diff --git a/Modules/DiffusionImaging/CMakeLists.txt b/Modules/DiffusionImaging/CMakeLists.txt index e9c04e34fd..4118291223 100644 --- a/Modules/DiffusionImaging/CMakeLists.txt +++ b/Modules/DiffusionImaging/CMakeLists.txt @@ -1,20 +1,20 @@ FIND_PACKAGE(ITK) IF(ITK_GDCM_DIR) INCLUDE(${ITK_GDCM_DIR}/GDCMConfig.cmake) IF(GDCM_MAJOR_VERSION EQUAL 2) ADD_DEFINITIONS(-DGDCM2) SET(ITK_USES_GDCM2 1) ENDIF(GDCM_MAJOR_VERSION EQUAL 2) ENDIF(ITK_GDCM_DIR) MITK_CREATE_MODULE( MitkDiffusionImaging SUBPROJECTS MITK-DTI - INCLUDE_DIRS Algorithms DicomImport IODataStructures/DiffusionWeightedImages IODataStructures/QBallImages IODataStructures/TensorImages IODataStructures Reconstruction Tractography Rendering ${CMAKE_CURRENT_BINARY_DIR} + INCLUDE_DIRS Algorithms DicomImport IODataStructures/DiffusionWeightedImages IODataStructures/QBallImages IODataStructures/TensorImages IODataStructures/FiberBundle IODataStructures/PlanarFigureComposite IODataStructures Reconstruction Tractography Rendering ${CMAKE_CURRENT_BINARY_DIR} DEPENDS MitkExt SceneSerializationBase PACKAGE_DEPENDS Boost ) ADD_SUBDIRECTORY(Testing) CONFIGURE_FILE(${CMAKE_CURRENT_SOURCE_DIR}/mitkDiffusionImagingConfigure.h.in ${CMAKE_CURRENT_BINARY_DIR}/mitkDiffusionImagingConfigure.h) diff --git a/Modules/DiffusionImaging/IODataStructures/FiberBundle/itkSlowPolyLineParametricPath.h b/Modules/DiffusionImaging/IODataStructures/FiberBundle/itkSlowPolyLineParametricPath.h new file mode 100644 index 0000000000..e4b0f53d37 --- /dev/null +++ b/Modules/DiffusionImaging/IODataStructures/FiberBundle/itkSlowPolyLineParametricPath.h @@ -0,0 +1,112 @@ +#ifndef _itkSlowPolyLineParametricPathPath_h +#define _itkSlowPolyLineParametricPathPath_h + +#include "itkPolyLineParametricPath.h" +#include "itkVectorContainer.h" +#include "itkContinuousIndex.h" +#include "itkIndex.h" +#include "itkOffset.h" +#include "itkVector.h" + +namespace itk +{ + + +/** \class SlowPolyLineParametricPath + * \brief Represent a path of line segments through ND Space + * + * This class is intended to represent parametric paths through an image, where + * the paths are composed of line segments. Each line segment traverses one + * unit of input. A classic application of this class is the representation of + * contours in 2D images, especially when the contours only need to be + * approximately correct. Another use of a path is to guide the movement of an + * iterator through an image. + * + * \sa EllipseParametricPath + * \sa FourierSeriesPath + * \sa OrthogonallyCorrectedParametricPath + * \sa ParametricPath + * \sa ChainCodePath + * \sa Path + * \sa ContinuousIndex + * \sa Index + * \sa Offset + * \sa Vector + * + * \ingroup PathObjects + */ +template +class ITK_EXPORT SlowPolyLineParametricPath : public +PolyLineParametricPath< VDimension > +{ +public: + /** Standard class typedefs. */ + typedef SlowPolyLineParametricPath Self; + typedef PolyLineParametricPath Superclass; + typedef SmartPointer Pointer; + typedef SmartPointer ConstPointer; + + /** Run-time type information (and related methods). */ + itkTypeMacro(SlowPolyLineParametricPath, PolyLineParametricPath); + + /** Input type */ + typedef typename Superclass::InputType InputType; + + /** Output type */ + typedef typename Superclass::OutputType OutputType; + + + /** Basic data-structure types used */ + typedef typename Superclass::ContinuousIndexType ContinuousIndexType; + typedef typename Superclass::IndexType IndexType; + typedef typename Superclass::OffsetType OffsetType; + typedef typename Superclass::PointType PointType; + typedef typename Superclass::VectorType VectorType; + typedef typename Superclass::VertexType VertexType; + typedef typename Superclass::VertexListType VertexListType; + typedef typename Superclass::VertexListPointer VertexListPointer; + + /** Increment the input variable passed by reference such that the ND index of + * the path moves to its next vertex-connected (8-connected in 2D) neighbor. + * Return the Index-space offset of the path from its prior input to its new + * input. If the path is unable to increment, input is not changed and an + * offset of Zero is returned. Children are not required to implement bounds + * checking. + * + * This is a fairly slow, iterative algorithm that numerically converges to + * the next index along the path, in a vertex-connected (8-connected in 2D) + * fashion. When possible, children of this class should overload this + * function with something more efficient. + * + * WARNING: This default implementation REQUIRES that the ND endpoint of + * the path be either unique or coincident only with the startpoint, since it + * uses the endpoint as a stopping condition. */ + virtual OffsetType IncrementInput(InputType & input) const; + + + ///** Evaluate the first derivative of the ND output with respect to the 1D + // * input. This is an exact, algebraic function. */ + //virtual VectorType EvaluateDerivative(const InputType & input) const; + + + /** New() method for dynamic construction */ + itkNewMacro( Self ); + + +protected: + SlowPolyLineParametricPath(); + ~SlowPolyLineParametricPath(){} + void PrintSelf(std::ostream& os, Indent indent) const; + +private: + SlowPolyLineParametricPath(const Self&); //purposely not implemented + void operator=(const Self&); //purposely not implemented +}; + +} // namespace itk + +#ifndef ITK_MANUAL_INSTANTIATION +#include "itkSlowPolyLineParametricPath.txx" +#endif + +#endif diff --git a/Modules/DiffusionImaging/IODataStructures/FiberBundle/itkSlowPolyLineParametricPath.txx b/Modules/DiffusionImaging/IODataStructures/FiberBundle/itkSlowPolyLineParametricPath.txx new file mode 100644 index 0000000000..e0852d1614 --- /dev/null +++ b/Modules/DiffusionImaging/IODataStructures/FiberBundle/itkSlowPolyLineParametricPath.txx @@ -0,0 +1,115 @@ +#ifndef _itkSlowPolyLineParametricPath_txx +#define _itkSlowPolyLineParametricPath_txx + +#include "itkSlowPolyLineParametricPath.h" +#include + + + +namespace itk +{ + +//template +//typename SlowPolyLineParametricPath::VectorType +//SlowPolyLineParametricPath +//::EvaluateDerivative(const InputType & input) const +//{ +//} + + + +/** + * Constructor + */ +template +SlowPolyLineParametricPath +::SlowPolyLineParametricPath() +{ + this->SetDefaultInputStepSize( 0.3 ); +} + + +template +typename SlowPolyLineParametricPath::OffsetType +SlowPolyLineParametricPath +::IncrementInput(InputType & input) const +{ + int iterationCount; + bool tooSmall; + bool tooBig; + InputType inputStepSize; + InputType finalInputValue; + OffsetType offset; + IndexType currentImageIndex; + IndexType nextImageIndex; + IndexType finalImageIndex; + + iterationCount = 0; + inputStepSize = this->GetDefaultInputStepSize(); + + // Are we already at (or past) the end of the input? + finalInputValue = this->EndOfInput(); + currentImageIndex = this->EvaluateToIndex( input ); + finalImageIndex = this->EvaluateToIndex( finalInputValue ); + offset = finalImageIndex - currentImageIndex; + if( ( offset == this->GetZeroOffset() && input != this->StartOfInput() ) || + ( input >=finalInputValue ) ) + { + return this->GetZeroOffset(); + } + + do + { + if( iterationCount++ > 10000 ) {itkExceptionMacro(<<"Too many iterations");} + + nextImageIndex = this->EvaluateToIndex( input + inputStepSize ); + offset = nextImageIndex - currentImageIndex; + + tooBig = false; + tooSmall = ( offset == this->GetZeroOffset() ); + if( tooSmall ) + { + // increase the input step size, but don't go past the end of the input + inputStepSize *= 2; + if( (input + inputStepSize) >= finalInputValue ){ + //inputStepSize = finalInputValue - input; + inputStepSize += this->GetDefaultInputStepSize(); + } + } + else + { + // Search for an offset dimension that is too big + for( unsigned int i=0; i= 2 || offset[i] <= -2 ); + } + + if( tooBig ){ + //inputStepSize /= 1.5; + inputStepSize -= (this->GetDefaultInputStepSize()/0.5); + } + } + } + while( tooSmall || tooBig ); + + input += inputStepSize; + return offset; +} + + +/** + * Standard "PrintSelf" method + */ +template +void +SlowPolyLineParametricPath +::PrintSelf( std::ostream& os, Indent indent) const +{ + Superclass::PrintSelf( os, indent ); +} + + + +} // end namespaceitk + +#endif diff --git a/Modules/DiffusionImaging/IODataStructures/FiberBundle/mitkFiberBundle.cpp b/Modules/DiffusionImaging/IODataStructures/FiberBundle/mitkFiberBundle.cpp new file mode 100644 index 0000000000..3c0926f731 --- /dev/null +++ b/Modules/DiffusionImaging/IODataStructures/FiberBundle/mitkFiberBundle.cpp @@ -0,0 +1,1664 @@ +/*========================================================================= + + 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]; + +} + +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->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; + } + +} + +/* 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 new file mode 100644 index 0000000000..6f2126e67e --- /dev/null +++ b/Modules/DiffusionImaging/IODataStructures/FiberBundle/mitkFiberBundle.h @@ -0,0 +1,162 @@ + +/*========================================================================= + + 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 "MitkDiffusionImagingMBIExports.h" +#include "mitkPlanarFigure.h" + +/* 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" + +namespace mitk { + + /** + * \brief Base Class for Fiber Bundles; */ + class MitkDiffusionImagingMBI_EXPORT FiberBundle : public BaseData + { + + /* 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 + + + + /** 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); + 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); + + protected: + FiberBundle(); + virtual ~FiberBundle(); + + private: + FiberGroupType::Pointer m_GroupFiberBundle; + ContainerType::Pointer m_TractContainer; + itkStochTractContainerType::Pointer m_debugITKContainer; + + 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); + + + }; + +} // namespace mitk + +#endif /* _MITK_FiberBundle_H */ diff --git a/Modules/DiffusionImaging/IODataStructures/FiberBundle/mitkFiberBundleIOFactory.cpp b/Modules/DiffusionImaging/IODataStructures/FiberBundle/mitkFiberBundleIOFactory.cpp new file mode 100644 index 0000000000..c4134a9c20 --- /dev/null +++ b/Modules/DiffusionImaging/IODataStructures/FiberBundle/mitkFiberBundleIOFactory.cpp @@ -0,0 +1,54 @@ +/*========================================================================= + +Program: Medical Imaging & Interaction Toolkit +Language: C++ +Date: $Date: 2007-12-11 14:46:19 +0100 (Di, 11 Dez 2007) $ +Version: $Revision: 6607 $ + +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 "mitkFiberBundleIOFactory.h" +#include "mitkIOAdapter.h" +#include "mitkFiberBundleReader.h" + +#include "itkVersion.h" + +//NOTE>umbenennen in FBReaderType + + +namespace mitk +{ + +FiberBundleIOFactory::FiberBundleIOFactory() +{ + typedef FiberBundleReader FiberBundleReaderType; + this->RegisterOverride("mitkIOAdapter", //beibehalten + "mitkFiberBundleReader", //umbenennen + "Fiber Bundle IO", //angezeigter name + 1, + itk::CreateObjectFunction >::New()); +} + +FiberBundleIOFactory::~FiberBundleIOFactory() +{ +} + +const char* FiberBundleIOFactory::GetITKSourceVersion() const +{ + return ITK_SOURCE_VERSION; +} + +const char* FiberBundleIOFactory::GetDescription() const +{ + return "FibreBundleIOFactory, allows the loading of FibreBundles"; +} + +} // end namespace mitk diff --git a/Modules/DiffusionImaging/IODataStructures/FiberBundle/mitkFiberBundleIOFactory.h b/Modules/DiffusionImaging/IODataStructures/FiberBundle/mitkFiberBundleIOFactory.h new file mode 100644 index 0000000000..5277b11ab5 --- /dev/null +++ b/Modules/DiffusionImaging/IODataStructures/FiberBundle/mitkFiberBundleIOFactory.h @@ -0,0 +1,76 @@ +/*========================================================================= + +Program: Medical Imaging & Interaction Toolkit +Language: C++ +Date: $Date: 2009-05-13 18:06:46 +0200 (Mi, 13 Mai 2009) $ +Version: $Revision: 6590 $ + +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_FIBER_BUNDLE_IO_FACTORY_H_HEADER__ +#define __MITK_FIBER_BUNDLE_IO_FACTORY_H_HEADER__ + +#ifdef _MSC_VER +#pragma warning ( disable : 4786 ) +#endif + +#include "itkObjectFactoryBase.h" +#include "mitkBaseData.h" +#include "MitkDiffusionImagingMBIExports.h" + +//NOTE>umbenennen in internal FiberBundleIOFactory + + +namespace mitk +{ +//##Documentation +//## @brief Create instances of NrrdQBallImageReader objects using an object factory. +//## +//## @ingroup IO +class MitkDiffusionImagingMBI_EXPORT FiberBundleIOFactory : public itk::ObjectFactoryBase +{ +public: + /** Standard class typedefs. */ + typedef FiberBundleIOFactory Self; + typedef itk::ObjectFactoryBase Superclass; + typedef itk::SmartPointer Pointer; + typedef itk::SmartPointer ConstPointer; + + /** Class methods used to interface with the registered factories. */ + virtual const char* GetITKSourceVersion(void) const; + virtual const char* GetDescription(void) const; + + /** Method for class instantiation. */ + itkFactorylessNewMacro(Self); + static FiberBundleIOFactory* FactoryNew() { return new FiberBundleIOFactory;} + /** Run-time type information (and related methods). */ + itkTypeMacro(FiberBundleIOFactory, ObjectFactoryBase); + + /** Register one factory of this type */ + static void RegisterOneFactory(void) + { + FiberBundleIOFactory::Pointer FiberBundleIOFactory = FiberBundleIOFactory::New(); + ObjectFactoryBase::RegisterFactory(FiberBundleIOFactory); + } + +protected: + FiberBundleIOFactory(); + ~FiberBundleIOFactory(); + +private: + FiberBundleIOFactory(const Self&); //purposely not implemented + void operator=(const Self&); //purposely not implemented + +}; + + +} // end namespace mitk + +#endif // __MITK_FIBER_BUNDLE_IO_FACTORY_H_HEADER__ diff --git a/Modules/DiffusionImaging/IODataStructures/FiberBundle/mitkFiberBundleReader.cpp b/Modules/DiffusionImaging/IODataStructures/FiberBundle/mitkFiberBundleReader.cpp new file mode 100644 index 0000000000..c9825a5478 --- /dev/null +++ b/Modules/DiffusionImaging/IODataStructures/FiberBundle/mitkFiberBundleReader.cpp @@ -0,0 +1,314 @@ +/*========================================================================= + +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 "itkAffineGeometryFrame.h" +#include "mitkSlicedGeometry3D.h" +#include "mitkPlaneGeometry.h" +#include "mitkGeometry2D.h" + +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(); + + if ( m_FileName == "") + { + + } + else + { + 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 "; + } + } + } + + 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*/) + { + // First check the extension + if( filename == "" ) + { + return false; + } + std::string ext = itksys::SystemTools::GetFilenameLastExtension(filename); + ext = itksys::SystemTools::LowerCase(ext); + + if (ext == ".fib" ) + { + return true; + } + + return false; + } + +} //namespace MITK diff --git a/Modules/DiffusionImaging/IODataStructures/FiberBundle/mitkFiberBundleReader.h b/Modules/DiffusionImaging/IODataStructures/FiberBundle/mitkFiberBundleReader.h new file mode 100644 index 0000000000..09b32561a9 --- /dev/null +++ b/Modules/DiffusionImaging/IODataStructures/FiberBundle/mitkFiberBundleReader.h @@ -0,0 +1,147 @@ +/*========================================================================= + +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. + +=========================================================================*/ + +#ifndef __mitkFiberBundleReader_h +#define __mitkFiberBundleReader_h + +#include "mitkCommon.h" +#include "itkVectorContainer.h" +#include "mitkFileReader.h" +#include "mitkFiberBundle.h" +#include "itkSlowPolyLineParametricPath.h" + +//NOTE>umbenennen in FiberBundleSource + +namespace mitk +{ + + /** \brief + */ + + class FiberBundleReader : public FileReader, public BaseProcess + { + public: + + /** Types for the standardized TractContainer **/ + /* direct linked includes of mitkFiberBundle DataStructure */ + typedef mitk::FiberBundle::ContainerPointType ContainerPointType; + typedef mitk::FiberBundle::ContainerTractType ContainerTractType; + typedef mitk::FiberBundle::ContainerType ContainerType; + + + typedef mitk::FiberBundle OutputType; + + mitkClassMacro( FiberBundleReader, BaseProcess ); + itkNewMacro(Self); + + const char* GetFileName() const; + void SetFileName(const char* aFileName); + const char* GetFilePrefix() const; + void SetFilePrefix(const char* aFilePrefix); + const char* GetFilePattern() const; + void SetFilePattern(const char* aFilePattern); + + static bool CanReadFile(const std::string filename, const std::string filePrefix, const std::string filePattern); + +// itkGetMacro(GroupFiberBundle, FiberGroupType::Pointer); +// itkGetMacro(TractContainer, ContainerType::Pointer); + + virtual void 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; + + protected: + + /** Does the real work. */ + virtual void GenerateData(); + virtual void GenerateOutputInformation(); + + OutputType::Pointer m_OutputCache; + + std::string m_FileName; + std::string m_FilePrefix; + std::string m_FilePattern; + ContainerType::Pointer m_TractContainer; + + private: + void operator=(const Self&); //purposely not implemented + }; + +} //namespace MITK + +#endif // __mitkFiberBundleReader_h diff --git a/Modules/DiffusionImaging/IODataStructures/FiberBundle/mitkFiberBundleSerializer.cpp b/Modules/DiffusionImaging/IODataStructures/FiberBundle/mitkFiberBundleSerializer.cpp new file mode 100644 index 0000000000..dec8bd70e9 --- /dev/null +++ b/Modules/DiffusionImaging/IODataStructures/FiberBundle/mitkFiberBundleSerializer.cpp @@ -0,0 +1,75 @@ +/*========================================================================= + +Program: Medical Imaging & Interaction Toolkit +Language: C++ +Date: $Date$ +Version: $Revision: 1.12 $ + +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 "mitkFiberBundleSerializer.h" +#include "mitkFiberBundle.h" +#include "mitkFiberBundleWriter.h" + +#include + + +MITK_REGISTER_SERIALIZER(FiberBundleSerializer) + + +mitk::FiberBundleSerializer::FiberBundleSerializer() +{ +} + + +mitk::FiberBundleSerializer::~FiberBundleSerializer() +{ +} + + +std::string mitk::FiberBundleSerializer::Serialize() +{ + const FiberBundle* fb = dynamic_cast( m_Data.GetPointer() ); + if (fb == NULL) + { + MITK_ERROR << " Object at " << (const void*) this->m_Data + << " is not an mitk::FiberBundle. Cannot serialize as FiberBundle."; + return ""; + } + + std::string filename( this->GetUniqueFilenameInWorkingDirectory() ); + filename += "_"; + filename += m_FilenameHint; + filename += ".fib"; + + std::string fullname(m_WorkingDirectory); + fullname += "/"; + fullname += itksys::SystemTools::ConvertToOutputPath(filename.c_str()); + + try + { + FiberBundleWriter::Pointer writer = FiberBundleWriter::New(); + writer->SetFileName(fullname); + writer->SetInput(const_cast(fb)); + writer->Write(); + } + catch (std::exception& e) + { + MITK_ERROR << " Error serializing object at " << (const void*) this->m_Data + << " to " + << fullname + << ": " + << e.what(); + return ""; + } + return filename; +} + diff --git a/Modules/DiffusionImaging/IODataStructures/FiberBundle/mitkFiberBundleSerializer.h b/Modules/DiffusionImaging/IODataStructures/FiberBundle/mitkFiberBundleSerializer.h new file mode 100644 index 0000000000..726e1e61bd --- /dev/null +++ b/Modules/DiffusionImaging/IODataStructures/FiberBundle/mitkFiberBundleSerializer.h @@ -0,0 +1,40 @@ +/*========================================================================= + +Program: Medical Imaging & Interaction Toolkit +Language: C++ +Date: $Date$ +Version: $Revision: 1.12 $ + +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 mitkFiberBundleSerializer_h_included +#define mitkFiberBundleSerializer_h_included + +#include "MitkDiffusionImagingMBIExports.h" +#include "mitkBaseDataSerializer.h" + +namespace mitk +{ +/** + \brief Serializes mitk::Surface for mitk::SceneIO +*/ +class MitkDiffusionImagingMBI_EXPORT FiberBundleSerializer : public BaseDataSerializer +{ + public: + mitkClassMacro( FiberBundleSerializer, BaseDataSerializer ); + itkNewMacro(Self); + virtual std::string Serialize(); + protected: + FiberBundleSerializer(); + virtual ~FiberBundleSerializer(); +}; +} // namespace +#endif diff --git a/Modules/DiffusionImaging/IODataStructures/FiberBundle/mitkFiberBundleSource.cpp b/Modules/DiffusionImaging/IODataStructures/FiberBundle/mitkFiberBundleSource.cpp new file mode 100644 index 0000000000..0c780e249f --- /dev/null +++ b/Modules/DiffusionImaging/IODataStructures/FiberBundle/mitkFiberBundleSource.cpp @@ -0,0 +1,35 @@ +/*========================================================================= + +Program: Medical Imaging & Interaction Toolkit +Language: C++ +Date: $Date: 2009-05-12 19:56:03 +0200 (Di, 12 Mai 2009) $ +Version: $Revision: 17179 $ + +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 "mitkQBallImageSource.h" + + +mitk::QBallImageSource::QBallImageSource() +{ + // Create the output. We use static_cast<> here because we know the default + // output must be of type TOutputImage + OutputImageType::Pointer output + = static_cast(this->MakeOutput(0).GetPointer()); + Superclass::SetNumberOfRequiredOutputs(1); + Superclass::SetNthOutput(0, output.GetPointer()); +} + +mitk::QBallImageSource::DataObjectPointer mitk::QBallImageSource::MakeOutput( unsigned int /*idx*/ ) +{ + return static_cast(OutputImageType::New().GetPointer()); +} diff --git a/Modules/DiffusionImaging/IODataStructures/FiberBundle/mitkFiberBundleSource.h b/Modules/DiffusionImaging/IODataStructures/FiberBundle/mitkFiberBundleSource.h new file mode 100644 index 0000000000..ce50970b88 --- /dev/null +++ b/Modules/DiffusionImaging/IODataStructures/FiberBundle/mitkFiberBundleSource.h @@ -0,0 +1,52 @@ +/*========================================================================= + +Program: Medical Imaging & Interaction Toolkit +Language: C++ +Date: $Date: 2009-05-12 19:56:03 +0200 (Di, 12 Mai 2009) $ +Version: $Revision: 17179 $ + +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 QBallImageSource_H_HEADER_INCLUDED_C1E7D6EC +#define QBallImageSource_H_HEADER_INCLUDED_C1E7D6EC + +#include "mitkImageSource.h" +#include "mitkQBallImage.h" + +//NOTE>umbenennen .. ableiten von DataSource + + +namespace mitk { + +class QBallImageSource : public ImageSource +{ +public: + + typedef mitk::QBallImage OutputImageType; + typedef OutputImageType::Pointer OutputImagePointer; + typedef SlicedData::RegionType OutputImageRegionType; + typedef itk::DataObject::Pointer DataObjectPointer; + + mitkClassMacro(QBallImageSource,ImageSource); + itkNewMacro(Self); + + virtual DataObjectPointer MakeOutput(unsigned int idx); + +protected: + QBallImageSource(); + virtual ~QBallImageSource() {} + +}; + +} // namespace mitk + +#endif /* QBallImageSource_H_HEADER_INCLUDED_C1E7D6EC */ diff --git a/Modules/DiffusionImaging/IODataStructures/FiberBundle/mitkFiberBundleWriter.cpp b/Modules/DiffusionImaging/IODataStructures/FiberBundle/mitkFiberBundleWriter.cpp new file mode 100644 index 0000000000..773462ae1d --- /dev/null +++ b/Modules/DiffusionImaging/IODataStructures/FiberBundle/mitkFiberBundleWriter.cpp @@ -0,0 +1,214 @@ +/*========================================================================= + +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" ; + +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(); + 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"; +} + + +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"); + return possibleFileExtensions; +} diff --git a/Modules/DiffusionImaging/IODataStructures/FiberBundle/mitkFiberBundleWriter.h b/Modules/DiffusionImaging/IODataStructures/FiberBundle/mitkFiberBundleWriter.h new file mode 100644 index 0000000000..4e684751a5 --- /dev/null +++ b/Modules/DiffusionImaging/IODataStructures/FiberBundle/mitkFiberBundleWriter.h @@ -0,0 +1,211 @@ +/*========================================================================= + +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" + + +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 * GetDefaultExtension() { return ".fib"; } + virtual bool CanWriteDataType(BaseData::Pointer data) { return (dynamic_cast(data.GetPointer()) != NULL); }; + virtual void DoWrite(BaseData::Pointer data) { + if (CanWriteDataType(data)) { + this->SetInput(dynamic_cast(data.GetPointer())); + 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; + +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/FiberBundle/mitkFiberBundleWriterFactory.cpp b/Modules/DiffusionImaging/IODataStructures/FiberBundle/mitkFiberBundleWriterFactory.cpp new file mode 100644 index 0000000000..0b4bc55c37 --- /dev/null +++ b/Modules/DiffusionImaging/IODataStructures/FiberBundle/mitkFiberBundleWriterFactory.cpp @@ -0,0 +1,76 @@ +/*========================================================================= + +Program: Medical Imaging & Interaction Toolkit +Language: C++ +Date: $Date: 2007-12-11 14:46:19 +0100 (Di, 11 Dez 2007) $ +Version: $Revision: 11215 $ + +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 "mitkFiberBundleWriterFactory.h" + +#include "itkCreateObjectFunction.h" +#include "itkVersion.h" + +#include "mitkFiberBundleWriter.h" + +namespace mitk +{ + +template +class CreateFiberBundleWriter : public itk::CreateObjectFunctionBase +{ +public: + + /** Standard class typedefs. */ + typedef CreateFiberBundleWriter Self; + typedef itk::SmartPointer Pointer; + + /** Methods from itk:LightObject. */ + itkFactorylessNewMacro(Self); + LightObject::Pointer CreateObject() { typename T::Pointer p = T::New(); + p->Register(); + return p.GetPointer(); + } + +protected: + CreateFiberBundleWriter() {} + ~CreateFiberBundleWriter() {} + +private: + CreateFiberBundleWriter(const Self&); //purposely not implemented + void operator=(const Self&); //purposely not implemented +}; + +FiberBundleWriterFactory::FiberBundleWriterFactory() +{ + this->RegisterOverride("IOWriter", + "FiberBundleWriter", + "FiberBundle Writer", + 1, + mitk::CreateFiberBundleWriter< mitk::FiberBundleWriter >::New()); +} + +FiberBundleWriterFactory::~FiberBundleWriterFactory() +{ +} + +const char* FiberBundleWriterFactory::GetITKSourceVersion() const +{ + return ITK_SOURCE_VERSION; +} + +const char* FiberBundleWriterFactory::GetDescription() const +{ + return "FiberBundleWriterFactory"; +} + +} // end namespace mitk diff --git a/Modules/DiffusionImaging/IODataStructures/FiberBundle/mitkFiberBundleWriterFactory.h b/Modules/DiffusionImaging/IODataStructures/FiberBundle/mitkFiberBundleWriterFactory.h new file mode 100644 index 0000000000..9b54b25856 --- /dev/null +++ b/Modules/DiffusionImaging/IODataStructures/FiberBundle/mitkFiberBundleWriterFactory.h @@ -0,0 +1,68 @@ +/*========================================================================= + +Program: Medical Imaging & Interaction Toolkit +Language: C++ +Date: $Date: 2009-05-13 18:06:46 +0200 (Mi, 13 Mai 2009) $ +Version: $Revision: 11215 $ + +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 FIBERBUNDLE_WRITERFACTORY_H_HEADER_INCLUDED +#define FIBERBUNDLE_WRITERFACTORY_H_HEADER_INCLUDED + +#include "itkObjectFactoryBase.h" +#include "mitkBaseData.h" +#include "MitkDiffusionImagingMBIExports.h" + +namespace mitk +{ + +class MitkDiffusionImagingMBI_EXPORT FiberBundleWriterFactory : public itk::ObjectFactoryBase +{ +public: + + mitkClassMacro( mitk::FiberBundleWriterFactory, itk::ObjectFactoryBase ) + + /** Class methods used to interface with the registered factories. */ + virtual const char* GetITKSourceVersion(void) const; + virtual const char* GetDescription(void) const; + + /** Method for class instantiation. */ + itkFactorylessNewMacro(Self); + + /** Register one factory of this type */ + static void RegisterOneFactory(void) + { + static bool IsRegistered = false; + if ( !IsRegistered ) + { + FiberBundleWriterFactory::Pointer ugVtkWriterFactory = FiberBundleWriterFactory::New(); + ObjectFactoryBase::RegisterFactory( ugVtkWriterFactory ); + IsRegistered = true; + } + } + +protected: + FiberBundleWriterFactory(); + ~FiberBundleWriterFactory(); + +private: + FiberBundleWriterFactory(const Self&); //purposely not implemented + void operator=(const Self&); //purposely not implemented + +}; + +} // end namespace mitk + +#endif // FIBERBUNDLE_WRITERFACTORY_H_HEADER_INCLUDED + + + diff --git a/Modules/DiffusionImaging/IODataStructures/PlanarFigureComposite/mitkPlanarFigureComposite.cpp b/Modules/DiffusionImaging/IODataStructures/PlanarFigureComposite/mitkPlanarFigureComposite.cpp new file mode 100644 index 0000000000..a59aaefbf0 --- /dev/null +++ b/Modules/DiffusionImaging/IODataStructures/PlanarFigureComposite/mitkPlanarFigureComposite.cpp @@ -0,0 +1,132 @@ +/* + * mitkPlanarFigureComposite.cpp + * mitk-all + * + * Created by HAL9000 on 2/4/11. + * Copyright 2011 __MyCompanyName__. All rights reserved. + * + */ + +#include "mitkPlanarFigureComposite.h" + + +mitk::PlanarFigureComposite::PlanarFigureComposite() + +{ + m_PFVector = CompositionContainer::New(); + m_DNVector = DataNodeContainer::New(); + +} + +mitk::PlanarFigureComposite::~PlanarFigureComposite() +{ + +} + +void mitk::PlanarFigureComposite::addDataNode(mitk::DataNode::Pointer dnode) +{ + + m_DNVector->InsertElement(m_DNVector->Size(), dnode); + +} + + +void mitk::PlanarFigureComposite::addPlanarFigure(PlanarFigure::Pointer pf) +{ + + MITK_INFO << "addPlanarFigure: size before: " << this->getNumberOfChildren(); + m_PFVector->InsertElement(m_PFVector->Size(), pf); + MITK_INFO << "addPlanarFigure: size after: " << this->getNumberOfChildren(); + + + + +} + +void mitk::PlanarFigureComposite::replaceDataNodeAt(int idx, mitk::DataNode::Pointer dn) +{ + MITK_INFO << "replace: size before: " << this->getNumberOfChildren(); + m_DNVector->SetElement( idx, dn ); + MITK_INFO << "replace: size after: " << this->getNumberOfChildren(); + +} + +void mitk::PlanarFigureComposite::setOperationType(PFCompositionOperation pfcOp) +{ + this->m_compOperation = pfcOp; + MITK_INFO << "Composition set to: " << this->getOperationType(); + +} + + +mitk::PFCompositionOperation mitk::PlanarFigureComposite::getOperationType() +{ + return this->m_compOperation; + + +} + +void mitk::PlanarFigureComposite::setDisplayName(std::string displName) +{ + + m_name = displName; + +} + + +std::string mitk::PlanarFigureComposite::getDisplayName() +{ + return m_name; +} + + +int mitk::PlanarFigureComposite::getNumberOfChildren() +{ + return m_PFVector->Size(); + +} + +mitk::PlanarFigure::Pointer mitk::PlanarFigureComposite::getChildAt(int idx) +{ + + return m_PFVector->ElementAt(idx); +} + + +mitk::DataNode::Pointer mitk::PlanarFigureComposite::getDataNodeAt(int idx) +{ + + return m_DNVector->ElementAt(idx); + +} + + + + + + +//musthave implementations from superclass.... not sure if return true makes sense +bool mitk::PlanarFigureComposite::SetControlPoint( unsigned int index, const Point2D &point, bool createIfDoesNotExist ) +{ + return true; +} + +void mitk::PlanarFigureComposite::GeneratePolyLine() +{ + +} + +void mitk::PlanarFigureComposite::GenerateHelperPolyLine(double /*mmPerDisplayUnit*/, unsigned int /*displayHeight*/) +{ + // A circle does not require a helper object +} + +void mitk::PlanarFigureComposite::EvaluateFeaturesInternal() +{ + +} + +void mitk::PlanarFigureComposite::PrintSelf( std::ostream& os, itk::Indent indent) const +{ + +} diff --git a/Modules/DiffusionImaging/IODataStructures/PlanarFigureComposite/mitkPlanarFigureComposite.h b/Modules/DiffusionImaging/IODataStructures/PlanarFigureComposite/mitkPlanarFigureComposite.h new file mode 100644 index 0000000000..b545595fe4 --- /dev/null +++ b/Modules/DiffusionImaging/IODataStructures/PlanarFigureComposite/mitkPlanarFigureComposite.h @@ -0,0 +1,110 @@ +/* + * mitkPlanarFigureComposite.h + * mitk-all + * + * Created by HAL9000 on 2/4/11. + * Copyright 2011 __MyCompanyName__. All rights reserved. + * + */ + +#ifndef _MITK_PLANARFIGURECOMPOSITE_H +#define _MITK_PLANARFIGURECOMPOSITE_H + +#include "mitkCommon.h" +#include "mitkBaseData.h" +#include "MitkDiffusionImagingMBIExports.h" +#include "mitkPlanarFigure.h" +#include "itkVectorContainer.h" +#include "mitkDataNode.h" + + +namespace mitk { + + enum PFCompositionOperation { + PFCOMPOSITION_AND_OPERATION, + PFCOMPOSITION_OR_OPERATION, + PFCOMPOSITION_NOT_OPERATION, + }; + + + + + class MitkDiffusionImagingMBI_EXPORT PlanarFigureComposite : public PlanarFigure + { + + typedef itk::VectorContainer CompositionContainer; + typedef itk::VectorContainer DataNodeContainer; + + + public: + mitkClassMacro(PlanarFigureComposite, PlanarFigure); + itkNewMacro( Self ); + + // ///MUST HAVE IMPLEMENTATION////// + bool SetControlPoint( unsigned int index, const Point2D &point, bool createIfDoesNotExist ); + unsigned int GetMinimumNumberOfControlPoints() const + { + return 0; + } + /** \brief Circle has 2 control points per definition. */ + unsigned int GetMaximumNumberOfControlPoints() const + { + return 0; + } + // ///////////////////////// + + + + int getNumberOfChildren(); + mitk::PlanarFigure::Pointer getChildAt(int); + void addPlanarFigure(PlanarFigure::Pointer); + + + mitk::DataNode::Pointer getDataNodeAt(int); + void addDataNode(mitk::DataNode::Pointer); + void replaceDataNodeAt(int, mitk::DataNode::Pointer); + + // set if this compsition is AND, OR, NOT + void setOperationType(PFCompositionOperation); + PFCompositionOperation getOperationType(); + + void setDisplayName(std::string); + std::string getDisplayName(); + + protected: + PlanarFigureComposite(); + virtual ~PlanarFigureComposite(); + + + + // ///MUST HAVE IMPLEMENTATION////// + /** \brief Generates the poly-line representation of the planar figure. */ + virtual void GeneratePolyLine(); + + /** \brief Generates the poly-lines that should be drawn the same size regardless of zoom.*/ + virtual void GenerateHelperPolyLine(double mmPerDisplayUnit, unsigned int displayHeight); + + /** \brief Calculates feature quantities of the planar figure. */ + virtual void EvaluateFeaturesInternal(); + + virtual void PrintSelf( std::ostream &os, itk::Indent indent ) const; + // //////////////////// + + + + + private: + //this vector takes planarfigures and planarfigureComosite types + CompositionContainer::Pointer m_PFVector; + PFCompositionOperation m_compOperation; + + DataNodeContainer::Pointer m_DNVector; + std::string m_name; + + + + }; + +} + +#endif diff --git a/Modules/DiffusionImaging/IODataStructures/mitkDiffusionImagingObjectFactory.cpp b/Modules/DiffusionImaging/IODataStructures/mitkDiffusionImagingObjectFactory.cpp index 57a93e78ea..dc52290f31 100644 --- a/Modules/DiffusionImaging/IODataStructures/mitkDiffusionImagingObjectFactory.cpp +++ b/Modules/DiffusionImaging/IODataStructures/mitkDiffusionImagingObjectFactory.cpp @@ -1,213 +1,236 @@ /*========================================================================= 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 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() { 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() { 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_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")); } 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; } } diff --git a/Modules/DiffusionImaging/Rendering/mitkFiberBundleMapper3D.cpp b/Modules/DiffusionImaging/Rendering/mitkFiberBundleMapper3D.cpp new file mode 100644 index 0000000000..126e80b35c --- /dev/null +++ b/Modules/DiffusionImaging/Rendering/mitkFiberBundleMapper3D.cpp @@ -0,0 +1,1136 @@ +/*========================================================================= + + Program: Medical Imaging & Interaction Toolkit + Language: C++ + Date: $Date: 2009-05-12 19:56:03 +0200 (Di, 12 Mai 2009) $ + Version: $Revision: 17179 $ + + 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 "mitkProperties.h" +#include "mitkFiberBundleMapper3D.h" + + +#include +#include +#include +#include +#include +#include +#include +#include +#include +#include +#include +#include "vtkVertex.h" + +#include +#include +#include +#include +#include + +//template +mitk::FiberBundleMapper3D::FiberBundleMapper3D() +: m_vtkFiberList(NULL), +m_VtkFiberDataMapperGL(NULL), +m_vtkTubeMapper(NULL) + +{ + //MITK_INFO << "FiberBundleMapper3D()"; + m_FiberAssembly = vtkPropAssembly::New(); + m_FiberActor = vtkOpenGLActor::New(); + m_TubeActor = vtkOpenGLActor::New(); + + + /* + vtkUnsignedCharArray *colorsT = vtkUnsignedCharArray::New(); + colorsT->SetName("Colors"); + colorsT->SetNumberOfComponents(4); + + unsigned char red1[4] = {255, 0, 0 , 10}; + colorsT->InsertNextTupleValue(red1); + + unsigned char red2[4] = {255,0, 0 , 255}; + colorsT->InsertNextTupleValue(red2); + + colorsT->SetValue(3, (unsigned char)(255)); + colorsT->SetValue(7, (unsigned char)(255)); + + + + + + + + //Create points for polyline1. + double origin[3] = {100.0, 400.0, 0.0}; + double p0[3] = {300.0, 400.0, 0.0}; + double p1[3] = {300.0, 200.0, 0.0}; + double p2[3] = {100.0, 300.0, 0.0}; + double p3[3] = {130.0, 250.0, 0.0}; + + //create points for polyline2 + //double p01[3] = {50.0, 50.0, 13.0}; + //double p11[3] = {200.0, 100.0, 13.0}; + + //insert points to vtkPointarray + vtkPoints *pnts = vtkPoints::New(); + pnts->InsertPoint(0,origin); + pnts->InsertPoint(1,p0); + pnts->InsertPoint(2,p1); + pnts->InsertPoint(3,p2); + //pnts->InsertPoint(4,p01); + //pnts->InsertPoint(5,p11); + pnts->InsertPoint(4,p3); + + //generate and define polyline1 + vtkPolyLine *polyLine = vtkPolyLine::New(); + polyLine->GetPointIds()->SetNumberOfIds(4); + polyLine->GetPointIds()->SetId(0,0); + polyLine->GetPointIds()->SetId(1,1); + polyLine->GetPointIds()->SetId(2,2); + polyLine->GetPointIds()->SetId(3,3); + + /*generate and define polyline2 + vtkPolyLine *polyLine2 = vtkPolyLine::New(); + polyLine2->GetPointIds()->SetNumberOfIds(2); + polyLine2->GetPointIds()->SetId(0,4); + polyLine2->GetPointIds()->SetId(1,5); + */ + + /* + vtkVertex *vtx = vtkVertex::New(); + vtx->GetPointIds()->SetNumberOfIds(1); + vtx->GetPointIds()->SetId(0,4); + + vtkCellArray *lines = vtkCellArray::New(); + lines->InsertNextCell(polyLine); + //lines->InsertNextCell(vtx); + //lines->InsertNextCell(polyLine2); + + + vtkCellArray *vertx = vtkCellArray::New(); + vertx->InsertNextCell(vtx); + + vtkPolyData *polyDataT = vtkPolyData::New(); + polyDataT->SetPoints(pnts); + polyDataT->SetLines(lines); + polyDataT->SetVerts(vertx); + + //color and opacity handling + vtkUnsignedCharArray *colorT = vtkUnsignedCharArray::New(); + colorT->SetName("Colors"); + + colorT->SetNumberOfComponents(4); //4 components cuz of RGBA + unsigned char rgba[4] = {255,0,0,255}; + unsigned char rgba2[4] = {0,255,0,255}; + + //if just 1 point in there + colorT->InsertNextTupleValue(rgba); + colorT->InsertNextTupleValue(rgba2); + colorT->InsertNextTupleValue(rgba); + colorT->InsertNextTupleValue(rgba2); + colorT->InsertNextTupleValue(rgba); + + /*for(int i=0; i<6; i++) + { + + + double vtkPntTmp[3]; + pnts->GetPoint(i, vtkPntTmp); + double vtkPntTmpNxt[3]; + pnts->GetPoint(i+1, vtkPntTmpNxt); + + vnl_vector_fixed< double, 3 > tmpPntvtk( vtkPntTmp[0], vtkPntTmp[1],vtkPntTmp[2]); + vnl_vector_fixed< double, 3 > nxttmpPntvtk(vtkPntTmpNxt[0], vtkPntTmpNxt[1], vtkPntTmpNxt[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); + + + if(i==3) + { + colorT->InsertNextTupleValue(rgba); + colorT->InsertNextTupleValue(rgba); + }else if(i==4) + { + //do nothing + }else{ + colorT->InsertNextTupleValue(rgba); + } + + + + } + + /* + unsigned char red[4] = {255, 0, 0 , 20}; + unsigned char green[4] = {0, 255, 0 , 190}; + unsigned char blue[4] = {0, 0, 255, 255}; + unsigned char white[4] = {255, 255, 255, 255}; + + colorT->InsertNextTupleValue(red); //color for point0 + colorT->InsertNextTupleValue(green); //color for point1 + colorT->InsertNextTupleValue(blue); + colorT->InsertNextTupleValue(white); + colorT->InsertNextTupleValue(white); + colorT->InsertNextTupleValue(white); //color for point5 + + polyDataT->GetPointData()->AddArray(colorT); + + + vtkTubeFilter *tube = vtkTubeFilter::New(); + tube->SetInput(polyDataT); + tube->SetNumberOfSides(8); + tube->SetRadius(5); + + vtkSmartPointer mapper = + vtkSmartPointer::New(); + mapper->SetInput(polyDataT); + //mapper->SetInputConnection(tube->GetOutputPort()); + mapper->ScalarVisibilityOn(); + mapper->SetScalarModeToUsePointFieldData(); + //mapper->SetColorModeToMapScalars(); + mapper->SelectColorArray("Colors"); + + vtkSmartPointer actor = + vtkSmartPointer::New(); + actor->SetMapper(mapper); + actor->GetProperty()->SetOpacity(1.0); + //actor->GetProperty()->SetLineWidth(20); + actor->GetProperty()->SetPointSize(5.0); + + + vtkSmartPointer renderer = + vtkSmartPointer::New(); + renderer->AddActor(actor); + //renderer->SetBackground(.2, .3, .4); + + // Make an oblique view + renderer->GetActiveCamera()->Azimuth(30); + renderer->GetActiveCamera()->Elevation(30); + renderer->ResetCamera(); + + vtkSmartPointer renWin = + vtkSmartPointer::New(); + vtkSmartPointer + iren = vtkSmartPointer::New(); + + iren->SetRenderWindow(renWin); + renWin->AddRenderer(renderer); + //renWin->LineSmoothingOff(); + renWin->SetSize(500, 500); + renWin->Render(); + + vtkSmartPointer style = + vtkSmartPointer::New(); + iren->SetInteractorStyle(style); + + iren->Start(); + MITK_INFO << "swerwas"; + + /* + + + // Spiral tube + double vX, vY, vZ; + unsigned int nV = 256; // No. of vertices + unsigned int nCyc = 5; // No. of spiral cycles + double rT1 = 0.1, rT2 = 0.5;// Start/end tube radii + double rS = 2; // Spiral radius + double h = 10; // Height + unsigned int nTv = 8; // No. of surface elements for each tube vertex + + unsigned int i; + + // Create points and cells for the spiral + vtkSmartPointer points = vtkSmartPointer::New(); + for(i = 0; i < nV; i++) + { + // Spiral coordinates + vX = rS * cos(2 * 3 * nCyc * i / (nV - 1)); + vY = rS * sin(2 * 3 * nCyc * i / (nV - 1)); + vZ = h * i / nV; + points->InsertPoint(i, vX, vY, vZ); + } + + vtkSmartPointer lines = + vtkSmartPointer::New(); + lines->InsertNextCell(nV); + for (i = 0; i < nV; i++) + { + lines->InsertCellPoint(i); + } + + + vtkSmartPointer polyData = + vtkSmartPointer::New(); + polyData->SetPoints(points); + polyData->SetLines(lines); + + + // RBG array (could add Alpha channel too I guess...) + // Varying from blue to red + vtkSmartPointer colors = + vtkSmartPointer::New(); + colors->SetName("Colors"); + colors->SetNumberOfComponents(3); + colors->SetNumberOfTuples(nV); + for (i = 0; i < nV ;i++) + { + + unsigned char red[3] = {char(255 * i/ (nV - 1)),0,char(255 * (nV - 1 - i)/(nV - 1))}; + + colors->InsertNextTupleValue( red); + } + polyData->GetPointData()->AddArray(colors); + + + + vtkSmartPointer mapper = + vtkSmartPointer::New(); + mapper->SetInput(polyData); + mapper->ScalarVisibilityOn(); + mapper->SetScalarModeToUsePointFieldData(); + mapper->SelectColorArray("Colors"); + + vtkSmartPointer actor = + vtkSmartPointer::New(); + actor->SetMapper(mapper); + + vtkSmartPointer renderer = + vtkSmartPointer::New(); + renderer->AddActor(actor); + renderer->SetBackground(.2, .3, .4); + + // Make an oblique view + renderer->GetActiveCamera()->Azimuth(30); + renderer->GetActiveCamera()->Elevation(30); + renderer->ResetCamera(); + + vtkSmartPointer renWin = + vtkSmartPointer::New(); + vtkSmartPointer + iren = vtkSmartPointer::New(); + + iren->SetRenderWindow(renWin); + renWin->AddRenderer(renderer); + renWin->SetSize(500, 500); + renWin->Render(); + + vtkSmartPointer style = + vtkSmartPointer::New(); + iren->SetInteractorStyle(style); + + iren->Start(); + + + + + /* + + double origin[3] = {0.0, 0.0, 0.0}; + double p0[3] = {10.0, 0.0, 0.0}; + double p1[3] = {10.0, 10.0, 0.0}; + double p2[3] = {0.0, 10.0, 0.0}; + double p3[3] = {10.0, 10.0, 0.0}; + double p4[3] = {10.0, 20.0, 0.0}; + double p5[3] = {0.0, 20.0, 0.0}; + + //create a vtkPoints object and store the points in it + vtkSmartPointer points = + vtkSmartPointer::New(); + points->InsertNextPoint(origin); + points->InsertNextPoint(p0); + points->InsertNextPoint(p1); + points->InsertNextPoint(p2); + points->InsertNextPoint(p3); + points->InsertNextPoint(p4); + points->InsertNextPoint(p5); + + vtkSmartPointer polyLine = + vtkSmartPointer::New(); + polyLine->GetPointIds()->SetNumberOfIds(7); + for(unsigned int i = 0; i < 7; i++) + { + polyLine->GetPointIds()->SetId(i,i); + } + + double origin2[3] = {30.0, 0.0, 0.0}; + double p02[3] = {40.0, 0.0, 0.0}; + double p12[3] = {40.0, 20.0, 0.0}; + double p22[3] = {30.0, 20.0, 0.0}; + double p23[3] = {30.0, 0.0, 0.0}; + + + points->InsertNextPoint(origin2); + points->InsertNextPoint(p02); + points->InsertNextPoint(p12); + points->InsertNextPoint(p22); + points->InsertNextPoint(p23); + + vtkSmartPointer polyLine2 = + vtkSmartPointer::New(); + polyLine2->GetPointIds()->SetNumberOfIds(5); + for(unsigned int i = 0; i < 5; i++) + { + polyLine2->GetPointIds()->SetId(i,i+7); + } + + //Create a cell array to store the lines in and add the lines to it + vtkSmartPointer cells = + vtkSmartPointer::New(); + cells->InsertNextCell(polyLine); + cells->InsertNextCell(polyLine2); + + + //Create a polydata to store everything in + vtkSmartPointer polyData = + vtkSmartPointer::New(); + + //add the points to the dataset + polyData->SetPoints(points); + + //add the lines to the dataset + polyData->SetLines(cells); + //setup actor and mapper + vtkSmartPointer mapper = + vtkSmartPointer::New(); + mapper->SetInput(polyData); + + vtkSmartPointer actor = + vtkSmartPointer::New(); + actor->SetMapper(mapper); + + m_FiberAssembly->AddPart(actor); + */ + + + +} + +//template +mitk::FiberBundleMapper3D::~FiberBundleMapper3D() +{ + //MITK_INFO << "FiberBundleMapper3D(destructor)"; + m_FiberActor->Delete(); + m_FiberAssembly->Delete(); + //m_vtkFiberList->Delete(); + //m_VtkFiberDataMapperGL->Delete(); + //m_VtkFiberDataMapper->Delete(); + +} + + +const mitk::FiberBundle* mitk::FiberBundleMapper3D::GetInput() +{ + //MITK_INFO << "FiberBundleMapper3D GetInput()" ; + + return static_cast ( GetData() ); +} + +/* + This method is called once the mapper gets new input, + for UI rotation or changes in colorcoding this method is NOT called + */ +void mitk::FiberBundleMapper3D::GenerateData() +{ + /* ######## FIBER PREPARATION START ######### */ + //get fiberbundle + mitk::FiberBundle::Pointer PFiberBundle = dynamic_cast< mitk::FiberBundle* > (this->GetData()); + + //get groupFiberBundle, which is a datastructure containing single fibers + mitk::FiberBundle::FiberGroupType::Pointer groupFiberBundle = PFiberBundle->GetGroupFiberBundle(); + + //extractn single fibers + //in the groupFiberBundle all smartPointers to single fibers are stored in in a ChildrenList + mitk::FiberBundle::ChildrenListType * FiberList; + FiberList = groupFiberBundle->GetChildren(); + + /* ######## FIBER PREPARATION END ######### */ + + /* ######## VTK FIBER REPRESENTATION ######## */ + //create a vtkPoints object and store the all the brainFiber points in it + + vtkPoints* vtkSmoothPoints = vtkPoints::New(); //in smoothpoints the interpolated points representing a fiber are stored. + + //in vtkcells all polylines are stored, actually all id's of them are stored + vtkCellArray *vtkSmoothCells = vtkCellArray::New(); //cellcontainer for smoothed lines + + //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 = vtkpointsDTI->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; } + + //get list of points + int fibrNrPnts = dtiTract->GetNumberOfPoints(); + mitk::FiberBundle::DTITubeType::PointListType dtiPntList = dtiTract->GetPoints(); + + //MITK_INFO << "REAL AMOUNT OF FIBERS: " << fibrNrPnts; + + vtkPoints *vtkpointsDTI = vtkPoints::New(); + + if (fibrNrPnts <= 0) { //this should never occour! but who knows + MITK_INFO << "HyperERROR in fiberBundleMapper3D.cpp ...no point in fiberBundle!!! .. check ur trackingAlgorithm"; + continue; + } + + + ///////PROCESS ON FIBERS//////// + for (int i=0; i1 + PFiberBundle->GetGeometry()->IndexToWorld(indexPnt, worldPnt); + double worldFbrPnt[3] = {worldPnt[0], worldPnt[1], worldPnt[2]}; + vtkpointsDTI->InsertNextPoint(worldFbrPnt); + } + + //MITK_INFO << "REDUCED AMOUNT OF FIBERS: " << vtkpointsDTI->GetNumberOfPoints(); + + ////POINTS OF DTI ARE READY FOR FUTHER VTK PROCESSING//// + } + + + /////PROCESS POLYLINE SMOOTHING///// + vtkKochanekSpline* xSpline = vtkKochanekSpline::New(); + vtkKochanekSpline* ySpline = vtkKochanekSpline::New(); + vtkKochanekSpline* zSpline = vtkKochanekSpline::New(); + + vtkParametricSpline* spline = vtkParametricSpline::New(); + spline->SetXSpline(xSpline); + spline->SetYSpline(ySpline); + spline->SetZSpline(zSpline); + spline->SetPoints(vtkpointsDTI); + + + vtkParametricFunctionSource* functionSource = vtkParametricFunctionSource::New(); + functionSource->SetParametricFunction(spline); + functionSource->SetUResolution(200); + functionSource->SetVResolution(200); + functionSource->SetWResolution(200); + functionSource->Update(); + + + + vtkPolyData* outputFunction = functionSource->GetOutput(); + vtkPoints* tmpSmoothPnts = outputFunction->GetPoints(); //smoothPoints of current fiber + + vtkPolyLine* smoothLine = vtkPolyLine::New(); + smoothLine->GetPointIds()->SetNumberOfIds(tmpSmoothPnts->GetNumberOfPoints()); +// MITK_INFO << "SMOOTHED AMOUNT OF POINTS:" << tmpSmoothPnts->GetNumberOfPoints(); + + + /////CREATE SMOOTH POLYLINE OBJECT//// + /////MANAGE LINE AND CORRELATED POINTS///// + int pointHelperCnt = vtkSmoothPoints->GetNumberOfPoints(); //also put current points into global smooth pointcontainer + int nrSmPnts = tmpSmoothPnts->GetNumberOfPoints(); + tubeRadius->SetNumberOfTuples(nrSmPnts); + double tbradius = 1;//default value for radius + + for(int ism=0; ismGetPointIds()->SetId(ism, ism+pointHelperCnt); + vtkSmoothPoints->InsertNextPoint(tmpSmoothPnts->GetPoint(ism)); + + // MITK_INFO << "LinePntID: " << ism << " linked to: " << ism+pointHelperCnt << " val: " << tmpSmoothPnts->GetPoint(ism)[0] << " " << tmpSmoothPnts->GetPoint(ism)[1] << " " << tmpSmoothPnts->GetPoint(ism)[2]; + tubeRadius->SetTuple1(ism,tbradius); //tuple with 1 argument + + + //colorcoding orientation based + unsigned char rgba[4] = {0,0,0,0}; + if (ism < nrSmPnts-1 && ism>0) + { + + // MITK_INFO << "inbetween fiber, at position:" << ism; +// //nimm nur diff1 + vnl_vector_fixed< double, 3 > tmpPntvtk(tmpSmoothPnts->GetPoint(ism)[0], tmpSmoothPnts->GetPoint(ism)[1],tmpSmoothPnts->GetPoint(ism)[2]); + vnl_vector_fixed< double, 3 > nxttmpPntvtk(tmpSmoothPnts->GetPoint(ism+1)[0], tmpSmoothPnts->GetPoint(ism+1)[1], tmpSmoothPnts->GetPoint(ism+1)[2]); + vnl_vector_fixed< double, 3 > prevtmpPntvtk(tmpSmoothPnts->GetPoint(ism-1)[0], tmpSmoothPnts->GetPoint(ism-1)[1], tmpSmoothPnts->GetPoint(ism-1)[2]); + + vnl_vector_fixed< double, 3 > diff1; + diff1 = tmpPntvtk - nxttmpPntvtk; + diff1.normalize(); + + vnl_vector_fixed< double, 3 > diff2; + diff2 = tmpPntvtk - prevtmpPntvtk; + diff2.normalize(); + + vnl_vector_fixed< double, 3 > diff; + diff = (diff1 - diff2)/2.0; + + + rgba[0] = (unsigned char) (255.0 * std::abs(diff[0])); + rgba[1] = (unsigned char) (255.0 * std::abs(diff[1])); + rgba[2] = (unsigned char) (255.0 * std::abs(diff[2])); + rgba[3] = (unsigned char) (255.0); + + + + } else if(ism==0) { + //explicit handling of startpoint of line + + //nimm nur diff1 + vnl_vector_fixed< double, 3 > tmpPntvtk(tmpSmoothPnts->GetPoint(ism)[0], tmpSmoothPnts->GetPoint(ism)[1],tmpSmoothPnts->GetPoint(ism)[2]); + vnl_vector_fixed< double, 3 > nxttmpPntvtk(tmpSmoothPnts->GetPoint(ism+1)[0], tmpSmoothPnts->GetPoint(ism+1)[1], tmpSmoothPnts->GetPoint(ism+1)[2]); + + + vnl_vector_fixed< double, 3 > diff1; + diff1 = tmpPntvtk - nxttmpPntvtk; + diff1.normalize(); + + rgba[0] = (unsigned char) (255.0 * std::abs(diff1[0])); + rgba[1] = (unsigned char) (255.0 * std::abs(diff1[1])); + rgba[2] = (unsigned char) (255.0 * std::abs(diff1[2])); + rgba[3] = (unsigned char) (255.0); + +// MITK_INFO << "first point color: " << rgba[0] << " " << rgba[1] << " " << rgba[2]; + + + } else if(ism==nrSmPnts-1) { +// last point in fiber + + // nimm nur diff2 + vnl_vector_fixed< double, 3 > tmpPntvtk(tmpSmoothPnts->GetPoint(ism)[0], tmpSmoothPnts->GetPoint(ism)[1],tmpSmoothPnts->GetPoint(ism)[2]); + vnl_vector_fixed< double, 3 > prevtmpPntvtk(tmpSmoothPnts->GetPoint(ism-1)[0], tmpSmoothPnts->GetPoint(ism-1)[1], tmpSmoothPnts->GetPoint(ism-1)[2]); + + vnl_vector_fixed< double, 3 > diff2; + diff2 = tmpPntvtk - prevtmpPntvtk; + diff2.normalize(); + + rgba[0] = (unsigned char) (255.0 * std::abs(diff2[0])); + rgba[1] = (unsigned char) (255.0 * std::abs(diff2[1])); + rgba[2] = (unsigned char) (255.0 * std::abs(diff2[2])); + rgba[3] = (unsigned char) (255.0); +// +// MITK_INFO << "last point color: " << rgba[0] << " " << rgba[1] << " " << rgba[2]; + } //end colorcoding +// + colorsT->InsertNextTupleValue(rgba); + + }//end of smoothline + + ///////smooth Fiber ready//////// + vtkSmoothCells->InsertNextCell(smoothLine); + } + + //vtkpointsDTI->Delete();//points are not needed anymore TODO uncomment! + + + /* + + //get FA value ... for that FA has to be interpolated as well as DTItracktLine + 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->InitTraversal(); + + // Put points and lines together in one polyData structure + vtkPolyData *polyData = vtkPolyData::New(); + polyData->SetPoints(vtkSmoothPoints); + polyData->SetLines(vtkSmoothCells); + + if (vtkVrtxs->GetSize() > 0) { + polyData->SetVerts(vtkVrtxs); + } + polyData->GetPointData()->AddArray(colorsT); + //polyData->GetPointData()->AddArray(faColors); + //polyData->GetPointData()->AddArray(tubeRadius); + + + vtkLookupTable *lut = vtkLookupTable::New(); + lut->Build(); + + + m_VtkFiberDataMapperGL = vtkOpenGLPolyDataMapper::New(); + m_VtkFiberDataMapperGL->SetInput(polyData); + m_VtkFiberDataMapperGL->ScalarVisibilityOn(); + + m_VtkFiberDataMapperGL->SetScalarModeToUsePointFieldData(); + //m_VtkFiberDataMapperGL->SelectColorArray("FaColors"); + m_VtkFiberDataMapperGL->SelectColorArray("ColorValues"); + m_VtkFiberDataMapperGL->SetLookupTable(lut); + + m_vtkTubeMapper = vtkOpenGLPolyDataMapper::New(); + + //m_FiberActor = vtkOpenGLActor::New(); + m_FiberActor->SetMapper(m_VtkFiberDataMapperGL); + m_FiberActor->GetProperty()->SetOpacity(1.0); + m_FiberActor->GetProperty()->SetPointSize(4.0f); + // m_FiberActor->GetProperty()->SetColor(255.0, 0.0, 0.0); + + + + m_FiberAssembly->AddPart(m_FiberActor); + + //setting color and opacity in the fiberActor itself is not recommended + //here cuz color and opacity of dataNode will be considered in GetData(baserenderer*) anyway + this->GetDataNode()->SetColor(255.0,0,0); + this->GetDataNode()->SetOpacity(1.0); + + +} + + + + +//template +void mitk::FiberBundleMapper3D::GenerateData( mitk::BaseRenderer *renderer ) +{ + + + //MITK_INFO << "FiberBundleMapper3D GenerateData(BaseRenderer)" ; + + // nodeCC = 1 ... ROI colorcoding + // 2 ... orientation colorcoding + // 3 ... FA colorcoding + + + int nodeCC; + bool isCCd = this->GetDataNode()->GetPropertyValue("ColorCoding", nodeCC); + if ( isCCd && nodeCC == 1 ) { + + + //get color and opacity from DataNode + int tmpline; + + bool isLineProp = this->GetDataNode()->GetPropertyValue("LineWidth",tmpline); + + bool isPointRep; + bool successPointProp = this->GetDataNode()->GetPropertyValue("RepPoints", isPointRep); + float pointSize; + bool successPointSize = this->GetDataNode()->GetPropertyValue("pointSize", pointSize); + + if (isLineProp) { + m_FiberActor->GetProperty()->SetLineWidth(tmpline); + } + + if(isPointRep) { + m_FiberActor->GetProperty()->SetRepresentationToPoints(); + m_FiberActor->GetProperty()->SetPointSize(pointSize); + } + + } else if (isCCd && nodeCC == 2) { + float tmpopa; + this->GetDataNode()->GetOpacity(tmpopa, NULL); + m_FiberActor->GetProperty()->SetOpacity((double) tmpopa); + + } else if (isCCd && nodeCC == 3) { + + float temprgb[3]; + this->GetDataNode()->GetColor( temprgb, NULL ); + double trgb[3] = { (double) temprgb[0], (double) temprgb[1], (double) temprgb[2] }; + m_FiberActor->GetProperty()->SetColor(trgb); + + if(m_VtkFiberDataMapperGL->GetScalarVisibility()) //can be 0 or 1, for scalarVis On or Off + { + m_VtkFiberDataMapperGL->ScalarVisibilityOff(); + } + + + + } else if (isCCd && nodeCC == 4) { + + if(!m_VtkFiberDataMapperGL->GetScalarVisibility()) //can be 0 or 1, for scalarVis On or Off + { + m_VtkFiberDataMapperGL->ScalarVisibilityOn(); + } + m_VtkFiberDataMapperGL->SelectColorArray("ColorValues"); + + } else if (isCCd && nodeCC == 5){ + + if(!m_VtkFiberDataMapperGL->GetScalarVisibility()) //if visibility is off, switch it on + { + m_VtkFiberDataMapperGL->ScalarVisibilityOn(); + } + m_VtkFiberDataMapperGL->SelectColorArray("FaColors"); + + } else if (isCCd && nodeCC == 6){ + //orientationbased colorcoding + FA as opacity + //get FA out of polydata, which is saved in faColor vtkDoubleArray + + vtkPolyData *tmpPolyData = m_VtkFiberDataMapperGL->GetInput(); + vtkPointData *tmpPointData = tmpPolyData->GetPointData(); + + + + int hasAr = tmpPointData->HasArray("FaColors"); + if(!hasAr) + return; + + vtkDoubleArray *tmpFAarray = (vtkDoubleArray*)(tmpPointData->GetArray("FaColors")) ; + + /*for(int i=0; iGetNumberOfTuples(); i++) + { + + double *tmpTuple; + tmpFAarray->GetTuple(i, tmpTuple); + + for(int j=0; jGetNumberOfComponents(); j++) + { + MITK_INFO << "FA Value: at index " << i << ": " << tmpTuple[j]; + } + + + } + */ + + //since we have our FA values, lets replace the alpha values in colorT + //we know each 4th entry is a A value of RGBA + int hasArCV = tmpPointData->HasArray("ColorValues"); + if(!hasArCV) + return; + + vtkUnsignedCharArray *colorsTtmp = dynamic_cast (tmpPointData->GetArray("ColorValues")); + + for(int i=0; iGetNumberOfTuples(); i++) + { + + //double *tmpTupleCV = colorsTtmp->GetTuple4(i); + double tmpTupleFA = tmpFAarray->GetTuple1(i); + tmpTupleFA = tmpTupleFA * 255.0; + + colorsTtmp->SetComponent(i,3, tmpTupleFA ); + + // MITK_INFO << "----" << i; + //MITK_INFO << tmpTupleCV[0]; + //MITK_INFO << tmpTupleCV[1]; + //MITK_INFO << tmpTupleCV[2]; + //MITK_INFO << tmpTupleCV[3]; + //double *test = m_VtkFiberDataMapperGL->GetInput()->GetPointData()->GetArray("ColorValues")->GetTuple4(i); + //MITK_INFO << test[0]; + //MITK_INFO << test[1]; + //MITK_INFO << test[2]; + //MITK_INFO << test[3]; + + + } + + m_VtkFiberDataMapperGL->SelectColorArray(""); + m_VtkFiberDataMapperGL->SelectColorArray("ColorValues"); + + + } else if (isCCd && nodeCC == 7){ + + vtkPolyData *tmpPolyData = m_VtkFiberDataMapperGL->GetInput(); + vtkPointData *tmpPointData = tmpPolyData->GetPointData(); + int hasArCV = tmpPointData->HasArray("ColorValues"); + if(!hasArCV) + return; + + vtkUnsignedCharArray *colorsTtmp = dynamic_cast (tmpPointData->GetArray("ColorValues")); + + for(int i=0; iGetNumberOfTuples(); i++) + { + + double tmpTupleFA = 255.0; + colorsTtmp->SetComponent(i,3, tmpTupleFA ); + } + m_VtkFiberDataMapperGL->SelectColorArray(""); + m_VtkFiberDataMapperGL->SelectColorArray("ColorValues"); + + + } else if (isCCd && nodeCC == 8) { + /* something is still missing to activate smoothing or make it work.... */ + if (!renderer->GetRenderWindow()->GetLineSmoothing()) { + renderer->GetRenderWindow()->SetLineSmoothing(1); + renderer->GetRenderWindow()->Modified(); + } + if (!renderer->GetRenderWindow()->GetPointSmoothing()) { + renderer->GetRenderWindow()->SetPointSmoothing(1); + renderer->GetRenderWindow()->Modified(); + } + if (!renderer->GetRenderWindow()->GetPolygonSmoothing()) { + renderer->GetRenderWindow()->SetPolygonSmoothing(1); + renderer->GetRenderWindow()->Modified(); + } + + + } else if (isCCd && nodeCC == 9) { + if (renderer->GetRenderWindow()->GetLineSmoothing()) { + renderer->GetRenderWindow()->SetLineSmoothing(0); + renderer->GetRenderWindow()->Modified(); + } + if (renderer->GetRenderWindow()->GetPointSmoothing()) { + renderer->GetRenderWindow()->SetPointSmoothing(0); + renderer->GetRenderWindow()->Modified(); + } + if (renderer->GetRenderWindow()->GetPolygonSmoothing()) { + renderer->GetRenderWindow()->SetPolygonSmoothing(0); + renderer->GetRenderWindow()->Modified(); + } + + } else if (isCCd && nodeCC == 10) { + // manipulate X Coordinates of selected FiberBundle + int tmpXmove; + + bool isXmove = this->GetDataNode()->GetPropertyValue("Xmove",tmpXmove); + + if (!isXmove) + return; + + vtkPolyData *tmpPolyData = m_VtkFiberDataMapperGL->GetInput(); + vtkPoints* tmpVtkPnts = tmpPolyData->GetPoints(); + double PtmpPntVal[3]; + + for (int i=0; iGetNumberOfPoints(); ++i ) + { + tmpVtkPnts->GetPoint(i,PtmpPntVal); + + PtmpPntVal[0] = PtmpPntVal[0] + (double) tmpXmove; + tmpVtkPnts->SetPoint(i, PtmpPntVal); + + tmpPolyData->Modified(); + + } + + } else if (isCCd && nodeCC == 11) { + // manipulate Y Coordinates of selected FiberBundle + int tmpYmove; + + bool isYmove = this->GetDataNode()->GetPropertyValue("Ymove",tmpYmove); + + if (!isYmove) + return; + + vtkPolyData *tmpPolyData = m_VtkFiberDataMapperGL->GetInput(); + vtkPoints* tmpVtkPnts = tmpPolyData->GetPoints(); + double PtmpPntVal[3]; + + for (int i=0; iGetNumberOfPoints(); ++i ) + { + tmpVtkPnts->GetPoint(i,PtmpPntVal); + + PtmpPntVal[1] = PtmpPntVal[1] + (double) tmpYmove; + tmpVtkPnts->SetPoint(i, PtmpPntVal); + + tmpPolyData->Modified(); + + } + + } else if (isCCd && nodeCC == 12) { + // manipulate Z Coordinates of selected FiberBundle + int tmpZmove; + + bool isZmove = this->GetDataNode()->GetPropertyValue("Zmove",tmpZmove); + if (!isZmove) + return; + + vtkPolyData *tmpPolyData = m_VtkFiberDataMapperGL->GetInput(); + vtkPoints* tmpVtkPnts = tmpPolyData->GetPoints(); + double PtmpPntVal[3]; + + for (int i=0; iGetNumberOfPoints(); ++i ) + { + tmpVtkPnts->GetPoint(i,PtmpPntVal); + + PtmpPntVal[2] = PtmpPntVal[2] + (double) tmpZmove; + //PtmpPntVal[2] = PtmpPntVal[2] + 1; + tmpVtkPnts->SetPoint(i, PtmpPntVal); + + tmpPolyData->Modified(); + + } + + } else if (isCCd && nodeCC == 13) { + int tmpTubeSides; + bool isTubeSides = this->GetDataNode()->GetPropertyValue("TubeSides",tmpTubeSides); + + float tmpRadius; + bool isRadius = this->GetDataNode()->GetPropertyValue("TubeRadius",tmpRadius); + + if (!isTubeSides) + return; + + vtkPolyData *tmpPolyData = m_VtkFiberDataMapperGL->GetInput(); + + + m_tubes = vtkTubeFilter::New(); + m_tubes->SetInput(tmpPolyData); + m_tubes->SidesShareVerticesOn(); + m_tubes->SetRadius((double)(tmpRadius)); + m_tubes->SetNumberOfSides(tmpTubeSides); + m_tubes->Modified(); + // m_tubes->Update(); + + + m_vtkTubeMapper->SetInputConnection(m_tubes->GetOutputPort()); + m_vtkTubeMapper->ScalarVisibilityOn(); + m_vtkTubeMapper->SetScalarModeToUsePointFieldData(); + m_vtkTubeMapper->SelectColorArray(""); + m_vtkTubeMapper->SelectColorArray("ColorValues"); + + + + m_TubeActor->SetMapper(m_vtkTubeMapper); + m_TubeActor->GetProperty()->SetOpacity(1); + m_TubeActor->GetProperty()->BackfaceCullingOn(); + + m_FiberAssembly->AddPart(m_TubeActor); + m_FiberAssembly->Modified(); + + } else if (isCCd && nodeCC == 14) { + + float temprgb[3]; + this->GetDataNode()->GetColor( temprgb, NULL ); + double trgb[3] = { (double) temprgb[0], (double) temprgb[1], (double) temprgb[2] }; + m_TubeActor->GetProperty()->SetColor(trgb); + + if(m_vtkTubeMapper->GetScalarVisibility()) //can be 0 or 1, for scalarVis On or Off + { + m_vtkTubeMapper->ScalarVisibilityOff(); + } + + } else if (isCCd && nodeCC == 15) { + m_TubeActor->GetProperty()->SetOpacity(0); + m_FiberAssembly->RemovePart(m_TubeActor); + m_FiberAssembly->Modified(); + + }else if (isCCd && nodeCC == 16) { + float tmpTubeOpacity; + bool isTubeOpacity = this->GetDataNode()->GetPropertyValue("TubeOpacity",tmpTubeOpacity); + + m_TubeActor->GetProperty()->SetOpacity((double) tmpTubeOpacity); + m_TubeActor->Modified(); + + } else if (isCCd && nodeCC == 17) { + m_FiberActor->GetProperty()->SetOpacity(0); + m_FiberAssembly->RemovePart(m_FiberActor); + m_FiberAssembly->Modified(); + + }else if (isCCd && nodeCC == 18) { + m_FiberActor->GetProperty()->SetOpacity(0); + m_FiberAssembly->AddPart(m_FiberActor); + m_FiberAssembly->Modified(); + + } + + + + //MITK_INFO << m_VtkFiberDataMapperGL->GetArrayName(); + + + /* int displayIndex(0); + this->GetDataNode()->GetIntProperty( "DisplayChannel", displayIndex, renderer ); + InputImageType *input = const_cast< InputImageType* >( + this->GetInput() + ); + mitk::DiffusionImage *input2 = dynamic_cast< mitk::DiffusionImage* >( + input + ); + input2->SetDisplayIndexForRendering(displayIndex); + Superclass::GenerateData(renderer); + */ +} + +//template +void mitk::FiberBundleMapper3D::SetDefaultProperties(mitk::DataNode* node, mitk::BaseRenderer* renderer, bool overwrite) +{ + //MITK_INFO << "FiberBundleMapper3D SetDefault Properties(...)"; + node->AddProperty( "DisplayChannel", mitk::IntProperty::New( true ), renderer, overwrite ); + node->AddProperty( "LineWidth", mitk::IntProperty::New( true ), renderer, overwrite ); + node->AddProperty( "ColorCoding", mitk::IntProperty::New( 0 ), renderer, overwrite); + node->AddProperty( "VertexOpacity_1", mitk::BoolProperty::New( false ), renderer, overwrite); + node->AddProperty( "Set_FA_VertexAlpha", mitk::BoolProperty::New( false ), renderer, overwrite); + node->AddProperty( "pointSize", mitk::FloatProperty::New(0.5), renderer, overwrite); + node->AddProperty( "setShading", mitk::IntProperty::New(1), renderer, overwrite); + node->AddProperty( "Xmove", mitk::IntProperty::New( 0 ), renderer, overwrite); + node->AddProperty( "Ymove", mitk::IntProperty::New( 0 ), renderer, overwrite); + node->AddProperty( "Zmove", mitk::IntProperty::New( 0 ), renderer, overwrite); + node->AddProperty( "RepPoints", mitk::BoolProperty::New( false ), renderer, overwrite); + node->AddProperty( "TubeSides", mitk::IntProperty::New( 8 ), renderer, overwrite); + node->AddProperty( "TubeRadius", mitk::FloatProperty::New( 0.15 ), renderer, overwrite); + node->AddProperty( "TubeOpacity", mitk::FloatProperty::New( 1.0 ), renderer, overwrite); + + + Superclass::SetDefaultProperties(node, renderer, overwrite); + + + +} + +vtkProp* mitk::FiberBundleMapper3D::GetVtkProp(mitk::BaseRenderer *renderer) +{ + + //MITK_INFO << "FiberBundleMapper3D GetVtkProp(renderer)"; + return m_FiberAssembly; + +} + +void mitk::FiberBundleMapper3D::ApplyProperties(mitk::BaseRenderer* renderer) +{ + // MITK_INFO << "FiberBundleMapper3D ApplyProperties(renderer)"; +} + +void mitk::FiberBundleMapper3D::UpdateVtkObjects() +{ + // MITK_INFO << "FiberBundleMapper3D UpdateVtkObjects()"; + + +} + +void mitk::FiberBundleMapper3D::SetVtkMapperImmediateModeRendering(vtkMapper *) +{ + + + +} + + + diff --git a/Modules/DiffusionImaging/Rendering/mitkFiberBundleMapper3D.h b/Modules/DiffusionImaging/Rendering/mitkFiberBundleMapper3D.h new file mode 100644 index 0000000000..ea9cb42ca5 --- /dev/null +++ b/Modules/DiffusionImaging/Rendering/mitkFiberBundleMapper3D.h @@ -0,0 +1,103 @@ +/*========================================================================= + +Program: Medical Imaging & Interaction Toolkit +Language: C++ +Date: $Date: 2009-05-12 19:56:03 +0200 (Di, 12 Mai 2009) $ +Version: $Revision: 17179 $ + +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 FiberBundleMapper3D_H_HEADER_INCLUDED +#define FiberBundleMapper3D_H_HEADER_INCLUDED + +//#include "mitkCommon.h" +//#include "mitkBaseRenderer.h" + +#include "mitkFiberBundle.h" +#include +#include "mitkVtkMapper3D.h" +#include "MitkDiffusionImagingMBIExports.h" +#include "mitkBaseData.h" +#include "vtkAppendPolyData.h" +#include "vtkOpenGLPolyDataMapper.h" +#include "vtkOpenGLActor.h" +#include "vtkPropAssembly.h" +#include "vtkProperty.h" +#include "vtkUnsignedCharArray.h" +#include "vtkTubeFilter.h" + + +namespace mitk { + + //##Documentation + //## @brief Mapper for FiberBundles + //## @ingroup Mapper +// template + class MitkDiffusionImagingMBI_EXPORT FiberBundleMapper3D : public VtkMapper3D + { + public: + + mitkClassMacro(FiberBundleMapper3D, VtkMapper3D); + itkNewMacro(Self); + + + const mitk::FiberBundle* GetInput(); + + virtual vtkProp *GetVtkProp(mitk::BaseRenderer *renderer); //looks like depricated.. should be replaced bz GetViewProp() + static void SetDefaultProperties(DataNode* node, BaseRenderer* renderer = NULL, bool overwrite = false ); + + virtual void ApplyProperties(mitk::BaseRenderer* renderer); + static void SetVtkMapperImmediateModeRendering(vtkMapper *mapper); + + virtual void GenerateData(mitk::BaseRenderer* renderer); + virtual void GenerateData(); + + + protected: + + FiberBundleMapper3D(); + virtual ~FiberBundleMapper3D(); + + void UpdateVtkObjects(); + + + vtkAppendPolyData *m_vtkFiberList; + //vtkSmartPointer m_vtkFiberList; + + vtkOpenGLPolyDataMapper *m_VtkFiberDataMapperGL; + //vtkPainterPolyDataMapper *m_VtkFiberDataMapperGL; + //vtkSmartPointer m_VtkFiberDataMapperGL; + + //vtkOpenGLPolyDataMapper *m_VtkFiberDataMapper; + //vtkSmartPointer m_VtkFiberDataMapper; + + vtkOpenGLActor *m_FiberActor; + //vtkSmartPointer m_FiberActor; + + vtkTubeFilter *m_tubes; + vtkOpenGLActor *m_TubeActor; + vtkOpenGLPolyDataMapper *m_vtkTubeMapper; + + + vtkPropAssembly *m_FiberAssembly; + + + + }; + +} // namespace mitk + + + + +#endif /* FiberBundleMapper3D_H_HEADER_INCLUDED */ + diff --git a/Modules/DiffusionImaging/files.cmake b/Modules/DiffusionImaging/files.cmake index 64b4ae5645..f9771d1825 100644 --- a/Modules/DiffusionImaging/files.cmake +++ b/Modules/DiffusionImaging/files.cmake @@ -1,78 +1,92 @@ SET(CPP_FILES # Algorithms Algorithms/itkDiffusionQballGeneralizedFaImageFilter.h Algorithms/itkDiffusionQballPrepareVisualizationImageFilter.h Algorithms/itkTensorDerivedMeasurementsFilter.h Algorithms/itkBrainMaskExtractionImageFilter.h Algorithms/itkB0ImageExtractionImageFilter.h Algorithms/itkTensorImageToDiffusionImageFilter.h Algorithms/itkTensorToL2NormImageFilter.h # DicomImport DicomImport/mitkDicomDiffusionImageReader.cpp DicomImport/mitkGroupDiffusionHeadersFilter.cpp DicomImport/mitkDicomDiffusionImageHeaderReader.cpp DicomImport/mitkGEDicomDiffusionImageHeaderReader.cpp DicomImport/mitkPhilipsDicomDiffusionImageHeaderReader.cpp DicomImport/mitkSiemensDicomDiffusionImageHeaderReader.cpp DicomImport/mitkSiemensMosaicDicomDiffusionImageHeaderReader.cpp # DataStructures IODataStructures/mitkDiffusionImagingObjectFactory.cpp # DataStructures -> DWI IODataStructures/DiffusionWeightedImages/mitkDiffusionImageHeaderInformation.cpp IODataStructures/DiffusionWeightedImages/mitkDiffusionImageSource.cpp IODataStructures/DiffusionWeightedImages/mitkNrrdDiffusionImageReader.cpp IODataStructures/DiffusionWeightedImages/mitkNrrdDiffusionImageWriter.cpp IODataStructures/DiffusionWeightedImages/mitkNrrdDiffusionImageIOFactory.cpp IODataStructures/DiffusionWeightedImages/mitkNrrdDiffusionImageWriterFactory.cpp IODataStructures/DiffusionWeightedImages/mitkDiffusionImageSerializer.cpp # DataStructures -> QBall IODataStructures/QBallImages/mitkQBallImageSource.cpp IODataStructures/QBallImages/mitkNrrdQBallImageReader.cpp IODataStructures/QBallImages/mitkNrrdQBallImageWriter.cpp IODataStructures/QBallImages/mitkNrrdQBallImageIOFactory.cpp IODataStructures/QBallImages/mitkNrrdQBallImageWriterFactory.cpp IODataStructures/QBallImages/mitkQBallImage.cpp IODataStructures/QBallImages/mitkQBallImageSerializer.cpp # DataStructures -> Tensor IODataStructures/TensorImages/mitkTensorImageSource.cpp IODataStructures/TensorImages/mitkNrrdTensorImageReader.cpp IODataStructures/TensorImages/mitkNrrdTensorImageWriter.cpp IODataStructures/TensorImages/mitkNrrdTensorImageIOFactory.cpp IODataStructures/TensorImages/mitkNrrdTensorImageWriterFactory.cpp IODataStructures/TensorImages/mitkTensorImage.cpp IODataStructures/TensorImages/mitkTensorImageSerializer.cpp + # DataStructures -> FiberBundle + IODataStructures/FiberBundle/mitkFiberBundle.cpp + IODataStructures/FiberBundle/mitkFiberBundleWriter.cpp + IODataStructures/FiberBundle/mitkFiberBundleReader.cpp + IODataStructures/FiberBundle/mitkFiberBundleIOFactory.cpp + IODataStructures/FiberBundle/mitkFiberBundleWriterFactory.cpp + IODataStructures/FiberBundle/mitkFiberBundleSerializer.cpp + + # DataStructures -> PlanarFigureComposite + IODataStructures/PlanarFigureComposite/mitkPlanarFigureComposite.cpp + # Rendering Rendering/vtkMaskedProgrammableGlyphFilter.cpp Rendering/mitkCompositeMapper.cpp Rendering/mitkVectorImageVtkGlyphMapper3D.cpp Rendering/vtkOdfSource.cxx Rendering/vtkThickPlane.cxx Rendering/mitkOdfNormalizationMethodProperty.cpp Rendering/mitkOdfScaleByProperty.cpp + Rendering/mitkFiberBundleMapper3D.cpp + ) SET(H_FILES Rendering/mitkDiffusionImageMapper.h Reconstruction/itkDiffusionQballReconstructionImageFilter.h Reconstruction/mitkTeemDiffusionTensor3DReconstructionImageFilter.h Reconstruction/itkAnalyticalDiffusionQballReconstructionImageFilter.h Reconstruction/itkPointShell.h Reconstruction/itkOrientationDistributionFunction.h - IODataStructures/DiffusionWeightedImages/mitkDiffusionImage.h + IODataStructures/DiffusionWeightedImages/mitkDiffusionImage.h + IODataStructures/FiberBundle/itkSlowPolyLineParametricPath.h Rendering/mitkOdfVtkMapper2D.h ) SET( TOOL_FILES ) IF(WIN32) ENDIF(WIN32) #MITK_MULTIPLEX_PICTYPE( Algorithms/mitkImageRegistrationMethod-TYPE.cpp )