XML_ORIGIN_X; static const char* XML_ORIGIN_Y; static const char* XML_ORIGIN_Z; static const char* XML_SPACING_X; static const char* XML_SPACING_Y; static const char* XML_SPACING_Z; static const char* XML_SIZE_X; static const char* XML_SIZE_Y; static const char* XML_SIZE_Z; static const char* XML_FIBER_BUNDLE; static const char* XML_FIBER; static const char* XML_PARTICLE; static const char* XML_ID; static const char* XML_POS_X; static const char* XML_POS_Y; static const char* XML_POS_Z; static const char* VERSION_STRING; static const char* XML_FIBER_BUNDLE_FILE; static const char* XML_FILE_VERSION; static const char* XML_NUM_FIBERS; static const char* XML_NUM_PARTICLES; + static const char* ASCII_FILE; + + static const char* FILE_NAME; + protected: - + FiberBundleWriter(); virtual ~FiberBundleWriter(); virtual void GenerateData(); - + std::string m_FileName; std::string m_FilePrefix; std::string m_FilePattern; - + bool m_Success; - -}; - + +}; + } // end of namespace mitk #endif //__mitkFiberBundleWriter_h diff --git a/Modules/DiffusionImaging/IODataStructures/mitkDiffusionImagingObjectFactory.cpp b/Modules/DiffusionImaging/IODataStructures/mitkDiffusionImagingObjectFactory.cpp index dc52290f31..5452438247 100644 --- a/Modules/DiffusionImaging/IODataStructures/mitkDiffusionImagingObjectFactory.cpp +++ b/Modules/DiffusionImaging/IODataStructures/mitkDiffusionImagingObjectFactory.cpp @@ -1,236 +1,239 @@ /*========================================================================= - + Program: Medical Imaging & Interaction Toolkit Language: C++ Date: $Date: 2009-06-18 15:59:04 +0200 (Do, 18 Jun 2009) $ Version: $Revision: 16916 $ - + 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 "mitkDiffusionImagingObjectFactory.h" #include "mitkProperties.h" #include "mitkBaseRenderer.h" #include "mitkDataNode.h" #include "mitkNrrdDiffusionImageIOFactory.h" #include "mitkNrrdDiffusionImageWriterFactory.h" #include "mitkNrrdDiffusionImageWriter.h" #include "mitkDiffusionImage.h" #include "mitkNrrdQBallImageIOFactory.h" #include "mitkNrrdQBallImageWriterFactory.h" #include "mitkNrrdQBallImageWriter.h" #include "mitkNrrdTensorImageIOFactory.h" #include "mitkNrrdTensorImageWriterFactory.h" #include "mitkNrrdTensorImageWriter.h" #include "mitkCompositeMapper.h" #include "mitkDiffusionImageMapper.h" #include "mitkGPUVolumeMapper3D.h" #include "mitkFiberBundle.h" #include "mitkFiberBundleMapper3D.h" #include "mitkFiberBundleIOFactory.h" #include "mitkFiberBundleWriterFactory.h" #include "mitkFiberBundleWriter.h" typedef short DiffusionPixelType; typedef mitk::DiffusionImage DiffusionImageShort; typedef std::multimap MultimapType; mitk::DiffusionImagingObjectFactory::DiffusionImagingObjectFactory(bool /*registerSelf*/) :CoreObjectFactoryBase() { static bool alreadyDone = false; if (!alreadyDone) { MITK_INFO << "DiffusionImagingObjectFactory c'tor" << std::endl; RegisterIOFactories(); mitk::NrrdDiffusionImageIOFactory::RegisterOneFactory(); mitk::NrrdQBallImageIOFactory::RegisterOneFactory(); mitk::NrrdTensorImageIOFactory::RegisterOneFactory(); mitk::FiberBundleIOFactory::RegisterOneFactory(); mitk::NrrdDiffusionImageWriterFactory::RegisterOneFactory(); mitk::NrrdQBallImageWriterFactory::RegisterOneFactory(); mitk::NrrdTensorImageWriterFactory::RegisterOneFactory(); mitk::FiberBundleWriterFactory::RegisterOneFactory(); m_FileWriters.push_back( NrrdDiffusionImageWriter::New().GetPointer() ); m_FileWriters.push_back( NrrdQBallImageWriter::New().GetPointer() ); m_FileWriters.push_back( NrrdTensorImageWriter::New().GetPointer() ); m_FileWriters.push_back( mitk::FiberBundleWriter::New().GetPointer() ); mitk::CoreObjectFactory::GetInstance()->RegisterExtraFactory(this); CreateFileExtensionsMap(); alreadyDone = true; } } -mitk::Mapper::Pointer mitk::DiffusionImagingObjectFactory::CreateMapper(mitk::DataNode* node, MapperSlotId id) +mitk::Mapper::Pointer mitk::DiffusionImagingObjectFactory::CreateMapper(mitk::DataNode* node, MapperSlotId id) { mitk::Mapper::Pointer newMapper=NULL; if ( id == mitk::BaseRenderer::Standard2D ) { std::string classname("QBallImage"); if(node->GetData() && classname.compare(node->GetData()->GetNameOfClass())==0) { newMapper = mitk::CompositeMapper::New(); newMapper->SetDataNode(node); node->SetMapper(3, ((CompositeMapper*)newMapper.GetPointer())->GetImageMapper()); } classname = "TensorImage"; if(node->GetData() && classname.compare(node->GetData()->GetNameOfClass())==0) { newMapper = mitk::CompositeMapper::New(); newMapper->SetDataNode(node); node->SetMapper(3, ((CompositeMapper*)newMapper.GetPointer())->GetImageMapper()); } classname = "DiffusionImage"; if(node->GetData() && classname.compare(node->GetData()->GetNameOfClass())==0) { newMapper = mitk::DiffusionImageMapper::New(); newMapper->SetDataNode(node); } } else if ( id == mitk::BaseRenderer::Standard3D ) { std::string classname("QBallImage"); if(node->GetData() && classname.compare(node->GetData()->GetNameOfClass())==0) { newMapper = mitk::GPUVolumeMapper3D::New(); newMapper->SetDataNode(node); } classname = "TensorImage"; if(node->GetData() && classname.compare(node->GetData()->GetNameOfClass())==0) { newMapper = mitk::GPUVolumeMapper3D::New(); newMapper->SetDataNode(node); } classname = "DiffusionImage"; if(node->GetData() && classname.compare(node->GetData()->GetNameOfClass())==0) { newMapper = mitk::GPUVolumeMapper3D::New(); newMapper->SetDataNode(node); } classname = "FiberBundle"; if(node->GetData() && classname.compare(node->GetData()->GetNameOfClass())==0) { newMapper = mitk::FiberBundleMapper3D::New(); newMapper->SetDataNode(node); } } return newMapper; } void mitk::DiffusionImagingObjectFactory::SetDefaultProperties(mitk::DataNode* node) { std::string classname = "QBallImage"; if(node->GetData() && classname.compare(node->GetData()->GetNameOfClass())==0) { mitk::CompositeMapper::SetDefaultProperties(node); mitk::GPUVolumeMapper3D::SetDefaultProperties(node); } classname = "TensorImage"; if(node->GetData() && classname.compare(node->GetData()->GetNameOfClass())==0) { mitk::CompositeMapper::SetDefaultProperties(node); mitk::GPUVolumeMapper3D::SetDefaultProperties(node); } classname = "DiffusionImage"; if(node->GetData() && classname.compare(node->GetData()->GetNameOfClass())==0) { mitk::DiffusionImageMapper::SetDefaultProperties(node); mitk::GPUVolumeMapper3D::SetDefaultProperties(node); } classname = "FiberBundle"; if(node->GetData() && classname.compare(node->GetData()->GetNameOfClass())==0) { mitk::FiberBundleMapper3D::SetDefaultProperties(node); } } -const char* mitk::DiffusionImagingObjectFactory::GetFileExtensions() +const char* mitk::DiffusionImagingObjectFactory::GetFileExtensions() { std::string fileExtension; this->CreateFileExtensions(m_FileExtensionsMap, fileExtension); return fileExtension.c_str(); }; mitk::CoreObjectFactoryBase::MultimapType mitk::DiffusionImagingObjectFactory::GetFileExtensionsMap() { return m_FileExtensionsMap; } -const char* mitk::DiffusionImagingObjectFactory::GetSaveFileExtensions() -{ +const char* mitk::DiffusionImagingObjectFactory::GetSaveFileExtensions() +{ std::string fileExtension; this->CreateFileExtensions(m_SaveFileExtensionsMap, fileExtension); return fileExtension.c_str(); }; mitk::CoreObjectFactoryBase::MultimapType mitk::DiffusionImagingObjectFactory::GetSaveFileExtensionsMap() { return m_SaveFileExtensionsMap; } void mitk::DiffusionImagingObjectFactory::CreateFileExtensionsMap() { m_FileExtensionsMap.insert(std::pair("*.dwi", "Diffusion Weighted Images")); m_FileExtensionsMap.insert(std::pair("*.hdwi", "Diffusion Weighted Images")); m_FileExtensionsMap.insert(std::pair("*.nii", "Diffusion Weighted Images for FSL")); m_FileExtensionsMap.insert(std::pair("*.fsl", "Diffusion Weighted Images for FSL")); m_FileExtensionsMap.insert(std::pair("*.fslgz", "Diffusion Weighted Images for FSL")); m_FileExtensionsMap.insert(std::pair("*.qbi", "Q-Ball Images")); m_FileExtensionsMap.insert(std::pair("*.hqbi", "Q-Ball Images")); m_FileExtensionsMap.insert(std::pair("*.dti", "Tensor Images")); m_FileExtensionsMap.insert(std::pair("*.hdti", "Tensor Images")); m_FileExtensionsMap.insert(std::pair("*.fib", "Fiber Bundle")); + m_FileExtensionsMap.insert(std::pair("*.afib", "Fiber Bundle Polydata")); + m_FileExtensionsMap.insert(std::pair("*.vtk", "Fiber Bundle Polydata")); m_SaveFileExtensionsMap.insert(std::pair("*.dwi", "Diffusion Weighted Images")); m_SaveFileExtensionsMap.insert(std::pair("*.hdwi", "Diffusion Weighted Images")); m_SaveFileExtensionsMap.insert(std::pair("*.nii", "Diffusion Weighted Images for FSL")); m_SaveFileExtensionsMap.insert(std::pair("*.fsl", "Diffusion Weighted Images for FSL")); m_SaveFileExtensionsMap.insert(std::pair("*.fslgz", "Diffusion Weighted Images for FSL")); m_SaveFileExtensionsMap.insert(std::pair("*.qbi", "Q-Ball Images")); m_SaveFileExtensionsMap.insert(std::pair("*.hqbi", "Q-Ball Images")); m_SaveFileExtensionsMap.insert(std::pair("*.dti", "Tensor Images")); m_SaveFileExtensionsMap.insert(std::pair("*.hdti", "Tensor Images")); m_SaveFileExtensionsMap.insert(std::pair("*.fib", "Fiber Bundle")); + m_SaveFileExtensionsMap.insert(std::pair("*.vtk", "Fiber Bundle Polydata")); } -void mitk::DiffusionImagingObjectFactory::RegisterIOFactories() +void mitk::DiffusionImagingObjectFactory::RegisterIOFactories() { } void RegisterDiffusionImagingObjectFactory() { static bool oneDiffusionImagingObjectFactoryRegistered = false; if ( ! oneDiffusionImagingObjectFactoryRegistered ) { MITK_INFO << "Registering DiffusionImagingObjectFactory..." << std::endl; mitk::CoreObjectFactory::GetInstance()->RegisterExtraFactory(mitk::DiffusionImagingObjectFactory::New()); oneDiffusionImagingObjectFactoryRegistered = true; } }