diff --git a/Modules/DiffusionImaging/DiffusionCore/Rendering/mitkOdfVtkMapper2D.txx b/Modules/DiffusionImaging/DiffusionCore/Rendering/mitkOdfVtkMapper2D.txx index c6bc7b0d53..91bb189c78 100644 --- a/Modules/DiffusionImaging/DiffusionCore/Rendering/mitkOdfVtkMapper2D.txx +++ b/Modules/DiffusionImaging/DiffusionCore/Rendering/mitkOdfVtkMapper2D.txx @@ -1,881 +1,882 @@ /*=================================================================== The Medical Imaging Interaction Toolkit (MITK) Copyright (c) German Cancer Research Center, Division of Medical and Biological Informatics. All rights reserved. This software is distributed WITHOUT ANY WARRANTY; without even the implied warranty of MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See LICENSE.txt or http://www.mitk.org for details. ===================================================================*/ #ifndef __mitkOdfVtkMapper2D_txx__ #define __mitkOdfVtkMapper2D_txx__ #include "mitkOdfVtkMapper2D.h" #include "mitkDataNode.h" #include "mitkBaseRenderer.h" #include "mitkMatrixConvert.h" #include "mitkGeometry3D.h" #include "mitkTimeGeometry.h" #include "mitkOdfNormalizationMethodProperty.h" #include "mitkOdfScaleByProperty.h" #include "mitkProperties.h" #include "mitkTensorImage.h" #include "vtkSphereSource.h" #include "vtkPropCollection.h" #include "vtkMaskedGlyph3D.h" #include "vtkGlyph2D.h" #include "vtkGlyph3D.h" #include "vtkMaskedProgrammableGlyphFilter.h" #include "vtkImageData.h" #include "vtkLinearTransform.h" #include "vtkCamera.h" #include "vtkPointData.h" #include "vtkTransformPolyDataFilter.h" #include "vtkTransform.h" #include "vtkOdfSource.h" #include "vtkDoubleArray.h" #include "vtkLookupTable.h" #include "vtkProperty.h" #include "vtkPolyDataNormals.h" #include "vtkLight.h" #include "vtkLightCollection.h" #include "vtkMath.h" #include "vtkFloatArray.h" #include "vtkDelaunay2D.h" #include "vtkMapper.h" #include "vtkRenderer.h" #include "itkOrientationDistributionFunction.h" #include "itkFixedArray.h" #include #include "vtkOpenGLRenderer.h" #define _USE_MATH_DEFINES #include template vtkSmartPointer mitk::OdfVtkMapper2D::m_OdfTransform = vtkSmartPointer::New(); template vtkSmartPointer mitk::OdfVtkMapper2D::m_OdfSource = vtkSmartPointer::New(); template float mitk::OdfVtkMapper2D::m_Scaling; template int mitk::OdfVtkMapper2D::m_Normalization; template int mitk::OdfVtkMapper2D::m_ScaleBy; template float mitk::OdfVtkMapper2D::m_IndexParam1; template float mitk::OdfVtkMapper2D::m_IndexParam2; #define ODF_MAPPER_PI M_PI template mitk::OdfVtkMapper2D::LocalStorage::LocalStorage() { m_PropAssemblies.push_back(vtkPropAssembly::New()); m_PropAssemblies.push_back(vtkPropAssembly::New()); m_PropAssemblies.push_back(vtkPropAssembly::New()); m_OdfsPlanes.push_back(vtkAppendPolyData::New()); m_OdfsPlanes.push_back(vtkAppendPolyData::New()); m_OdfsPlanes.push_back(vtkAppendPolyData::New()); m_OdfsPlanes[0]->AddInputData(vtkPolyData::New()); m_OdfsPlanes[1]->AddInputData(vtkPolyData::New()); m_OdfsPlanes[2]->AddInputData(vtkPolyData::New()); m_OdfsActors.push_back(vtkActor::New()); m_OdfsActors.push_back(vtkActor::New()); m_OdfsActors.push_back(vtkActor::New()); m_OdfsActors[0]->GetProperty()->SetInterpolationToGouraud(); m_OdfsActors[1]->GetProperty()->SetInterpolationToGouraud(); m_OdfsActors[2]->GetProperty()->SetInterpolationToGouraud(); m_OdfsMappers.push_back(vtkPolyDataMapper::New()); m_OdfsMappers.push_back(vtkPolyDataMapper::New()); m_OdfsMappers.push_back(vtkPolyDataMapper::New()); vtkLookupTable *lut = vtkLookupTable::New(); m_OdfsMappers[0]->SetLookupTable(lut); m_OdfsMappers[1]->SetLookupTable(lut); m_OdfsMappers[2]->SetLookupTable(lut); m_OdfsActors[0]->SetMapper(m_OdfsMappers[0]); m_OdfsActors[1]->SetMapper(m_OdfsMappers[1]); m_OdfsActors[2]->SetMapper(m_OdfsMappers[2]); } template mitk::OdfVtkMapper2D ::OdfVtkMapper2D() { m_Planes.push_back(vtkPlane::New()); m_Planes.push_back(vtkPlane::New()); m_Planes.push_back(vtkPlane::New()); m_Cutters.push_back(vtkCutter::New()); m_Cutters.push_back(vtkCutter::New()); m_Cutters.push_back(vtkCutter::New()); m_Cutters[0]->SetCutFunction( m_Planes[0] ); m_Cutters[0]->GenerateValues( 1, 0, 1 ); m_Cutters[1]->SetCutFunction( m_Planes[1] ); m_Cutters[1]->GenerateValues( 1, 0, 1 ); m_Cutters[2]->SetCutFunction( m_Planes[2] ); m_Cutters[2]->GenerateValues( 1, 0, 1 ); // Windowing the cutted planes in direction 1 m_ThickPlanes1.push_back(vtkThickPlane::New()); m_ThickPlanes1.push_back(vtkThickPlane::New()); m_ThickPlanes1.push_back(vtkThickPlane::New()); m_Clippers1.push_back(vtkClipPolyData::New()); m_Clippers1.push_back(vtkClipPolyData::New()); m_Clippers1.push_back(vtkClipPolyData::New()); m_Clippers1[0]->SetClipFunction( m_ThickPlanes1[0] ); m_Clippers1[1]->SetClipFunction( m_ThickPlanes1[1] ); m_Clippers1[2]->SetClipFunction( m_ThickPlanes1[2] ); // Windowing the cutted planes in direction 2 m_ThickPlanes2.push_back(vtkThickPlane::New()); m_ThickPlanes2.push_back(vtkThickPlane::New()); m_ThickPlanes2.push_back(vtkThickPlane::New()); m_Clippers2.push_back(vtkClipPolyData::New()); m_Clippers2.push_back(vtkClipPolyData::New()); m_Clippers2.push_back(vtkClipPolyData::New()); m_Clippers2[0]->SetClipFunction( m_ThickPlanes2[0] ); m_Clippers2[1]->SetClipFunction( m_ThickPlanes2[1] ); m_Clippers2[2]->SetClipFunction( m_ThickPlanes2[2] ); m_ShowMaxNumber = 500; } template mitk::OdfVtkMapper2D ::~OdfVtkMapper2D() { } template mitk::Image* mitk::OdfVtkMapper2D ::GetInput() { return static_cast ( m_DataNode->GetData() ); } template vtkProp* mitk::OdfVtkMapper2D ::GetVtkProp(mitk::BaseRenderer* renderer) { LocalStorage *localStorage = m_LSH.GetLocalStorage(renderer); return localStorage->m_PropAssemblies[GetIndex(renderer)]; } template int mitk::OdfVtkMapper2D ::GetIndex(mitk::BaseRenderer* renderer) { if(!strcmp(renderer->GetName(),"stdmulti.widget1")) return 0; if(!strcmp(renderer->GetName(),"stdmulti.widget2")) return 1; if(!strcmp(renderer->GetName(),"stdmulti.widget3")) return 2; return 0; } template void mitk::OdfVtkMapper2D ::GlyphMethod(void *arg) { vtkMaskedProgrammableGlyphFilter* pfilter=(vtkMaskedProgrammableGlyphFilter*)arg; double point[3]; double debugpoint[3]; pfilter->GetPoint(point); pfilter->GetPoint(debugpoint); itk::Point p(point); Vector3D spacing = pfilter->GetGeometry()->GetSpacing(); p[0] /= spacing[0]; p[1] /= spacing[1]; p[2] /= spacing[2]; mitk::Point3D p2; pfilter->GetGeometry()->IndexToWorld( p, p2 ); point[0] = p2[0]; point[1] = p2[1]; point[2] = p2[2]; vtkPointData* data = pfilter->GetPointData(); vtkDataArray* odfvals = data->GetArray("vector"); vtkIdType id = pfilter->GetPointId(); m_OdfTransform->Identity(); m_OdfTransform->Translate(point[0],point[1],point[2]); typedef itk::OrientationDistributionFunction OdfType; OdfType odf; if(odfvals->GetNumberOfComponents()==6) { float tensorelems[6] = { (float)odfvals->GetComponent(id,0), (float)odfvals->GetComponent(id,1), (float)odfvals->GetComponent(id,2), (float)odfvals->GetComponent(id,3), (float)odfvals->GetComponent(id,4), (float)odfvals->GetComponent(id,5), }; itk::DiffusionTensor3D tensor(tensorelems); odf.InitFromTensor(tensor); } else { for(int i=0; iGetComponent(id,i); } switch(m_ScaleBy) { case ODFSB_NONE: m_OdfSource->SetScale(m_Scaling); break; case ODFSB_GFA: m_OdfSource->SetScale(m_Scaling*odf.GetGeneralizedGFA(m_IndexParam1, m_IndexParam2)); break; case ODFSB_PC: m_OdfSource->SetScale(m_Scaling*odf.GetPrincipleCurvature(m_IndexParam1, m_IndexParam2, 0)); break; } m_OdfSource->SetNormalization(m_Normalization); m_OdfSource->SetOdf(odf); m_OdfSource->Modified(); } template typename mitk::OdfVtkMapper2D::OdfDisplayGeometry mitk::OdfVtkMapper2D ::MeasureDisplayedGeometry(mitk::BaseRenderer* renderer) { PlaneGeometry::ConstPointer worldPlaneGeometry = renderer->GetCurrentWorldPlaneGeometry(); // set up the cutter orientation according to the current geometry of // the renderers plane double vp[ 3 ], vnormal[ 3 ]; Point3D point = worldPlaneGeometry->GetOrigin(); Vector3D normal = worldPlaneGeometry->GetNormal(); normal.Normalize(); vnl2vtk( point.GetVnlVector(), vp ); vnl2vtk( normal.GetVnlVector(), vnormal ); mitk::DisplayGeometry::Pointer dispGeometry = renderer->GetDisplayGeometry(); mitk::Vector2D size = dispGeometry->GetSizeInMM(); mitk::Vector2D origin = dispGeometry->GetOriginInMM(); // // |------O------| // | d2 | // L d1 M | // | | // |-------------| // mitk::Vector2D M; mitk::Vector2D L; mitk::Vector2D O; M[0] = origin[0] + size[0]/2; M[1] = origin[1] + size[1]/2; L[0] = origin[0]; L[1] = origin[1] + size[1]/2; O[0] = origin[0] + size[0]/2; O[1] = origin[1] + size[1]; mitk::Point2D point1; point1[0] = M[0]; point1[1] = M[1]; mitk::Point3D M3D; dispGeometry->Map(point1, M3D); point1[0] = L[0]; point1[1] = L[1]; mitk::Point3D L3D; dispGeometry->Map(point1, L3D); point1[0] = O[0]; point1[1] = O[1]; mitk::Point3D O3D; dispGeometry->Map(point1, O3D); double d1 = sqrt((M3D[0]-L3D[0])*(M3D[0]-L3D[0]) + (M3D[1]-L3D[1])*(M3D[1]-L3D[1]) + (M3D[2]-L3D[2])*(M3D[2]-L3D[2])); double d2 = sqrt((M3D[0]-O3D[0])*(M3D[0]-O3D[0]) + (M3D[1]-O3D[1])*(M3D[1]-O3D[1]) + (M3D[2]-O3D[2])*(M3D[2]-O3D[2])); double d = d1>d2 ? d1 : d2; d = d2; OdfDisplayGeometry retval; retval.vp[0] = vp[0]; retval.vp[1] = vp[1]; retval.vp[2] = vp[2]; retval.vnormal[0] = vnormal[0]; retval.vnormal[1] = vnormal[1]; retval.vnormal[2] = vnormal[2]; retval.normal[0] = normal[0]; retval.normal[1] = normal[1]; retval.normal[2] = normal[2]; retval.d = d; retval.d1 = d1; retval.d2 = d2; retval.M3D[0] = M3D[0]; retval.M3D[1] = M3D[1]; retval.M3D[2] = M3D[2]; retval.L3D[0] = L3D[0]; retval.L3D[1] = L3D[1]; retval.L3D[2] = L3D[2]; retval.O3D[0] = O3D[0]; retval.O3D[1] = O3D[1]; retval.O3D[2] = O3D[2]; retval.vp_original[0] = vp[0]; retval.vp_original[1] = vp[1]; retval.vp_original[2] = vp[2]; retval.vnormal_original[0] = vnormal[0]; retval.vnormal_original[1] = vnormal[1]; retval.vnormal_original[2] = vnormal[2]; retval.size[0] = size[0]; retval.size[1] = size[1]; retval.origin[0] = origin[0]; retval.origin[1] = origin[1]; return retval; } template void mitk::OdfVtkMapper2D ::Slice(mitk::BaseRenderer* renderer, OdfDisplayGeometry dispGeo) { LocalStorage *localStorage = m_LSH.GetLocalStorage(renderer); vtkLinearTransform * vtktransform = this->GetDataNode()->GetVtkTransform(this->GetTimestep()); int index = GetIndex(renderer); vtkSmartPointer inversetransform = vtkSmartPointer::New(); inversetransform->Identity(); inversetransform->Concatenate(vtktransform->GetLinearInverse()); double myscale[3]; ((vtkTransform*)vtktransform)->GetScale(myscale); inversetransform->PostMultiply(); inversetransform->Scale(1*myscale[0],1*myscale[1],1*myscale[2]); inversetransform->TransformPoint( dispGeo.vp, dispGeo.vp ); inversetransform->TransformNormalAtPoint( dispGeo.vp, dispGeo.vnormal, dispGeo.vnormal ); // vtk works in axis align coords // thus the normal also must be axis align, since // we do not allow arbitrary cutting through volume // // vnormal should already be axis align, but in order // to get rid of precision effects, we set the two smaller // components to zero here int dims[3]; m_VtkImage->GetDimensions(dims); double spac[3]; m_VtkImage->GetSpacing(spac); if(fabs(dispGeo.vnormal[0]) > fabs(dispGeo.vnormal[1]) && fabs(dispGeo.vnormal[0]) > fabs(dispGeo.vnormal[2]) ) { if(fabs(dispGeo.vp[0]/spac[0]) < 0.4) dispGeo.vp[0] = 0.4*spac[0]; if(fabs(dispGeo.vp[0]/spac[0]) > (dims[0]-1)-0.4) dispGeo.vp[0] = ((dims[0]-1)-0.4)*spac[0]; dispGeo.vnormal[1] = 0; dispGeo.vnormal[2] = 0; } if(fabs(dispGeo.vnormal[1]) > fabs(dispGeo.vnormal[0]) && fabs(dispGeo.vnormal[1]) > fabs(dispGeo.vnormal[2]) ) { if(fabs(dispGeo.vp[1]/spac[1]) < 0.4) dispGeo.vp[1] = 0.4*spac[1]; if(fabs(dispGeo.vp[1]/spac[1]) > (dims[1]-1)-0.4) dispGeo.vp[1] = ((dims[1]-1)-0.4)*spac[1]; dispGeo.vnormal[0] = 0; dispGeo.vnormal[2] = 0; } if(fabs(dispGeo.vnormal[2]) > fabs(dispGeo.vnormal[1]) && fabs(dispGeo.vnormal[2]) > fabs(dispGeo.vnormal[0]) ) { if(fabs(dispGeo.vp[2]/spac[2]) < 0.4) dispGeo.vp[2] = 0.4*spac[2]; if(fabs(dispGeo.vp[2]/spac[2]) > (dims[2]-1)-0.4) dispGeo.vp[2] = ((dims[2]-1)-0.4)*spac[2]; dispGeo.vnormal[0] = 0; dispGeo.vnormal[1] = 0; } m_Planes[index]->SetTransform( (vtkAbstractTransform*)NULL ); m_Planes[index]->SetOrigin( dispGeo.vp ); m_Planes[index]->SetNormal( dispGeo.vnormal ); vtkSmartPointer points; vtkSmartPointer tmppoints; vtkSmartPointer polydata; vtkSmartPointer pointdata; vtkSmartPointer delaunay; vtkSmartPointer cuttedPlane; // the cutter only works if we do not have a 2D-image // or if we have a 2D-image and want to see the whole image. // // for side views of 2D-images, we need some special treatment if(!( (dims[0] == 1 && dispGeo.vnormal[0] != 0) || (dims[1] == 1 && dispGeo.vnormal[1] != 0) || (dims[2] == 1 && dispGeo.vnormal[2] != 0) )) { m_Cutters[index]->SetCutFunction( m_Planes[index] ); m_Cutters[index]->SetInputData( m_VtkImage ); m_Cutters[index]->Update(); cuttedPlane = m_Cutters[index]->GetOutput(); } else { // cutting of a 2D-Volume does not work, // so we have to build up our own polydata object cuttedPlane = vtkPolyData::New(); points = vtkPoints::New(); points->SetNumberOfPoints(m_VtkImage->GetNumberOfPoints()); for(int i=0; iGetNumberOfPoints(); i++) { points->SetPoint(i, m_VtkImage->GetPoint(i)); } cuttedPlane->SetPoints(points); pointdata = vtkFloatArray::New(); int comps = m_VtkImage->GetPointData()->GetScalars()->GetNumberOfComponents(); pointdata->SetNumberOfComponents(comps); int tuples = m_VtkImage->GetPointData()->GetScalars()->GetNumberOfTuples(); pointdata->SetNumberOfTuples(tuples); for(int i=0; iSetTuple(i,m_VtkImage->GetPointData()->GetScalars()->GetTuple(i)); pointdata->SetName( "vector" ); cuttedPlane->GetPointData()->AddArray(pointdata); int nZero1, nZero2; if(dims[0]==1) { nZero1 = 1; nZero2 = 2; } else if(dims[1]==1) { nZero1 = 0; nZero2 = 2; } else { nZero1 = 0; nZero2 = 1; } tmppoints = vtkPoints::New(); for(int j=0; jGetNumberOfPoints(); j++){ double pt[3]; m_VtkImage->GetPoint(j,pt); tmppoints->InsertNextPoint(pt[nZero1],pt[nZero2],0); } polydata = vtkPolyData::New(); polydata->SetPoints( tmppoints ); delaunay = vtkDelaunay2D::New(); delaunay->SetInputData( polydata ); delaunay->Update(); vtkCellArray* polys = delaunay->GetOutput()->GetPolys(); cuttedPlane->SetPolys(polys); } if(cuttedPlane->GetNumberOfPoints()) { // WINDOWING HERE inversetransform = vtkTransform::New(); inversetransform->Identity(); inversetransform->Concatenate(vtktransform->GetLinearInverse()); double myscale[3]; ((vtkTransform*)vtktransform)->GetScale(myscale); inversetransform->PostMultiply(); inversetransform->Scale(1*myscale[0],1*myscale[1],1*myscale[2]); dispGeo.vnormal[0] = dispGeo.M3D[0]-dispGeo.O3D[0]; dispGeo.vnormal[1] = dispGeo.M3D[1]-dispGeo.O3D[1]; dispGeo.vnormal[2] = dispGeo.M3D[2]-dispGeo.O3D[2]; vtkMath::Normalize(dispGeo.vnormal); dispGeo.vp[0] = dispGeo.M3D[0]; dispGeo.vp[1] = dispGeo.M3D[1]; dispGeo.vp[2] = dispGeo.M3D[2]; inversetransform->TransformPoint( dispGeo.vp, dispGeo.vp ); inversetransform->TransformNormalAtPoint( dispGeo.vp, dispGeo.vnormal, dispGeo.vnormal ); m_ThickPlanes1[index]->count = 0; m_ThickPlanes1[index]->SetTransform((vtkAbstractTransform*)NULL ); m_ThickPlanes1[index]->SetPose( dispGeo.vnormal, dispGeo.vp ); m_ThickPlanes1[index]->SetThickness(dispGeo.d2); m_Clippers1[index]->SetClipFunction( m_ThickPlanes1[index] ); m_Clippers1[index]->SetInputData( cuttedPlane ); m_Clippers1[index]->SetInsideOut(1); m_Clippers1[index]->Update(); dispGeo.vnormal[0] = dispGeo.M3D[0]-dispGeo.L3D[0]; dispGeo.vnormal[1] = dispGeo.M3D[1]-dispGeo.L3D[1]; dispGeo.vnormal[2] = dispGeo.M3D[2]-dispGeo.L3D[2]; vtkMath::Normalize(dispGeo.vnormal); dispGeo.vp[0] = dispGeo.M3D[0]; dispGeo.vp[1] = dispGeo.M3D[1]; dispGeo.vp[2] = dispGeo.M3D[2]; inversetransform->TransformPoint( dispGeo.vp, dispGeo.vp ); inversetransform->TransformNormalAtPoint( dispGeo.vp, dispGeo.vnormal, dispGeo.vnormal ); m_ThickPlanes2[index]->count = 0; m_ThickPlanes2[index]->SetTransform((vtkAbstractTransform*)NULL ); m_ThickPlanes2[index]->SetPose( dispGeo.vnormal, dispGeo.vp ); m_ThickPlanes2[index]->SetThickness(dispGeo.d1); m_Clippers2[index]->SetClipFunction( m_ThickPlanes2[index] ); m_Clippers2[index]->SetInputData( m_Clippers1[index]->GetOutput() ); m_Clippers2[index]->SetInsideOut(1); m_Clippers2[index]->Update(); cuttedPlane = m_Clippers2[index]->GetOutput (); if(cuttedPlane->GetNumberOfPoints()) { localStorage->m_OdfsPlanes[index]->RemoveAllInputs(); vtkSmartPointer normals = vtkSmartPointer::New(); normals->SetInputConnection( m_OdfSource->GetOutputPort() ); normals->SplittingOff(); normals->ConsistencyOff(); normals->AutoOrientNormalsOff(); normals->ComputePointNormalsOn(); normals->ComputeCellNormalsOff(); normals->FlipNormalsOff(); normals->NonManifoldTraversalOff(); vtkSmartPointer trans = vtkSmartPointer::New(); trans->SetInputConnection( normals->GetOutputPort() ); trans->SetTransform(m_OdfTransform); vtkSmartPointer glyphGenerator = vtkSmartPointer::New(); glyphGenerator->SetMaximumNumberOfPoints(std::min(m_ShowMaxNumber,(int)cuttedPlane->GetNumberOfPoints())); glyphGenerator->SetRandomMode(0); glyphGenerator->SetUseMaskPoints(1); glyphGenerator->SetSourceConnection(trans->GetOutputPort() ); glyphGenerator->SetInput(cuttedPlane); glyphGenerator->SetColorModeToColorBySource(); glyphGenerator->SetInputArrayToProcess(0,0,0, vtkDataObject::FIELD_ASSOCIATION_POINTS , "vector"); glyphGenerator->SetGeometry(this->GetDataNode()->GetData()->GetGeometry()); glyphGenerator->SetGlyphMethod(&(GlyphMethod),(void *)glyphGenerator); try { glyphGenerator->Update(); } catch( itk::ExceptionObject& err ) { std::cout << err << std::endl; } localStorage->m_OdfsPlanes[index]->AddInputConnection(glyphGenerator->GetOutputPort()); localStorage->m_OdfsPlanes[index]->Update(); } } localStorage->m_PropAssemblies[index]->VisibilityOn(); if(localStorage->m_PropAssemblies[index]->GetParts()->IsItemPresent(localStorage->m_OdfsActors[index])) localStorage->m_PropAssemblies[index]->RemovePart(localStorage->m_OdfsActors[index]); localStorage->m_OdfsMappers[index]->SetInputData(localStorage->m_OdfsPlanes[index]->GetOutput()); localStorage->m_PropAssemblies[index]->AddPart(localStorage->m_OdfsActors[index]); } template bool mitk::OdfVtkMapper2D ::IsVisibleOdfs(mitk::BaseRenderer* renderer) { mitk::Image::Pointer input = const_cast(this->GetInput()); const TimeGeometry *inputTimeGeometry = input->GetTimeGeometry(); if(inputTimeGeometry==NULL || inputTimeGeometry->CountTimeSteps()==0 || !inputTimeGeometry->IsValidTimeStep(this->GetTimestep())) return false; if(this->IsPlaneRotated(renderer)) return false; bool retval = false; switch(GetIndex(renderer)) { case 0: GetDataNode()->GetVisibility(retval, renderer, "VisibleOdfs_T"); break; case 1: GetDataNode()->GetVisibility(retval, renderer, "VisibleOdfs_S"); break; case 2: GetDataNode()->GetVisibility(retval, renderer, "VisibleOdfs_C"); break; } return retval; } template void mitk::OdfVtkMapper2D ::MitkRenderOverlay(mitk::BaseRenderer* renderer) { if ( this->IsVisibleOdfs(renderer)==false ) return; if ( this->GetVtkProp(renderer)->GetVisibility() ) this->GetVtkProp(renderer)->RenderOverlay(renderer->GetVtkRenderer()); } template void mitk::OdfVtkMapper2D ::MitkRenderOpaqueGeometry(mitk::BaseRenderer* renderer) { if ( this->IsVisibleOdfs( renderer )==false ) return; if ( this->GetVtkProp(renderer)->GetVisibility() ) { // adapt cam pos this->GetVtkProp(renderer)->RenderOpaqueGeometry( renderer->GetVtkRenderer() ); } } template void mitk::OdfVtkMapper2D ::MitkRenderTranslucentGeometry(mitk::BaseRenderer* renderer) { if ( this->IsVisibleOdfs(renderer)==false ) return; if ( this->GetVtkProp(renderer)->GetVisibility() ) this->GetVtkProp(renderer)->RenderTranslucentPolygonalGeometry(renderer->GetVtkRenderer()); } template void mitk::OdfVtkMapper2D ::Update(mitk::BaseRenderer* renderer) { bool visible = true; GetDataNode()->GetVisibility(visible, renderer, "visible"); if ( !visible ) return; mitk::Image::Pointer input = const_cast( this->GetInput() ); if ( input.IsNull() ) return ; std::string classname("TensorImage"); if(classname.compare(input->GetNameOfClass())==0) m_VtkImage = dynamic_cast( this->GetInput() )->GetNonRgbVtkImageData(); std::string qclassname("QBallImage"); if(qclassname.compare(input->GetNameOfClass())==0) m_VtkImage = dynamic_cast( this->GetInput() )->GetNonRgbVtkImageData(); if( m_VtkImage ) { // make sure, that we have point data with more than 1 component (as vectors) vtkPointData* pointData = m_VtkImage->GetPointData(); if ( pointData == NULL ) { itkWarningMacro( << "m_VtkImage->GetPointData() returns NULL!" ); return ; } if ( pointData->GetNumberOfArrays() == 0 ) { itkWarningMacro( << "m_VtkImage->GetPointData()->GetNumberOfArrays() is 0!" ); return ; } else if ( pointData->GetArray(0)->GetNumberOfComponents() != N && pointData->GetArray(0)->GetNumberOfComponents() != 6 /*for tensor visualization*/) { itkWarningMacro( << "number of components != number of directions in ODF!" ); return; } else if ( pointData->GetArrayName( 0 ) == NULL ) { m_VtkImage->GetPointData()->GetArray(0)->SetName("vector"); } GenerateDataForRenderer(renderer); } else { itkWarningMacro( << "m_VtkImage is NULL!" ); return ; } } template void mitk::OdfVtkMapper2D ::GenerateDataForRenderer( mitk::BaseRenderer *renderer ) { LocalStorage *localStorage = m_LSH.GetLocalStorage(renderer); OdfDisplayGeometry dispGeo = MeasureDisplayedGeometry( renderer); if ( (localStorage->m_LastUpdateTime >= m_DataNode->GetMTime()) //was the node modified? && (localStorage->m_LastUpdateTime >= m_DataNode->GetPropertyList()->GetMTime()) //was a property modified? && (localStorage->m_LastUpdateTime >= m_DataNode->GetPropertyList(renderer)->GetMTime()) && dispGeo.Equals(m_LastDisplayGeometry)) return; localStorage->m_LastUpdateTime.Modified(); if(!IsVisibleOdfs(renderer)) { localStorage->m_OdfsActors[0]->VisibilityOff(); localStorage->m_OdfsActors[1]->VisibilityOff(); localStorage->m_OdfsActors[2]->VisibilityOff(); } else { localStorage->m_OdfsActors[0]->VisibilityOn(); localStorage->m_OdfsActors[1]->VisibilityOn(); localStorage->m_OdfsActors[2]->VisibilityOn(); m_OdfSource->SetAdditionalScale(GetMinImageSpacing(GetIndex(renderer))); ApplyPropertySettings(); Slice(renderer, dispGeo); m_LastDisplayGeometry = dispGeo; } } template double mitk::OdfVtkMapper2D::GetMinImageSpacing( int index ) { // Spacing adapted scaling double spacing[3]; m_VtkImage->GetSpacing(spacing); double min = spacing[0]; if(index==0) { min = spacing[0]; min = min > spacing[1] ? spacing[1] : min; } if(index==1) { min = spacing[1]; min = min > spacing[2] ? spacing[2] : min; } if(index==2) { min = spacing[0]; min = min > spacing[2] ? spacing[2] : min; } return min; } template void mitk::OdfVtkMapper2D ::ApplyPropertySettings() { this->GetDataNode()->GetFloatProperty( "Scaling", m_Scaling ); this->GetDataNode()->GetIntProperty( "ShowMaxNumber", m_ShowMaxNumber ); OdfNormalizationMethodProperty* nmp = dynamic_cast(this->GetDataNode()->GetProperty( "Normalization" )); if(nmp) m_Normalization = nmp->GetNormalization(); OdfScaleByProperty* sbp = dynamic_cast(this->GetDataNode()->GetProperty( "ScaleBy" )); if(sbp) m_ScaleBy = sbp->GetScaleBy(); this->GetDataNode()->GetFloatProperty( "IndexParam1", m_IndexParam1); this->GetDataNode()->GetFloatProperty( "IndexParam2", m_IndexParam2); } template bool mitk::OdfVtkMapper2D ::IsPlaneRotated(mitk::BaseRenderer* renderer) { - PlaneGeometry::ConstPointer worldPlaneGeometry = - renderer->GetCurrentWorldPlaneGeometry(); + PlaneGeometry::ConstPointer worldPlaneGeometry = renderer->GetCurrentWorldPlaneGeometry(); double vnormal[ 3 ]; Vector3D normal = worldPlaneGeometry->GetNormal(); normal.Normalize(); vnl2vtk( normal.GetVnlVector(), vnormal ); - vtkLinearTransform * vtktransform = - this->GetDataNode()->GetVtkTransform(this->GetTimestep()); - - vtkSmartPointer inversetransform = vtkSmartPointer::New(); - inversetransform->Identity(); - inversetransform->Concatenate(vtktransform->GetLinearInverse()); - double* n = inversetransform->TransformNormal(vnormal); - - int nonZeros = 0; - for (int j=0; j<3; j++) - { - if (fabs(n[j])>mitk::eps){ - nonZeros++; - } - } - if(nonZeros>1) + mitk::Image* currentImage = dynamic_cast( this->GetDataNode()->GetData() ); + if( currentImage == NULL ) + return false; + mitk::Vector3D imageNormal0 = currentImage->GetSlicedGeometry()->GetAxisVector(0); + mitk::Vector3D imageNormal1 = currentImage->GetSlicedGeometry()->GetAxisVector(1); + mitk::Vector3D imageNormal2 = currentImage->GetSlicedGeometry()->GetAxisVector(2); + imageNormal0.Normalize(); + imageNormal1.Normalize(); + imageNormal2.Normalize(); + + double eps = 0.000001; + int test = 0; + if( fabs(fabs(dot_product(normal.GetVnlVector(),imageNormal0.GetVnlVector()))-1) > eps ) + test++; + if( fabs(fabs(dot_product(normal.GetVnlVector(),imageNormal1.GetVnlVector()))-1) > eps ) + test++; + if( fabs(fabs(dot_product(normal.GetVnlVector(),imageNormal2.GetVnlVector()))-1) > eps ) + test++; + if (test==3) return true; - return false; } template void mitk::OdfVtkMapper2D ::SetDefaultProperties(mitk::DataNode* node, mitk::BaseRenderer* /*renderer*/, bool /*overwrite*/) { node->SetProperty( "ShowMaxNumber", mitk::IntProperty::New( 150 ) ); node->SetProperty( "Scaling", mitk::FloatProperty::New( 1.0 ) ); node->SetProperty( "Normalization", mitk::OdfNormalizationMethodProperty::New()); node->SetProperty( "ScaleBy", mitk::OdfScaleByProperty::New()); node->SetProperty( "IndexParam1", mitk::FloatProperty::New(2)); node->SetProperty( "IndexParam2", mitk::FloatProperty::New(1)); node->SetProperty( "visible", mitk::BoolProperty::New( true ) ); node->SetProperty( "VisibleOdfs_T", mitk::BoolProperty::New( false ) ); node->SetProperty( "VisibleOdfs_C", mitk::BoolProperty::New( false ) ); node->SetProperty( "VisibleOdfs_S", mitk::BoolProperty::New( false ) ); node->SetProperty ("layer", mitk::IntProperty::New(100)); node->SetProperty( "DoRefresh", mitk::BoolProperty::New( true ) ); } #endif // __mitkOdfVtkMapper2D_txx__ diff --git a/Modules/DiffusionImaging/DiffusionIO/mitkFiberBundleXMapper2D.cpp b/Modules/DiffusionImaging/DiffusionIO/mitkFiberBundleXMapper2D.cpp index fd84df0658..77f4934755 100644 --- a/Modules/DiffusionImaging/DiffusionIO/mitkFiberBundleXMapper2D.cpp +++ b/Modules/DiffusionImaging/DiffusionIO/mitkFiberBundleXMapper2D.cpp @@ -1,212 +1,214 @@ /*=================================================================== The Medical Imaging Interaction Toolkit (MITK) Copyright (c) German Cancer Research Center, Division of Medical and Biological Informatics. All rights reserved. This software is distributed WITHOUT ANY WARRANTY; without even the implied warranty of MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See LICENSE.txt or http://www.mitk.org for details. ===================================================================*/ /* * mitkFiberBundleMapper2D.cpp * mitk-all * * Created by HAL9000 on 1/17/11. * Copyright 2011 __MyCompanyName__. All rights reserved. * */ #include "mitkFiberBundleXMapper2D.h" #include #include #include #include #include +#include //#include //#include #include #include #include #include #include #include #include #include //#include #include #include #include #include #include mitk::FiberBundleXMapper2D::FiberBundleXMapper2D() { m_lut = vtkLookupTable::New(); m_lut->Build(); } mitk::FiberBundleXMapper2D::~FiberBundleXMapper2D() { } mitk::FiberBundleX* mitk::FiberBundleXMapper2D::GetInput() { return dynamic_cast< mitk::FiberBundleX * > ( GetDataNode()->GetData() ); } void mitk::FiberBundleXMapper2D::Update(mitk::BaseRenderer * renderer) { bool visible = true; GetDataNode()->GetVisibility(visible, renderer, "visible"); if ( !visible ) return; // Calculate time step of the input data for the specified renderer (integer value) // this method is implemented in mitkMapper this->CalculateTimeStep( renderer ); //check if updates occured in the node or on the display FBXLocalStorage *localStorage = m_LocalStorageHandler.GetLocalStorage(renderer); //set renderer independent shader properties const DataNode::Pointer node = this->GetDataNode(); float thickness = 2.0; if(!this->GetDataNode()->GetPropertyValue("Fiber2DSliceThickness",thickness)) MITK_INFO << "FIBER2D SLICE THICKNESS PROPERTY ERROR"; bool fiberfading = false; if(!this->GetDataNode()->GetPropertyValue("Fiber2DfadeEFX",fiberfading)) MITK_INFO << "FIBER2D SLICE FADE EFX PROPERTY ERROR"; float fiberOpacity; this->GetDataNode()->GetOpacity(fiberOpacity, NULL); node->SetFloatProperty("shader.mitkShaderFiberClipping.fiberThickness",thickness); node->SetIntProperty("shader.mitkShaderFiberClipping.fiberFadingON",fiberfading); node->SetFloatProperty("shader.mitkShaderFiberClipping.fiberOpacity",fiberOpacity); mitk::FiberBundleX* fiberBundle = this->GetInput(); if (fiberBundle==NULL) return; if ( localStorage->m_LastUpdateTimeGetDisplayGeometry()->GetMTime() || localStorage->m_LastUpdateTimeGetUpdateTime2D() ) { this->UpdateShaderParameter(renderer); this->GenerateDataForRenderer( renderer ); } } void mitk::FiberBundleXMapper2D::UpdateShaderParameter(mitk::BaseRenderer * renderer) { //get information about current position of views mitk::SliceNavigationController::Pointer sliceContr = renderer->GetSliceNavigationController(); mitk::PlaneGeometry::ConstPointer planeGeo = sliceContr->GetCurrentPlaneGeometry(); //generate according cutting planes based on the view position float planeNormal[3]; planeNormal[0] = planeGeo->GetNormal()[0]; planeNormal[1] = planeGeo->GetNormal()[1]; planeNormal[2] = planeGeo->GetNormal()[2]; float tmp1 = planeGeo->GetOrigin()[0] * planeNormal[0]; float tmp2 = planeGeo->GetOrigin()[1] * planeNormal[1]; float tmp3 = planeGeo->GetOrigin()[2] * planeNormal[2]; float thickness = tmp1 + tmp2 + tmp3; //attention, correct normalvector DataNode::Pointer node = this->GetDataNode(); node->SetFloatProperty("shader.mitkShaderFiberClipping.slicingPlane.w",thickness,renderer); node->SetFloatProperty("shader.mitkShaderFiberClipping.slicingPlane.x",planeNormal[0],renderer); node->SetFloatProperty("shader.mitkShaderFiberClipping.slicingPlane.y",planeNormal[1],renderer); node->SetFloatProperty("shader.mitkShaderFiberClipping.slicingPlane.z",planeNormal[2],renderer); } // vtkActors and Mappers are feeded here void mitk::FiberBundleXMapper2D::GenerateDataForRenderer(mitk::BaseRenderer *renderer) { mitk::FiberBundleX* fiberBundle = this->GetInput(); //the handler of local storage gets feeded in this method with requested data for related renderwindow FBXLocalStorage *localStorage = m_LocalStorageHandler.GetLocalStorage(renderer); mitk::DataNode* node = this->GetDataNode(); if ( node == NULL ) return; + vtkSmartPointer fiberPolyData = fiberBundle->GetFiberPolyData(); + if (fiberPolyData == NULL) + return; + + fiberPolyData->GetPointData()->AddArray(fiberBundle->GetFiberColors()); localStorage->m_FiberMapper->ScalarVisibilityOn(); localStorage->m_FiberMapper->SetScalarModeToUsePointFieldData(); localStorage->m_FiberMapper->SetLookupTable(m_lut); //apply the properties after the slice was set localStorage->m_PointActor->GetProperty()->SetOpacity(0.999); + localStorage->m_FiberMapper->SelectColorArray("FIBER_COLORS"); - // set color - if (fiberBundle->GetCurrentColorCoding() != NULL) - { - localStorage->m_FiberMapper->SelectColorArray(fiberBundle->GetCurrentColorCoding()); +// if(fiberBundle->GetCurrentColorCoding() == fiberBundle->COLORCODING_CUSTOM){ +// float temprgb[3]; +// this->GetDataNode()->GetColor( temprgb, NULL ); +// double trgb[3] = { (double) temprgb[0], (double) temprgb[1], (double) temprgb[2] }; +// localStorage->m_PointActor->GetProperty()->SetColor(trgb); +// } - if(fiberBundle->GetCurrentColorCoding() == fiberBundle->COLORCODING_CUSTOM){ - float temprgb[3]; - this->GetDataNode()->GetColor( temprgb, NULL ); - double trgb[3] = { (double) temprgb[0], (double) temprgb[1], (double) temprgb[2] }; - localStorage->m_PointActor->GetProperty()->SetColor(trgb); - } - } int lineWidth = 1; node->GetIntProperty("LineWidth",lineWidth); - localStorage->m_FiberMapper->SetInputData(fiberBundle->GetFiberPolyData()); + localStorage->m_FiberMapper->SetInputData(fiberPolyData); localStorage->m_PointActor->SetMapper(localStorage->m_FiberMapper); localStorage->m_PointActor->GetProperty()->ShadingOn(); localStorage->m_PointActor->GetProperty()->SetLineWidth(lineWidth); // Applying shading properties this->ApplyShaderProperties(renderer); // We have been modified => save this for next Update() localStorage->m_LastUpdateTime.Modified(); } vtkProp* mitk::FiberBundleXMapper2D::GetVtkProp(mitk::BaseRenderer *renderer) { this->Update(renderer); return m_LocalStorageHandler.GetLocalStorage(renderer)->m_PointActor; } void mitk::FiberBundleXMapper2D::SetDefaultProperties(mitk::DataNode* node, mitk::BaseRenderer* renderer, bool overwrite) { + Superclass::SetDefaultProperties(node, renderer, overwrite); node->SetProperty("shader",mitk::ShaderProperty::New("mitkShaderFiberClipping")); // Shaders IShaderRepository* shaderRepo = CoreServices::GetShaderRepository(); if (shaderRepo) { shaderRepo->AddDefaultProperties(node, renderer, overwrite); } //add other parameters to propertylist - node->AddProperty( "Fiber2DSliceThickness", mitk::FloatProperty::New(2.0f), renderer, overwrite ); + node->AddProperty( "Fiber2DSliceThickness", mitk::FloatProperty::New(1.0f), renderer, overwrite ); node->AddProperty( "Fiber2DfadeEFX", mitk::BoolProperty::New(true), renderer, overwrite ); - - Superclass::SetDefaultProperties(node, renderer, overwrite); + node->AddProperty( "color", mitk::ColorProperty::New(1.0,1.0,1.0), renderer, overwrite); } mitk::FiberBundleXMapper2D::FBXLocalStorage::FBXLocalStorage() { m_PointActor = vtkSmartPointer::New(); m_FiberMapper = vtkSmartPointer::New(); } diff --git a/Modules/DiffusionImaging/DiffusionIO/mitkFiberBundleXMapper3D.cpp b/Modules/DiffusionImaging/DiffusionIO/mitkFiberBundleXMapper3D.cpp index caea82c3a1..31aa03a47a 100644 --- a/Modules/DiffusionImaging/DiffusionIO/mitkFiberBundleXMapper3D.cpp +++ b/Modules/DiffusionImaging/DiffusionIO/mitkFiberBundleXMapper3D.cpp @@ -1,168 +1,142 @@ /*=================================================================== The Medical Imaging Interaction Toolkit (MITK) Copyright (c) German Cancer Research Center, Division of Medical and Biological Informatics. All rights reserved. This software is distributed WITHOUT ANY WARRANTY; without even the implied warranty of MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See LICENSE.txt or http://www.mitk.org for details. ===================================================================*/ #include "mitkFiberBundleXMapper3D.h" #include //#include //#include #include #include #include #include //not essential for mapper // #include mitk::FiberBundleXMapper3D::FiberBundleXMapper3D() { m_lut = vtkLookupTable::New(); m_lut->Build(); } mitk::FiberBundleXMapper3D::~FiberBundleXMapper3D() { } const mitk::FiberBundleX* mitk::FiberBundleXMapper3D::GetInput() { return static_cast ( GetDataNode()->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::FiberBundleXMapper3D::InternalGenerateData(mitk::BaseRenderer *renderer) { mitk::FiberBundleX* fiberBundle = dynamic_cast (GetDataNode()->GetData()); if (fiberBundle == NULL) return; vtkSmartPointer fiberPolyData = fiberBundle->GetFiberPolyData(); if (fiberPolyData == NULL) return; FBXLocalStorage3D *localStorage = m_LocalStorageHandler.GetLocalStorage(renderer); - localStorage->m_FiberMapper->SetInputData(fiberPolyData); - - if ( fiberPolyData->GetPointData()->GetNumberOfArrays() > 0 ) - localStorage->m_FiberMapper->SelectColorArray( fiberBundle->GetCurrentColorCoding() ); + float tmpopa; + this->GetDataNode()->GetOpacity(tmpopa, NULL); + fiberPolyData->GetPointData()->AddArray(fiberBundle->GetFiberColors()); + localStorage->m_FiberMapper->SetInputData(fiberPolyData); + localStorage->m_FiberMapper->SelectColorArray("FIBER_COLORS"); localStorage->m_FiberMapper->ScalarVisibilityOn(); localStorage->m_FiberMapper->SetScalarModeToUsePointFieldData(); localStorage->m_FiberActor->SetMapper(localStorage->m_FiberMapper); localStorage->m_FiberMapper->SetLookupTable(m_lut); // set Opacity - float tmpopa; - this->GetDataNode()->GetOpacity(tmpopa, NULL); localStorage->m_FiberActor->GetProperty()->SetOpacity((double) tmpopa); int lineWidth = 1; this->GetDataNode()->GetIntProperty("LineWidth",lineWidth); localStorage->m_FiberActor->GetProperty()->SetLineWidth(lineWidth); - // set color - if (fiberBundle->GetCurrentColorCoding() != NULL){ - // localStorage->m_FiberMapper->SelectColorArray(""); - localStorage->m_FiberMapper->SelectColorArray(fiberBundle->GetCurrentColorCoding()); - MITK_DEBUG << "MapperFBX: " << fiberBundle->GetCurrentColorCoding(); - - if(fiberBundle->GetCurrentColorCoding() == fiberBundle->COLORCODING_CUSTOM) { - float temprgb[3]; - this->GetDataNode()->GetColor( temprgb, NULL ); - double trgb[3] = { (double) temprgb[0], (double) temprgb[1], (double) temprgb[2] }; - localStorage->m_FiberActor->GetProperty()->SetColor(trgb); - } - } - localStorage->m_FiberAssembly->AddPart(localStorage->m_FiberActor); localStorage->m_LastUpdateTime.Modified(); } void mitk::FiberBundleXMapper3D::GenerateDataForRenderer( mitk::BaseRenderer *renderer ) { bool visible = true; GetDataNode()->GetVisibility(visible, renderer, "visible"); if ( !visible ) return; const DataNode* node = this->GetDataNode(); FBXLocalStorage3D* localStorage = m_LocalStorageHandler.GetLocalStorage(renderer); mitk::FiberBundleX* fiberBundle = dynamic_cast(node->GetData()); if (localStorage->m_LastUpdateTime>=fiberBundle->GetUpdateTime3D()) return; // Calculate time step of the input data for the specified renderer (integer value) // this method is implemented in mitkMapper this->CalculateTimeStep( renderer ); this->InternalGenerateData(renderer); } void mitk::FiberBundleXMapper3D::SetDefaultProperties(mitk::DataNode* node, mitk::BaseRenderer* renderer, bool overwrite) { - // node->AddProperty( "DisplayChannel", mitk::IntProperty::New( true ), renderer, overwrite ); + Superclass::SetDefaultProperties(node, renderer, overwrite); node->AddProperty( "LineWidth", mitk::IntProperty::New( true ), renderer, overwrite ); node->AddProperty( "opacity", mitk::FloatProperty::New( 1.0 ), 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); + node->AddProperty( "color", mitk::ColorProperty::New(1.0,1.0,1.0), renderer, overwrite); node->AddProperty( "pickable", mitk::BoolProperty::New( true ), renderer, overwrite); - Superclass::SetDefaultProperties(node, renderer, overwrite); } vtkProp* mitk::FiberBundleXMapper3D::GetVtkProp(mitk::BaseRenderer *renderer) { //MITK_INFO << "FiberBundleXxXXMapper3D()GetVTKProp"; //this->GenerateData(); return m_LocalStorageHandler.GetLocalStorage(renderer)->m_FiberAssembly; } void mitk::FiberBundleXMapper3D::UpdateVtkObjects() { } void mitk::FiberBundleXMapper3D::SetVtkMapperImmediateModeRendering(vtkMapper *) { } mitk::FiberBundleXMapper3D::FBXLocalStorage3D::FBXLocalStorage3D() { m_FiberActor = vtkSmartPointer::New(); m_FiberMapper = vtkSmartPointer::New(); m_FiberAssembly = vtkSmartPointer::New(); } diff --git a/Modules/DiffusionImaging/DiffusionIO/mitkFiberBundleXReader.cpp b/Modules/DiffusionImaging/DiffusionIO/mitkFiberBundleXReader.cpp index f6ff88e5a5..ce9807f8a8 100644 --- a/Modules/DiffusionImaging/DiffusionIO/mitkFiberBundleXReader.cpp +++ b/Modules/DiffusionImaging/DiffusionIO/mitkFiberBundleXReader.cpp @@ -1,207 +1,229 @@ /*=================================================================== The Medical Imaging Interaction Toolkit (MITK) Copyright (c) German Cancer Research Center, Division of Medical and Biological Informatics. All rights reserved. This software is distributed WITHOUT ANY WARRANTY; without even the implied warranty of MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See LICENSE.txt or http://www.mitk.org for details. ===================================================================*/ #include "mitkFiberBundleXReader.h" #include #include #include #include #include #include #include +#include +#include +#include +#include #include #include #include #include #include #include "mitkDiffusionIOMimeTypes.h" mitk::FiberBundleXReader::FiberBundleXReader() : mitk::AbstractFileReader( CustomMimeType( mitk::DiffusionIOMimeTypes::FIBERBUNDLE_MIMETYPE_NAME() ), mitk::DiffusionIOMimeTypes::FIBERBUNDLE_MIMETYPE_DESCRIPTION() ) { m_ServiceReg = this->RegisterService(); } mitk::FiberBundleXReader::FiberBundleXReader(const FiberBundleXReader &other) :mitk::AbstractFileReader(other) { } mitk::FiberBundleXReader * mitk::FiberBundleXReader::Clone() const { return new FiberBundleXReader(*this); } std::vector > mitk::FiberBundleXReader::Read() { std::vector > result; try { const std::string& locale = "C"; const std::string& currLocale = setlocale( LC_ALL, NULL ); setlocale(LC_ALL, locale.c_str()); std::string filename = this->GetInputLocation(); std::string ext = itksys::SystemTools::GetFilenameLastExtension(filename); ext = itksys::SystemTools::LowerCase(ext); if (ext==".trk") { FiberBundleX::Pointer image = FiberBundleX::New(); TrackVisFiberReader reader; reader.open(this->GetInputLocation().c_str()); reader.read(image.GetPointer()); result.push_back(image.GetPointer()); return result; } vtkSmartPointer chooser=vtkSmartPointer::New(); chooser->SetFileName( this->GetInputLocation().c_str() ); if( chooser->IsFilePolyData()) { vtkSmartPointer reader = vtkSmartPointer::New(); reader->SetFileName( this->GetInputLocation().c_str() ); reader->Update(); if ( reader->GetOutput() != NULL ) { vtkSmartPointer fiberPolyData = reader->GetOutput(); - FiberBundleX::Pointer image = FiberBundleX::New(fiberPolyData); - result.push_back(image.GetPointer()); + FiberBundleX::Pointer fiberBundle = FiberBundleX::New(fiberPolyData); + + vtkSmartPointer weights = vtkFloatArray::SafeDownCast(fiberPolyData->GetCellData()->GetArray("FIBER_WEIGHTS")); + if (weights!=NULL) + { +// float weight=0; +// for (int i=0; iGetSize(); i++) +// if (!mitk::Equal(weights->GetValue(i),weight,0.00001)) +// { +// MITK_INFO << "Weight: " << weights->GetValue(i); +// weight = weights->GetValue(i); +// } + fiberBundle->SetFiberWeights(weights); + } + + vtkSmartPointer fiberColors = vtkUnsignedCharArray::SafeDownCast(fiberPolyData->GetPointData()->GetArray("FIBER_COLORS")); + if (fiberColors!=NULL) + fiberBundle->SetFiberColors(fiberColors); + + result.push_back(fiberBundle.GetPointer()); return result; } } else // try to read deprecated fiber bundle file format { MITK_INFO << "Reading xml fiber bundle"; vtkSmartPointer fiberPolyData = vtkSmartPointer::New(); vtkSmartPointer cellArray = vtkSmartPointer::New(); vtkSmartPointer points = vtkSmartPointer::New(); TiXmlDocument doc( this->GetInputLocation().c_str() ); if(doc.LoadFile()) { TiXmlHandle hDoc(&doc); TiXmlElement* pElem; TiXmlHandle hRoot(0); pElem = hDoc.FirstChildElement().Element(); // save this for later hRoot = TiXmlHandle(pElem); pElem = hRoot.FirstChildElement("geometry").Element(); // read geometry mitk::Geometry3D::Pointer geometry = mitk::Geometry3D::New(); // read origin mitk::Point3D origin; double temp = 0; pElem->Attribute("origin_x", &temp); origin[0] = temp; pElem->Attribute("origin_y", &temp); origin[1] = temp; pElem->Attribute("origin_z", &temp); origin[2] = temp; geometry->SetOrigin(origin); // read spacing ScalarType spacing[3]; pElem->Attribute("spacing_x", &temp); spacing[0] = temp; pElem->Attribute("spacing_y", &temp); spacing[1] = temp; pElem->Attribute("spacing_z", &temp); spacing[2] = temp; geometry->SetSpacing(spacing); // read transform vtkMatrix4x4* m = vtkMatrix4x4::New(); pElem->Attribute("xx", &temp); m->SetElement(0,0,temp); pElem->Attribute("xy", &temp); m->SetElement(1,0,temp); pElem->Attribute("xz", &temp); m->SetElement(2,0,temp); pElem->Attribute("yx", &temp); m->SetElement(0,1,temp); pElem->Attribute("yy", &temp); m->SetElement(1,1,temp); pElem->Attribute("yz", &temp); m->SetElement(2,1,temp); pElem->Attribute("zx", &temp); m->SetElement(0,2,temp); pElem->Attribute("zy", &temp); m->SetElement(1,2,temp); pElem->Attribute("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("size_x", &temp); bounds[1] = temp; pElem->Attribute("size_y", &temp); bounds[3] = temp; pElem->Attribute("size_z", &temp); bounds[5] = temp; geometry->SetFloatBounds(bounds); geometry->SetImageGeometry(true); pElem = hRoot.FirstChildElement("fiber_bundle").FirstChild().Element(); for( ; pElem ; pElem=pElem->NextSiblingElement()) { TiXmlElement* pElem2 = pElem->FirstChildElement(); vtkSmartPointer container = vtkSmartPointer::New(); for( ; pElem2; pElem2=pElem2->NextSiblingElement()) { Point3D point; pElem2->Attribute("pos_x", &temp); point[0] = temp; pElem2->Attribute("pos_y", &temp); point[1] = temp; pElem2->Attribute("pos_z", &temp); point[2] = temp; geometry->IndexToWorld(point, point); vtkIdType id = points->InsertNextPoint(point.GetDataPointer()); container->GetPointIds()->InsertNextId(id); } cellArray->InsertNextCell(container); } fiberPolyData->SetPoints(points); fiberPolyData->SetLines(cellArray); vtkSmartPointer cleaner = vtkSmartPointer::New(); cleaner->SetInputData(fiberPolyData); cleaner->Update(); fiberPolyData = cleaner->GetOutput(); FiberBundleX::Pointer image = FiberBundleX::New(fiberPolyData); result.push_back(image.GetPointer()); return result; } else { MITK_ERROR << "could not open xml file"; throw "could not open xml file"; } } setlocale(LC_ALL, currLocale.c_str()); MITK_INFO << "Fiber bundle read"; } catch(...) { throw; } return result; } diff --git a/Modules/DiffusionImaging/DiffusionIO/mitkFiberBundleXWriter.cpp b/Modules/DiffusionImaging/DiffusionIO/mitkFiberBundleXWriter.cpp index 643219e16d..0bc4d06310 100644 --- a/Modules/DiffusionImaging/DiffusionIO/mitkFiberBundleXWriter.cpp +++ b/Modules/DiffusionImaging/DiffusionIO/mitkFiberBundleXWriter.cpp @@ -1,133 +1,139 @@ /*=================================================================== The Medical Imaging Interaction Toolkit (MITK) Copyright (c) German Cancer Research Center, Division of Medical and Biological Informatics. All rights reserved. This software is distributed WITHOUT ANY WARRANTY; without even the implied warranty of MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See LICENSE.txt or http://www.mitk.org for details. ===================================================================*/ #include "mitkFiberBundleXWriter.h" #include #include #include #include #include - +#include +#include +#include #include #include #include "mitkDiffusionIOMimeTypes.h" mitk::FiberBundleXWriter::FiberBundleXWriter() : mitk::AbstractFileWriter(mitk::FiberBundleX::GetStaticNameOfClass(), CustomMimeType( mitk::DiffusionIOMimeTypes::FIBERBUNDLE_MIMETYPE_NAME() ), mitk::DiffusionIOMimeTypes::FIBERBUNDLE_MIMETYPE_DESCRIPTION()) { RegisterService(); } mitk::FiberBundleXWriter::FiberBundleXWriter(const mitk::FiberBundleXWriter & other) :mitk::AbstractFileWriter(other) {} mitk::FiberBundleXWriter::~FiberBundleXWriter() {} mitk::FiberBundleXWriter * mitk::FiberBundleXWriter::Clone() const { return new mitk::FiberBundleXWriter(*this); } void mitk::FiberBundleXWriter::Write() { std::ostream* out; std::ofstream outStream; if( this->GetOutputStream() ) { out = this->GetOutputStream(); }else{ outStream.open( this->GetOutputLocation().c_str() ); out = &outStream; } if ( !out->good() ) { mitkThrow() << "Stream not good."; } try { const std::string& locale = "C"; const std::string& currLocale = setlocale( LC_ALL, NULL ); setlocale(LC_ALL, locale.c_str()); std::locale previousLocale(out->getloc()); std::locale I("C"); out->imbue(I); std::string filename = this->GetOutputLocation().c_str(); mitk::FiberBundleX::ConstPointer input = dynamic_cast(this->GetInput()); std::string ext = itksys::SystemTools::GetFilenameLastExtension(this->GetOutputLocation().c_str()); + vtkSmartPointer fibPoly = input->GetFiberPolyData(); + fibPoly->GetCellData()->AddArray(input->GetFiberWeights()); + fibPoly->GetPointData()->AddArray(input->GetFiberColors()); + // default extension is .fib if(ext == "") { ext = ".fib"; this->SetOutputLocation(this->GetOutputLocation() + ext); } if (ext==".fib" || ext==".vtk") { MITK_INFO << "Writing fiber bundle as binary VTK"; vtkSmartPointer writer = vtkSmartPointer::New(); - writer->SetInputData(input->GetFiberPolyData()); - writer->SetFileName(this->GetOutputLocation().c_str()); + writer->SetInputData(fibPoly); + writer->SetFileName(filename.c_str()); writer->SetFileTypeToBinary(); writer->Write(); } else if (ext==".afib") { itksys::SystemTools::ReplaceString(filename,".afib",".fib"); MITK_INFO << "Writing fiber bundle as ascii VTK"; vtkSmartPointer writer = vtkSmartPointer::New(); - writer->SetInputData(input->GetFiberPolyData()); - writer->SetFileName(this->GetOutputLocation().c_str()); + writer->SetInputData(fibPoly); + writer->SetFileName(filename.c_str()); writer->SetFileTypeToASCII(); writer->Write(); } else if (ext==".avtk") { itksys::SystemTools::ReplaceString(filename,".avtk",".vtk"); MITK_INFO << "Writing fiber bundle as ascii VTK"; vtkSmartPointer writer = vtkSmartPointer::New(); - writer->SetInputData(input->GetFiberPolyData()); - writer->SetFileName(this->GetOutputLocation().c_str()); + writer->SetInputData(fibPoly); + writer->SetFileName(filename.c_str()); writer->SetFileTypeToASCII(); writer->Write(); } else if (ext==".trk") { MITK_INFO << "Writing fiber bundle as TRK"; TrackVisFiberReader trk; trk.create(filename, input.GetPointer()); trk.writeHdr(); trk.append(input.GetPointer()); } setlocale(LC_ALL, currLocale.c_str()); MITK_INFO << "Fiber bundle written"; } catch(...) { throw; } } diff --git a/Modules/DiffusionImaging/DiffusionIO/mitkFiberTrackingObjectFactory.cpp b/Modules/DiffusionImaging/DiffusionIO/mitkFiberTrackingObjectFactory.cpp index cf8846e1fa..cb78e2f291 100644 --- a/Modules/DiffusionImaging/DiffusionIO/mitkFiberTrackingObjectFactory.cpp +++ b/Modules/DiffusionImaging/DiffusionIO/mitkFiberTrackingObjectFactory.cpp @@ -1,127 +1,114 @@ /*=================================================================== The Medical Imaging Interaction Toolkit (MITK) Copyright (c) German Cancer Research Center, Division of Medical and Biological Informatics. All rights reserved. This software is distributed WITHOUT ANY WARRANTY; without even the implied warranty of MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See LICENSE.txt or http://www.mitk.org for details. ===================================================================*/ #include "mitkFiberTrackingObjectFactory.h" mitk::FiberTrackingObjectFactory::FiberTrackingObjectFactory() : CoreObjectFactoryBase() { } mitk::FiberTrackingObjectFactory::~FiberTrackingObjectFactory() { } mitk::Mapper::Pointer mitk::FiberTrackingObjectFactory::CreateMapper(mitk::DataNode* node, MapperSlotId id) { mitk::Mapper::Pointer newMapper=NULL; if ( id == mitk::BaseRenderer::Standard2D ) { std::string classname("FiberBundleX"); if(node->GetData() && classname.compare(node->GetData()->GetNameOfClass())==0) { newMapper = mitk::FiberBundleXMapper2D::New(); newMapper->SetDataNode(node); } } else if ( id == mitk::BaseRenderer::Standard3D ) { std::string classname("FiberBundleX"); if(node->GetData() && classname.compare(node->GetData()->GetNameOfClass())==0) { newMapper = mitk::FiberBundleXMapper3D::New(); newMapper->SetDataNode(node); } - -// classname = "FiberBundleXThreadMonitor"; -// if(node->GetData() && classname.compare(node->GetData()->GetNameOfClass())==0) -// { -// newMapper = mitk::FiberBundleXThreadMonitorMapper3D::New(); -// newMapper->SetDataNode(node); -// } } return newMapper; } void mitk::FiberTrackingObjectFactory::SetDefaultProperties(mitk::DataNode* node) { std::string classname("FiberBundleX"); if(node->GetData() && classname.compare(node->GetData()->GetNameOfClass())==0) { mitk::FiberBundleXMapper3D::SetDefaultProperties(node); mitk::FiberBundleXMapper2D::SetDefaultProperties(node); } - -// classname = "FiberBundleXThreadMonitor"; -// if(node->GetData() && classname.compare(node->GetData()->GetNameOfClass())==0) -// { -// mitk::FiberBundleXThreadMonitorMapper3D::SetDefaultProperties(node); -// } } const char* mitk::FiberTrackingObjectFactory::GetFileExtensions() { std::string fileExtension; this->CreateFileExtensions(m_FileExtensionsMap, fileExtension); return fileExtension.c_str(); } mitk::CoreObjectFactoryBase::MultimapType mitk::FiberTrackingObjectFactory::GetFileExtensionsMap() { return m_FileExtensionsMap; } const char* mitk::FiberTrackingObjectFactory::GetSaveFileExtensions() { std::string fileExtension; this->CreateFileExtensions(m_SaveFileExtensionsMap, fileExtension); return fileExtension.c_str(); } mitk::CoreObjectFactoryBase::MultimapType mitk::FiberTrackingObjectFactory::GetSaveFileExtensionsMap() { return m_SaveFileExtensionsMap; } void mitk::FiberTrackingObjectFactory::CreateFileExtensionsMap() { } void mitk::FiberTrackingObjectFactory::RegisterIOFactories() { } struct RegisterFiberTrackingObjectFactory{ RegisterFiberTrackingObjectFactory() : m_Factory( mitk::FiberTrackingObjectFactory::New() ) { mitk::CoreObjectFactory::GetInstance()->RegisterExtraFactory( m_Factory ); } ~RegisterFiberTrackingObjectFactory() { mitk::CoreObjectFactory::GetInstance()->UnRegisterExtraFactory( m_Factory ); } mitk::FiberTrackingObjectFactory::Pointer m_Factory; }; static RegisterFiberTrackingObjectFactory registerFiberTrackingObjectFactory; diff --git a/Modules/DiffusionImaging/FiberTracking/Algorithms/itkTractDensityImageFilter.cpp b/Modules/DiffusionImaging/FiberTracking/Algorithms/itkTractDensityImageFilter.cpp index c9dccdeb1b..13df693a5d 100644 --- a/Modules/DiffusionImaging/FiberTracking/Algorithms/itkTractDensityImageFilter.cpp +++ b/Modules/DiffusionImaging/FiberTracking/Algorithms/itkTractDensityImageFilter.cpp @@ -1,241 +1,248 @@ /*=================================================================== The Medical Imaging Interaction Toolkit (MITK) Coindex[1]right (c) German Cancer Research Center, Division of Medical and Biological Informatics. All rights reserved. This software is distributed WITHOUT ANY WARRANTY; without even the implied warranty of MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See LICENSE.txt or http://www.mitk.org for details. ===================================================================*/ #include "itkTractDensityImageFilter.h" // VTK #include #include #include #include // misc #include #include namespace itk{ template< class OutputImageType > TractDensityImageFilter< OutputImageType >::TractDensityImageFilter() : m_InvertImage(false) , m_FiberBundle(NULL) , m_UpsamplingFactor(1) , m_InputImage(NULL) , m_BinaryOutput(false) , m_UseImageGeometry(false) , m_OutputAbsoluteValues(false) , m_UseTrilinearInterpolation(false) + , m_DoFiberResampling(true) { } template< class OutputImageType > TractDensityImageFilter< OutputImageType >::~TractDensityImageFilter() { } template< class OutputImageType > itk::Point TractDensityImageFilter< OutputImageType >::GetItkPoint(double point[3]) { itk::Point itkPoint; itkPoint[0] = point[0]; itkPoint[1] = point[1]; itkPoint[2] = point[2]; return itkPoint; } template< class OutputImageType > void TractDensityImageFilter< OutputImageType >::GenerateData() { // generate upsampled image mitk::BaseGeometry::Pointer geometry = m_FiberBundle->GetGeometry(); typename OutputImageType::Pointer outImage = this->GetOutput(); // calculate new image parameters itk::Vector newSpacing; mitk::Point3D newOrigin; itk::Matrix newDirection; ImageRegion<3> upsampledRegion; if (m_UseImageGeometry && !m_InputImage.IsNull()) { MITK_INFO << "TractDensityImageFilter: using image geometry"; newSpacing = m_InputImage->GetSpacing()/m_UpsamplingFactor; upsampledRegion = m_InputImage->GetLargestPossibleRegion(); newOrigin = m_InputImage->GetOrigin(); typename OutputImageType::RegionType::SizeType size = upsampledRegion.GetSize(); size[0] *= m_UpsamplingFactor; size[1] *= m_UpsamplingFactor; size[2] *= m_UpsamplingFactor; upsampledRegion.SetSize(size); newDirection = m_InputImage->GetDirection(); } else { MITK_INFO << "TractDensityImageFilter: using fiber bundle geometry"; newSpacing = geometry->GetSpacing()/m_UpsamplingFactor; newOrigin = geometry->GetOrigin(); mitk::Geometry3D::BoundsArrayType bounds = geometry->GetBounds(); newOrigin[0] += bounds.GetElement(0); newOrigin[1] += bounds.GetElement(2); newOrigin[2] += bounds.GetElement(4); for (int i=0; i<3; i++) for (int j=0; j<3; j++) newDirection[j][i] = geometry->GetMatrixColumn(i)[j]; upsampledRegion.SetSize(0, geometry->GetExtent(0)*m_UpsamplingFactor); upsampledRegion.SetSize(1, geometry->GetExtent(1)*m_UpsamplingFactor); upsampledRegion.SetSize(2, geometry->GetExtent(2)*m_UpsamplingFactor); } typename OutputImageType::RegionType::SizeType upsampledSize = upsampledRegion.GetSize(); // apply new image parameters outImage->SetSpacing( newSpacing ); outImage->SetOrigin( newOrigin ); outImage->SetDirection( newDirection ); outImage->SetLargestPossibleRegion( upsampledRegion ); outImage->SetBufferedRegion( upsampledRegion ); outImage->SetRequestedRegion( upsampledRegion ); outImage->Allocate(); outImage->FillBuffer(0.0); int w = upsampledSize[0]; int h = upsampledSize[1]; int d = upsampledSize[2]; // set/initialize output OutPixelType* outImageBufferPointer = (OutPixelType*)outImage->GetBufferPointer(); // resample fiber bundle float minSpacing = 1; if(newSpacing[0]GetDeepCopy(); - m_FiberBundle->ResampleSpline(minSpacing/10); + if (m_DoFiberResampling) + { + m_FiberBundle = m_FiberBundle->GetDeepCopy(); + m_FiberBundle->ResampleSpline(minSpacing/10); + } MITK_INFO << "TractDensityImageFilter: starting image generation"; vtkSmartPointer fiberPolyData = m_FiberBundle->GetFiberPolyData(); vtkSmartPointer vLines = fiberPolyData->GetLines(); vLines->InitTraversal(); int numFibers = m_FiberBundle->GetNumFibers(); boost::progress_display disp(numFibers); for( int i=0; iGetNextCell ( numPoints, points ); + float weight = m_FiberBundle->GetFiberWeight(i); // fill output image for( int j=0; j vertex = GetItkPoint(fiberPolyData->GetPoint(points[j])); itk::Index<3> index; itk::ContinuousIndex contIndex; outImage->TransformPhysicalPointToIndex(vertex, index); outImage->TransformPhysicalPointToContinuousIndex(vertex, contIndex); if (!m_UseTrilinearInterpolation && outImage->GetLargestPossibleRegion().IsInside(index)) { if (m_BinaryOutput) outImage->SetPixel(index, 1); else - outImage->SetPixel(index, outImage->GetPixel(index)+0.01); + outImage->SetPixel(index, outImage->GetPixel(index)+0.01*weight); continue; } float frac_x = contIndex[0] - index[0]; float frac_y = contIndex[1] - index[1]; float frac_z = contIndex[2] - index[2]; if (frac_x<0) { index[0] -= 1; frac_x += 1; } if (frac_y<0) { index[1] -= 1; frac_y += 1; } if (frac_z<0) { index[2] -= 1; frac_z += 1; } frac_x = 1-frac_x; frac_y = 1-frac_y; frac_z = 1-frac_z; // int coordinates inside image? if (index[0] < 0 || index[0] >= w-1) continue; if (index[1] < 0 || index[1] >= h-1) continue; if (index[2] < 0 || index[2] >= d-1) continue; if (m_BinaryOutput) { outImageBufferPointer[( index[0] + w*(index[1] + h*index[2] ))] = 1; outImageBufferPointer[( index[0] + w*(index[1]+1+ h*index[2] ))] = 1; outImageBufferPointer[( index[0] + w*(index[1] + h*index[2]+h))] = 1; outImageBufferPointer[( index[0] + w*(index[1]+1+ h*index[2]+h))] = 1; outImageBufferPointer[( index[0]+1 + w*(index[1] + h*index[2] ))] = 1; outImageBufferPointer[( index[0]+1 + w*(index[1] + h*index[2]+h))] = 1; outImageBufferPointer[( index[0]+1 + w*(index[1]+1+ h*index[2] ))] = 1; outImageBufferPointer[( index[0]+1 + w*(index[1]+1+ h*index[2]+h))] = 1; } else { outImageBufferPointer[( index[0] + w*(index[1] + h*index[2] ))] += ( frac_x)*( frac_y)*( frac_z); outImageBufferPointer[( index[0] + w*(index[1]+1+ h*index[2] ))] += ( frac_x)*(1-frac_y)*( frac_z); outImageBufferPointer[( index[0] + w*(index[1] + h*index[2]+h))] += ( frac_x)*( frac_y)*(1-frac_z); outImageBufferPointer[( index[0] + w*(index[1]+1+ h*index[2]+h))] += ( frac_x)*(1-frac_y)*(1-frac_z); outImageBufferPointer[( index[0]+1 + w*(index[1] + h*index[2] ))] += (1-frac_x)*( frac_y)*( frac_z); outImageBufferPointer[( index[0]+1 + w*(index[1] + h*index[2]+h))] += (1-frac_x)*( frac_y)*(1-frac_z); outImageBufferPointer[( index[0]+1 + w*(index[1]+1+ h*index[2] ))] += (1-frac_x)*(1-frac_y)*( frac_z); outImageBufferPointer[( index[0]+1 + w*(index[1]+1+ h*index[2]+h))] += (1-frac_x)*(1-frac_y)*(1-frac_z); } } } if (!m_OutputAbsoluteValues && !m_BinaryOutput) { MITK_INFO << "TractDensityImageFilter: max-normalizing output image"; OutPixelType max = 0; for (int i=0; i0) for (int i=0; i #include #include #include #include namespace itk{ /** * \brief Generates tract density images from input fiberbundles (Calamante 2010). */ template< class OutputImageType > class TractDensityImageFilter : public ImageSource< OutputImageType > { public: typedef TractDensityImageFilter Self; typedef ProcessObject Superclass; typedef SmartPointer< Self > Pointer; typedef SmartPointer< const Self > ConstPointer; typedef typename OutputImageType::PixelType OutPixelType; itkFactorylessNewMacro(Self) itkCloneMacro(Self) itkTypeMacro( TractDensityImageFilter, ImageSource ) itkSetMacro( UpsamplingFactor, float) ///< use higher resolution for ouput image itkGetMacro( UpsamplingFactor, float) ///< use higher resolution for ouput image itkSetMacro( InvertImage, bool) ///< voxelvalue = 1-voxelvalue itkGetMacro( InvertImage, bool) ///< voxelvalue = 1-voxelvalue itkSetMacro( BinaryOutput, bool) ///< generate binary fiber envelope itkGetMacro( BinaryOutput, bool) ///< generate binary fiber envelope itkSetMacro( OutputAbsoluteValues, bool) ///< output absolute values of the number of fibers per voxel itkGetMacro( OutputAbsoluteValues, bool) ///< output absolute values of the number of fibers per voxel itkSetMacro( UseImageGeometry, bool) ///< use input image geometry to initialize output image itkGetMacro( UseImageGeometry, bool) ///< use input image geometry to initialize output image itkSetMacro( FiberBundle, mitk::FiberBundleX::Pointer) ///< input fiber bundle itkSetMacro( InputImage, typename OutputImageType::Pointer) ///< use input image geometry to initialize output image itkSetMacro( UseTrilinearInterpolation, bool ) + itkSetMacro( DoFiberResampling, bool ) void GenerateData(); protected: itk::Point GetItkPoint(double point[3]); TractDensityImageFilter(); virtual ~TractDensityImageFilter(); typename OutputImageType::Pointer m_InputImage; ///< use input image geometry to initialize output image mitk::FiberBundleX::Pointer m_FiberBundle; ///< input fiber bundle float m_UpsamplingFactor; ///< use higher resolution for ouput image bool m_InvertImage; ///< voxelvalue = 1-voxelvalue bool m_BinaryOutput; ///< generate binary fiber envelope bool m_UseImageGeometry; ///< use input image geometry to initialize output image bool m_OutputAbsoluteValues; ///< do not normalize image values to 0-1 bool m_UseTrilinearInterpolation; + bool m_DoFiberResampling; }; } #ifndef ITK_MANUAL_INSTANTIATION #include "itkTractDensityImageFilter.cpp" #endif #endif // __itkTractDensityImageFilter_h__ diff --git a/Modules/DiffusionImaging/FiberTracking/Algorithms/itkTractsToDWIImageFilter.cpp b/Modules/DiffusionImaging/FiberTracking/Algorithms/itkTractsToDWIImageFilter.cpp index 1805a97fb1..86093896aa 100755 --- a/Modules/DiffusionImaging/FiberTracking/Algorithms/itkTractsToDWIImageFilter.cpp +++ b/Modules/DiffusionImaging/FiberTracking/Algorithms/itkTractsToDWIImageFilter.cpp @@ -1,1301 +1,1302 @@ /*=================================================================== The Medical Imaging Interaction Toolkit (MITK) Copyright (c) German Cancer Research Center, Division of Medical and Biological Informatics. All rights reserved. This software is distributed WITHOUT ANY WARRANTY; without even the implied warranty of MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See LICENSE.txt or http://www.mitk.org for details. ===================================================================*/ #include "itkTractsToDWIImageFilter.h" #include #include #include #include #include #include #include #include #include #include #include #include #include #include #include #include #include #include #include #include #include #include #include #include #include #include #include #include #include #include #include #include namespace itk { template< class PixelType > TractsToDWIImageFilter< PixelType >::TractsToDWIImageFilter() : m_FiberBundle(NULL) , m_StatusText("") , m_UseConstantRandSeed(false) , m_RandGen(itk::Statistics::MersenneTwisterRandomVariateGenerator::New()) { m_RandGen->SetSeed(); } template< class PixelType > TractsToDWIImageFilter< PixelType >::~TractsToDWIImageFilter() { } template< class PixelType > TractsToDWIImageFilter< PixelType >::DoubleDwiType::Pointer TractsToDWIImageFilter< PixelType >::DoKspaceStuff( std::vector< DoubleDwiType::Pointer >& images ) { int numFiberCompartments = m_Parameters.m_FiberModelList.size(); // create slice object ImageRegion<2> sliceRegion; sliceRegion.SetSize(0, m_UpsampledImageRegion.GetSize()[0]); sliceRegion.SetSize(1, m_UpsampledImageRegion.GetSize()[1]); Vector< double, 2 > sliceSpacing; sliceSpacing[0] = m_UpsampledSpacing[0]; sliceSpacing[1] = m_UpsampledSpacing[1]; // frequency map slice SliceType::Pointer fMapSlice = NULL; if (m_Parameters.m_SignalGen.m_FrequencyMap.IsNotNull()) { fMapSlice = SliceType::New(); ImageRegion<2> region; region.SetSize(0, m_UpsampledImageRegion.GetSize()[0]); region.SetSize(1, m_UpsampledImageRegion.GetSize()[1]); fMapSlice->SetLargestPossibleRegion( region ); fMapSlice->SetBufferedRegion( region ); fMapSlice->SetRequestedRegion( region ); fMapSlice->Allocate(); fMapSlice->FillBuffer(0.0); } DoubleDwiType::Pointer newImage = DoubleDwiType::New(); newImage->SetSpacing( m_Parameters.m_SignalGen.m_ImageSpacing ); newImage->SetOrigin( m_Parameters.m_SignalGen.m_ImageOrigin ); newImage->SetDirection( m_Parameters.m_SignalGen.m_ImageDirection ); newImage->SetLargestPossibleRegion( m_Parameters.m_SignalGen.m_ImageRegion ); newImage->SetBufferedRegion( m_Parameters.m_SignalGen.m_ImageRegion ); newImage->SetRequestedRegion( m_Parameters.m_SignalGen.m_ImageRegion ); newImage->SetVectorLength( images.at(0)->GetVectorLength() ); newImage->Allocate(); std::vector< unsigned int > spikeVolume; for (unsigned int i=0; iGetIntegerVariate()%images.at(0)->GetVectorLength()); std::sort (spikeVolume.begin(), spikeVolume.end()); std::reverse (spikeVolume.begin(), spikeVolume.end()); m_StatusText += "0% 10 20 30 40 50 60 70 80 90 100%\n"; m_StatusText += "|----|----|----|----|----|----|----|----|----|----|\n*"; unsigned long lastTick = 0; boost::progress_display disp(2*images.at(0)->GetVectorLength()*images.at(0)->GetLargestPossibleRegion().GetSize(2)); for (unsigned int g=0; gGetVectorLength(); g++) { std::vector< unsigned int > spikeSlice; while (!spikeVolume.empty() && spikeVolume.back()==g) { spikeSlice.push_back(m_RandGen->GetIntegerVariate()%images.at(0)->GetLargestPossibleRegion().GetSize(2)); spikeVolume.pop_back(); } std::sort (spikeSlice.begin(), spikeSlice.end()); std::reverse (spikeSlice.begin(), spikeSlice.end()); for (unsigned int z=0; zGetLargestPossibleRegion().GetSize(2); z++) { std::vector< SliceType::Pointer > compartmentSlices; std::vector< double > t2Vector; for (unsigned int i=0; i* signalModel; if (iSetLargestPossibleRegion( sliceRegion ); slice->SetBufferedRegion( sliceRegion ); slice->SetRequestedRegion( sliceRegion ); slice->SetSpacing(sliceSpacing); slice->Allocate(); slice->FillBuffer(0.0); // extract slice from channel g for (unsigned int y=0; yGetLargestPossibleRegion().GetSize(1); y++) for (unsigned int x=0; xGetLargestPossibleRegion().GetSize(0); x++) { SliceType::IndexType index2D; index2D[0]=x; index2D[1]=y; DoubleDwiType::IndexType index3D; index3D[0]=x; index3D[1]=y; index3D[2]=z; slice->SetPixel(index2D, images.at(i)->GetPixel(index3D)[g]); if (fMapSlice.IsNotNull() && i==0) fMapSlice->SetPixel(index2D, m_Parameters.m_SignalGen.m_FrequencyMap->GetPixel(index3D)); } compartmentSlices.push_back(slice); t2Vector.push_back(signalModel->GetT2()); } if (this->GetAbortGenerateData()) return NULL; // create k-sapce (inverse fourier transform slices) itk::Size<2> outSize; outSize.SetElement(0, m_Parameters.m_SignalGen.m_ImageRegion.GetSize(0)); outSize.SetElement(1, m_Parameters.m_SignalGen.m_ImageRegion.GetSize(1)); itk::KspaceImageFilter< SliceType::PixelType >::Pointer idft = itk::KspaceImageFilter< SliceType::PixelType >::New(); idft->SetCompartmentImages(compartmentSlices); idft->SetT2(t2Vector); idft->SetUseConstantRandSeed(m_UseConstantRandSeed); idft->SetParameters(m_Parameters); idft->SetZ((double)z-(double)images.at(0)->GetLargestPossibleRegion().GetSize(2)/2.0); idft->SetDiffusionGradientDirection(m_Parameters.m_SignalGen.GetGradientDirection(g)); idft->SetFrequencyMapSlice(fMapSlice); idft->SetOutSize(outSize); int numSpikes = 0; while (!spikeSlice.empty() && spikeSlice.back()==z) { numSpikes++; spikeSlice.pop_back(); } idft->SetSpikesPerSlice(numSpikes); idft->Update(); ComplexSliceType::Pointer fSlice; fSlice = idft->GetOutput(); ++disp; unsigned long newTick = 50*disp.count()/disp.expected_count(); for (unsigned long tick = 0; tick<(newTick-lastTick); tick++) m_StatusText += "*"; lastTick = newTick; // fourier transform slice SliceType::Pointer newSlice; itk::DftImageFilter< SliceType::PixelType >::Pointer dft = itk::DftImageFilter< SliceType::PixelType >::New(); dft->SetInput(fSlice); dft->Update(); newSlice = dft->GetOutput(); // put slice back into channel g for (unsigned int y=0; yGetLargestPossibleRegion().GetSize(1); y++) for (unsigned int x=0; xGetLargestPossibleRegion().GetSize(0); x++) { DoubleDwiType::IndexType index3D; index3D[0]=x; index3D[1]=y; index3D[2]=z; SliceType::IndexType index2D; index2D[0]=x; index2D[1]=y; DoubleDwiType::PixelType pix3D = newImage->GetPixel(index3D); pix3D[g] = newSlice->GetPixel(index2D); newImage->SetPixel(index3D, pix3D); } ++disp; newTick = 50*disp.count()/disp.expected_count(); for (unsigned long tick = 0; tick<(newTick-lastTick); tick++) m_StatusText += "*"; lastTick = newTick; } } m_StatusText += "\n\n"; return newImage; } template< class PixelType > void TractsToDWIImageFilter< PixelType >::GenerateData() { m_TimeProbe.Start(); m_StatusText = "Starting simulation\n"; // check input data if (m_FiberBundle.IsNull()) itkExceptionMacro("Input fiber bundle is NULL!"); if (m_Parameters.m_FiberModelList.empty()) itkExceptionMacro("No diffusion model for fiber compartments defined!"); if (m_Parameters.m_NonFiberModelList.empty()) itkExceptionMacro("No diffusion model for non-fiber compartments defined!"); int baselineIndex = m_Parameters.m_SignalGen.GetFirstBaselineIndex(); if (baselineIndex<0) itkExceptionMacro("No baseline index found!"); if (!m_Parameters.m_SignalGen.m_SimulateKspaceAcquisition) m_Parameters.m_SignalGen.m_DoAddGibbsRinging = false; if (m_UseConstantRandSeed) // always generate the same random numbers? m_RandGen->SetSeed(0); else m_RandGen->SetSeed(); // initialize output dwi image ImageRegion<3> croppedRegion = m_Parameters.m_SignalGen.m_ImageRegion; croppedRegion.SetSize(1, croppedRegion.GetSize(1)*m_Parameters.m_SignalGen.m_CroppingFactor); itk::Point shiftedOrigin = m_Parameters.m_SignalGen.m_ImageOrigin; shiftedOrigin[1] += (m_Parameters.m_SignalGen.m_ImageRegion.GetSize(1)-croppedRegion.GetSize(1))*m_Parameters.m_SignalGen.m_ImageSpacing[1]/2; typename OutputImageType::Pointer outImage = OutputImageType::New(); outImage->SetSpacing( m_Parameters.m_SignalGen.m_ImageSpacing ); outImage->SetOrigin( shiftedOrigin ); outImage->SetDirection( m_Parameters.m_SignalGen.m_ImageDirection ); outImage->SetLargestPossibleRegion( croppedRegion ); outImage->SetBufferedRegion( croppedRegion ); outImage->SetRequestedRegion( croppedRegion ); outImage->SetVectorLength( m_Parameters.m_SignalGen.GetNumVolumes() ); outImage->Allocate(); typename OutputImageType::PixelType temp; temp.SetSize(m_Parameters.m_SignalGen.GetNumVolumes()); temp.Fill(0.0); outImage->FillBuffer(temp); // ADJUST GEOMETRY FOR FURTHER PROCESSING // is input slize size a power of two? unsigned int x=m_Parameters.m_SignalGen.m_ImageRegion.GetSize(0); unsigned int y=m_Parameters.m_SignalGen.m_ImageRegion.GetSize(1); ItkDoubleImgType::SizeType pad; pad[0]=x%2; pad[1]=y%2; pad[2]=0; m_Parameters.m_SignalGen.m_ImageRegion.SetSize(0, x+pad[0]); m_Parameters.m_SignalGen.m_ImageRegion.SetSize(1, y+pad[1]); if (m_Parameters.m_SignalGen.m_FrequencyMap.IsNotNull() && (pad[0]>0 || pad[1]>0)) { itk::ConstantPadImageFilter::Pointer zeroPadder = itk::ConstantPadImageFilter::New(); zeroPadder->SetInput(m_Parameters.m_SignalGen.m_FrequencyMap); zeroPadder->SetConstant(0); zeroPadder->SetPadUpperBound(pad); zeroPadder->Update(); m_Parameters.m_SignalGen.m_FrequencyMap = zeroPadder->GetOutput(); } if (m_Parameters.m_SignalGen.m_MaskImage.IsNotNull() && (pad[0]>0 || pad[1]>0)) { itk::ConstantPadImageFilter::Pointer zeroPadder = itk::ConstantPadImageFilter::New(); zeroPadder->SetInput(m_Parameters.m_SignalGen.m_MaskImage); zeroPadder->SetConstant(0); zeroPadder->SetPadUpperBound(pad); zeroPadder->Update(); m_Parameters.m_SignalGen.m_MaskImage = zeroPadder->GetOutput(); } // Apply in-plane upsampling for Gibbs ringing artifact double upsampling = 1; if (m_Parameters.m_SignalGen.m_DoAddGibbsRinging) upsampling = 2; m_UpsampledSpacing = m_Parameters.m_SignalGen.m_ImageSpacing; m_UpsampledSpacing[0] /= upsampling; m_UpsampledSpacing[1] /= upsampling; m_UpsampledImageRegion = m_Parameters.m_SignalGen.m_ImageRegion; m_UpsampledImageRegion.SetSize(0, m_Parameters.m_SignalGen.m_ImageRegion.GetSize()[0]*upsampling); m_UpsampledImageRegion.SetSize(1, m_Parameters.m_SignalGen.m_ImageRegion.GetSize()[1]*upsampling); m_UpsampledOrigin = m_Parameters.m_SignalGen.m_ImageOrigin; m_UpsampledOrigin[0] -= m_Parameters.m_SignalGen.m_ImageSpacing[0]/2; m_UpsampledOrigin[0] += m_UpsampledSpacing[0]/2; m_UpsampledOrigin[1] -= m_Parameters.m_SignalGen.m_ImageSpacing[1]/2; m_UpsampledOrigin[1] += m_UpsampledSpacing[1]/2; m_UpsampledOrigin[2] -= m_Parameters.m_SignalGen.m_ImageSpacing[2]/2; m_UpsampledOrigin[2] += m_UpsampledSpacing[2]/2; // generate double images to store the individual compartment signals m_CompartmentImages.clear(); int numFiberCompartments = m_Parameters.m_FiberModelList.size(); int numNonFiberCompartments = m_Parameters.m_NonFiberModelList.size(); for (int i=0; iSetSpacing( m_UpsampledSpacing ); doubleDwi->SetOrigin( m_UpsampledOrigin ); doubleDwi->SetDirection( m_Parameters.m_SignalGen.m_ImageDirection ); doubleDwi->SetLargestPossibleRegion( m_UpsampledImageRegion ); doubleDwi->SetBufferedRegion( m_UpsampledImageRegion ); doubleDwi->SetRequestedRegion( m_UpsampledImageRegion ); doubleDwi->SetVectorLength( m_Parameters.m_SignalGen.GetNumVolumes() ); doubleDwi->Allocate(); DoubleDwiType::PixelType pix; pix.SetSize(m_Parameters.m_SignalGen.GetNumVolumes()); pix.Fill(0.0); doubleDwi->FillBuffer(pix); m_CompartmentImages.push_back(doubleDwi); } // initialize output volume fraction images m_VolumeFractions.clear(); for (int i=0; iSetSpacing( m_UpsampledSpacing ); doubleImg->SetOrigin( m_UpsampledOrigin ); doubleImg->SetDirection( m_Parameters.m_SignalGen.m_ImageDirection ); doubleImg->SetLargestPossibleRegion( m_UpsampledImageRegion ); doubleImg->SetBufferedRegion( m_UpsampledImageRegion ); doubleImg->SetRequestedRegion( m_UpsampledImageRegion ); doubleImg->Allocate(); doubleImg->FillBuffer(0); m_VolumeFractions.push_back(doubleImg); } // get volume fraction images ItkDoubleImgType::Pointer sumImage = ItkDoubleImgType::New(); bool foundVolumeFractionImage = false; for (int i=0; iGetVolumeFractionImage().IsNotNull()) { foundVolumeFractionImage = true; itk::ConstantPadImageFilter::Pointer zeroPadder = itk::ConstantPadImageFilter::New(); zeroPadder->SetInput(m_Parameters.m_NonFiberModelList[i]->GetVolumeFractionImage()); zeroPadder->SetConstant(0); zeroPadder->SetPadUpperBound(pad); zeroPadder->Update(); m_Parameters.m_NonFiberModelList[i]->SetVolumeFractionImage(zeroPadder->GetOutput()); sumImage->SetSpacing( m_Parameters.m_NonFiberModelList[i]->GetVolumeFractionImage()->GetSpacing() ); sumImage->SetOrigin( m_Parameters.m_NonFiberModelList[i]->GetVolumeFractionImage()->GetOrigin() ); sumImage->SetDirection( m_Parameters.m_NonFiberModelList[i]->GetVolumeFractionImage()->GetDirection() ); sumImage->SetLargestPossibleRegion( m_Parameters.m_NonFiberModelList[i]->GetVolumeFractionImage()->GetLargestPossibleRegion() ); sumImage->SetBufferedRegion( m_Parameters.m_NonFiberModelList[i]->GetVolumeFractionImage()->GetLargestPossibleRegion() ); sumImage->SetRequestedRegion( m_Parameters.m_NonFiberModelList[i]->GetVolumeFractionImage()->GetLargestPossibleRegion() ); sumImage->Allocate(); sumImage->FillBuffer(0); break; } } if (!foundVolumeFractionImage) { sumImage->SetSpacing( m_UpsampledSpacing ); sumImage->SetOrigin( m_UpsampledOrigin ); sumImage->SetDirection( m_Parameters.m_SignalGen.m_ImageDirection ); sumImage->SetLargestPossibleRegion( m_UpsampledImageRegion ); sumImage->SetBufferedRegion( m_UpsampledImageRegion ); sumImage->SetRequestedRegion( m_UpsampledImageRegion ); sumImage->Allocate(); sumImage->FillBuffer(0.0); } for (int i=0; iGetVolumeFractionImage().IsNull()) { ItkDoubleImgType::Pointer doubleImg = ItkDoubleImgType::New(); doubleImg->SetSpacing( sumImage->GetSpacing() ); doubleImg->SetOrigin( sumImage->GetOrigin() ); doubleImg->SetDirection( sumImage->GetDirection() ); doubleImg->SetLargestPossibleRegion( sumImage->GetLargestPossibleRegion() ); doubleImg->SetBufferedRegion( sumImage->GetLargestPossibleRegion() ); doubleImg->SetRequestedRegion( sumImage->GetLargestPossibleRegion() ); doubleImg->Allocate(); doubleImg->FillBuffer(1.0/numNonFiberCompartments); m_Parameters.m_NonFiberModelList[i]->SetVolumeFractionImage(doubleImg); } ImageRegionIterator it(m_Parameters.m_NonFiberModelList[i]->GetVolumeFractionImage(), m_Parameters.m_NonFiberModelList[i]->GetVolumeFractionImage()->GetLargestPossibleRegion()); while(!it.IsAtEnd()) { sumImage->SetPixel(it.GetIndex(), sumImage->GetPixel(it.GetIndex())+it.Get()); ++it; } } for (int i=0; i it(m_Parameters.m_NonFiberModelList[i]->GetVolumeFractionImage(), m_Parameters.m_NonFiberModelList[i]->GetVolumeFractionImage()->GetLargestPossibleRegion()); while(!it.IsAtEnd()) { if (sumImage->GetPixel(it.GetIndex())>0) it.Set(it.Get()/sumImage->GetPixel(it.GetIndex())); ++it; } } // resample mask image and frequency map to fit upsampled geometry if (m_Parameters.m_SignalGen.m_DoAddGibbsRinging) { if (m_Parameters.m_SignalGen.m_MaskImage.IsNotNull()) { // rescale mask image (otherwise there are problems with the resampling) itk::RescaleIntensityImageFilter::Pointer rescaler = itk::RescaleIntensityImageFilter::New(); rescaler->SetInput(0,m_Parameters.m_SignalGen.m_MaskImage); rescaler->SetOutputMaximum(100); rescaler->SetOutputMinimum(0); rescaler->Update(); // resample mask image itk::ResampleImageFilter::Pointer resampler = itk::ResampleImageFilter::New(); resampler->SetInput(rescaler->GetOutput()); resampler->SetOutputParametersFromImage(m_Parameters.m_SignalGen.m_MaskImage); resampler->SetSize(m_UpsampledImageRegion.GetSize()); resampler->SetOutputSpacing(m_UpsampledSpacing); resampler->SetOutputOrigin(m_UpsampledOrigin); itk::NearestNeighborInterpolateImageFunction::Pointer nn_interpolator = itk::NearestNeighborInterpolateImageFunction::New(); resampler->SetInterpolator(nn_interpolator); resampler->Update(); m_Parameters.m_SignalGen.m_MaskImage = resampler->GetOutput(); itk::ImageFileWriter::Pointer w = itk::ImageFileWriter::New(); w->SetFileName("/local/mask_ups.nrrd"); w->SetInput(m_Parameters.m_SignalGen.m_MaskImage); w->Update(); } // resample frequency map if (m_Parameters.m_SignalGen.m_FrequencyMap.IsNotNull()) { itk::ResampleImageFilter::Pointer resampler = itk::ResampleImageFilter::New(); resampler->SetInput(m_Parameters.m_SignalGen.m_FrequencyMap); resampler->SetOutputParametersFromImage(m_Parameters.m_SignalGen.m_FrequencyMap); resampler->SetSize(m_UpsampledImageRegion.GetSize()); resampler->SetOutputSpacing(m_UpsampledSpacing); resampler->SetOutputOrigin(m_UpsampledOrigin); itk::NearestNeighborInterpolateImageFunction::Pointer nn_interpolator = itk::NearestNeighborInterpolateImageFunction::New(); resampler->SetInterpolator(nn_interpolator); resampler->Update(); m_Parameters.m_SignalGen.m_FrequencyMap = resampler->GetOutput(); } } // no input tissue mask is set -> create default m_MaskImageSet = true; if (m_Parameters.m_SignalGen.m_MaskImage.IsNull()) { m_StatusText += "No tissue mask set\n"; MITK_INFO << "No tissue mask set"; m_Parameters.m_SignalGen.m_MaskImage = ItkUcharImgType::New(); m_Parameters.m_SignalGen.m_MaskImage->SetSpacing( m_UpsampledSpacing ); m_Parameters.m_SignalGen.m_MaskImage->SetOrigin( m_UpsampledOrigin ); m_Parameters.m_SignalGen.m_MaskImage->SetDirection( m_Parameters.m_SignalGen.m_ImageDirection ); m_Parameters.m_SignalGen.m_MaskImage->SetLargestPossibleRegion( m_UpsampledImageRegion ); m_Parameters.m_SignalGen.m_MaskImage->SetBufferedRegion( m_UpsampledImageRegion ); m_Parameters.m_SignalGen.m_MaskImage->SetRequestedRegion( m_UpsampledImageRegion ); m_Parameters.m_SignalGen.m_MaskImage->Allocate(); m_Parameters.m_SignalGen.m_MaskImage->FillBuffer(1); m_MaskImageSet = false; } else { m_StatusText += "Using tissue mask\n"; MITK_INFO << "Using tissue mask"; } m_Parameters.m_SignalGen.m_ImageRegion = croppedRegion; x=m_Parameters.m_SignalGen.m_ImageRegion.GetSize(0); y=m_Parameters.m_SignalGen.m_ImageRegion.GetSize(1); if ( x%2 == 1 ) m_Parameters.m_SignalGen.m_ImageRegion.SetSize(0, x+1); if ( y%2 == 1 ) m_Parameters.m_SignalGen.m_ImageRegion.SetSize(1, y+1); // resample fiber bundle for sufficient voxel coverage m_StatusText += "\n"+this->GetTime()+" > Resampling fibers ...\n"; double segmentVolume = 0.0001; float minSpacing = 1; if(m_UpsampledSpacing[0]GetDeepCopy(); double volumeAccuracy = 10; m_FiberBundleWorkingCopy->ResampleSpline(minSpacing/volumeAccuracy); double mmRadius = m_Parameters.m_SignalGen.m_AxonRadius/1000; if (mmRadius>0) segmentVolume = M_PI*mmRadius*mmRadius*minSpacing/volumeAccuracy; double maxVolume = 0; m_VoxelVolume = m_UpsampledSpacing[0]*m_UpsampledSpacing[1]*m_UpsampledSpacing[2]; if (m_Parameters.m_SignalGen.m_DoAddMotion) { std::string fileName = "fiberfox_motion_0.log"; std::string filePath = mitk::IOUtil::GetTempPath(); if (m_Parameters.m_Misc.m_OutputPath.size()>0) filePath = m_Parameters.m_Misc.m_OutputPath; int c = 1; while (itksys::SystemTools::FileExists((filePath+fileName).c_str())) { fileName = "fiberfox_motion_"; fileName += boost::lexical_cast(c); fileName += ".log"; c++; } m_Logfile.open((filePath+fileName).c_str()); m_Logfile << "0 rotation: 0,0,0; translation: 0,0,0\n"; if (m_Parameters.m_SignalGen.m_DoRandomizeMotion) { m_StatusText += "Adding random motion artifacts:\n"; m_StatusText += "Maximum rotation: +/-" + boost::lexical_cast(m_Parameters.m_SignalGen.m_Rotation) + "°\n"; m_StatusText += "Maximum translation: +/-" + boost::lexical_cast(m_Parameters.m_SignalGen.m_Translation) + "mm\n"; } else { m_StatusText += "Adding linear motion artifacts:\n"; m_StatusText += "Maximum rotation: " + boost::lexical_cast(m_Parameters.m_SignalGen.m_Rotation) + "°\n"; m_StatusText += "Maximum translation: " + boost::lexical_cast(m_Parameters.m_SignalGen.m_Translation) + "mm\n"; } m_StatusText += "Motion logfile: " + (filePath+fileName) + "\n"; MITK_INFO << "Adding motion artifacts"; MITK_INFO << "Maximum rotation: " << m_Parameters.m_SignalGen.m_Rotation; MITK_INFO << "Maxmimum translation: " << m_Parameters.m_SignalGen.m_Translation; } maxVolume = 0; m_StatusText += "\n"+this->GetTime()+" > Generating " + boost::lexical_cast(numFiberCompartments+numNonFiberCompartments) + "-compartment diffusion-weighted signal.\n"; MITK_INFO << "Generating " << numFiberCompartments+numNonFiberCompartments << "-compartment diffusion-weighted signal."; int numFibers = m_FiberBundle->GetNumFibers(); boost::progress_display disp(numFibers*m_Parameters.m_SignalGen.GetNumVolumes()); // get transform for motion artifacts m_FiberBundleTransformed = m_FiberBundleWorkingCopy; m_Rotation = m_Parameters.m_SignalGen.m_Rotation/m_Parameters.m_SignalGen.GetNumVolumes(); m_Translation = m_Parameters.m_SignalGen.m_Translation/m_Parameters.m_SignalGen.GetNumVolumes(); // creat image to hold transformed mask (motion artifact) m_MaskImage = ItkUcharImgType::New(); itk::ImageDuplicator::Pointer duplicator = itk::ImageDuplicator::New(); duplicator->SetInputImage(m_Parameters.m_SignalGen.m_MaskImage); duplicator->Update(); m_MaskImage = duplicator->GetOutput(); // second upsampling needed for motion artifacts ImageRegion<3> upsampledImageRegion = m_UpsampledImageRegion; DoubleVectorType upsampledSpacing = m_UpsampledSpacing; upsampledSpacing[0] /= 4; upsampledSpacing[1] /= 4; upsampledSpacing[2] /= 4; upsampledImageRegion.SetSize(0, m_UpsampledImageRegion.GetSize()[0]*4); upsampledImageRegion.SetSize(1, m_UpsampledImageRegion.GetSize()[1]*4); upsampledImageRegion.SetSize(2, m_UpsampledImageRegion.GetSize()[2]*4); itk::Point upsampledOrigin = m_UpsampledOrigin; upsampledOrigin[0] -= m_UpsampledSpacing[0]/2; upsampledOrigin[0] += upsampledSpacing[0]/2; upsampledOrigin[1] -= m_UpsampledSpacing[1]/2; upsampledOrigin[1] += upsampledSpacing[1]/2; upsampledOrigin[2] -= m_UpsampledSpacing[2]/2; upsampledOrigin[2] += upsampledSpacing[2]/2; m_UpsampledMaskImage = ItkUcharImgType::New(); itk::ResampleImageFilter::Pointer upsampler = itk::ResampleImageFilter::New(); upsampler->SetInput(m_Parameters.m_SignalGen.m_MaskImage); upsampler->SetOutputParametersFromImage(m_Parameters.m_SignalGen.m_MaskImage); upsampler->SetSize(upsampledImageRegion.GetSize()); upsampler->SetOutputSpacing(upsampledSpacing); upsampler->SetOutputOrigin(upsampledOrigin); itk::NearestNeighborInterpolateImageFunction::Pointer nn_interpolator = itk::NearestNeighborInterpolateImageFunction::New(); upsampler->SetInterpolator(nn_interpolator); upsampler->Update(); m_UpsampledMaskImage = upsampler->GetOutput(); unsigned long lastTick = 0; int signalModelSeed = m_RandGen->GetIntegerVariate(); switch (m_Parameters.m_SignalGen.m_DiffusionDirectionMode) { case(SignalGenerationParameters::FIBER_TANGENT_DIRECTIONS): // use fiber tangent directions to determine diffusion direction { m_StatusText += "0% 10 20 30 40 50 60 70 80 90 100%\n"; m_StatusText += "|----|----|----|----|----|----|----|----|----|----|\n*"; for (unsigned int g=0; gSetSeed(signalModelSeed); for (int i=0; iSetSeed(signalModelSeed); ItkDoubleImgType::Pointer intraAxonalVolumeImage = ItkDoubleImgType::New(); intraAxonalVolumeImage->SetSpacing( m_UpsampledSpacing ); intraAxonalVolumeImage->SetOrigin( m_UpsampledOrigin ); intraAxonalVolumeImage->SetDirection( m_Parameters.m_SignalGen.m_ImageDirection ); intraAxonalVolumeImage->SetLargestPossibleRegion( m_UpsampledImageRegion ); intraAxonalVolumeImage->SetBufferedRegion( m_UpsampledImageRegion ); intraAxonalVolumeImage->SetRequestedRegion( m_UpsampledImageRegion ); intraAxonalVolumeImage->Allocate(); intraAxonalVolumeImage->FillBuffer(0); vtkPolyData* fiberPolyData = m_FiberBundleTransformed->GetFiberPolyData(); // generate fiber signal (if there are any fiber models present) if (!m_Parameters.m_FiberModelList.empty()) for( int i=0; iGetFiberWeight(i); vtkCell* cell = fiberPolyData->GetCell(i); int numPoints = cell->GetNumberOfPoints(); vtkPoints* points = cell->GetPoints(); if (numPoints<2) continue; for( int j=0; jGetAbortGenerateData()) { m_StatusText += "\n"+this->GetTime()+" > Simulation aborted\n"; return; } double* temp = points->GetPoint(j); itk::Point vertex = GetItkPoint(temp); itk::Vector v = GetItkVector(temp); itk::Vector dir(3); if (jGetPoint(j+1))-v; else dir = v-GetItkVector(points->GetPoint(j-1)); if (dir.GetSquaredNorm()<0.0001 || dir[0]!=dir[0] || dir[1]!=dir[1] || dir[2]!=dir[2]) continue; itk::Index<3> idx; itk::ContinuousIndex contIndex; m_MaskImage->TransformPhysicalPointToIndex(vertex, idx); m_MaskImage->TransformPhysicalPointToContinuousIndex(vertex, contIndex); if (!m_MaskImage->GetLargestPossibleRegion().IsInside(idx) || m_MaskImage->GetPixel(idx)<=0) continue; // generate signal for each fiber compartment for (int k=0; kSetFiberDirection(dir); DoubleDwiType::PixelType pix = m_CompartmentImages.at(k)->GetPixel(idx); - pix[g] += segmentVolume*m_Parameters.m_FiberModelList[k]->SimulateMeasurement(g); + pix[g] += fiberWeight*segmentVolume*m_Parameters.m_FiberModelList[k]->SimulateMeasurement(g); m_CompartmentImages.at(k)->SetPixel(idx, pix); } // update fiber volume image - double vol = intraAxonalVolumeImage->GetPixel(idx) + segmentVolume; + double vol = intraAxonalVolumeImage->GetPixel(idx) + segmentVolume*fiberWeight; intraAxonalVolumeImage->SetPixel(idx, vol); if (g==0 && vol>maxVolume) maxVolume = vol; } // progress report ++disp; unsigned long newTick = 50*disp.count()/disp.expected_count(); for (unsigned int tick = 0; tick<(newTick-lastTick); tick++) m_StatusText += "*"; lastTick = newTick; } // generate non-fiber signal ImageRegionIterator it3(m_MaskImage, m_MaskImage->GetLargestPossibleRegion()); double fact = 1; if (m_Parameters.m_SignalGen.m_AxonRadius<0.0001 || maxVolume>m_VoxelVolume) fact = m_VoxelVolume/maxVolume; while(!it3.IsAtEnd()) { if (it3.Get()>0) { DoubleDwiType::IndexType index = it3.GetIndex(); // adjust intra-axonal signal to abtain an only-fiber voxel if (fabs(fact-1.0)>0.0001) for (int i=0; iGetPixel(index); pix[g] *= fact; m_CompartmentImages.at(i)->SetPixel(index, pix); } // simulate other compartments SimulateNonFiberSignal(index, intraAxonalVolumeImage->GetPixel(index)*fact, g); } ++it3; } // move fibers SimulateMotion(g); } break; } case (SignalGenerationParameters::MAIN_FIBER_DIRECTIONS): // use main fiber directions to determine voxel-wise diffusion directions { typedef itk::Image< itk::Vector< float, 3>, 3 > ItkDirectionImage3DType; typedef itk::VectorContainer< unsigned int, ItkDirectionImage3DType::Pointer > ItkDirectionImageContainerType; // calculate main fiber directions itk::TractsToVectorImageFilter::Pointer fOdfFilter = itk::TractsToVectorImageFilter::New(); fOdfFilter->SetFiberBundle(m_FiberBundleTransformed); fOdfFilter->SetMaskImage(m_MaskImage); fOdfFilter->SetAngularThreshold(cos(m_Parameters.m_SignalGen.m_FiberSeparationThreshold*M_PI/180.0)); fOdfFilter->SetNormalizeVectors(false); fOdfFilter->SetUseWorkingCopy(true); fOdfFilter->SetSizeThreshold(0); fOdfFilter->SetMaxNumDirections(3); fOdfFilter->Update(); ItkDirectionImageContainerType::Pointer directionImageContainer = fOdfFilter->GetDirectionImageContainer(); // allocate image storing intra-axonal volume fraction information ItkDoubleImgType::Pointer intraAxonalVolumeImage = ItkDoubleImgType::New(); intraAxonalVolumeImage->SetSpacing( m_UpsampledSpacing ); intraAxonalVolumeImage->SetOrigin( m_UpsampledOrigin ); intraAxonalVolumeImage->SetDirection( m_Parameters.m_SignalGen.m_ImageDirection ); intraAxonalVolumeImage->SetLargestPossibleRegion( m_UpsampledImageRegion ); intraAxonalVolumeImage->SetBufferedRegion( m_UpsampledImageRegion ); intraAxonalVolumeImage->SetRequestedRegion( m_UpsampledImageRegion ); intraAxonalVolumeImage->Allocate(); intraAxonalVolumeImage->FillBuffer(0); // determine intra-axonal volume fraction using the tract density itk::TractDensityImageFilter< ItkDoubleImgType >::Pointer tdiFilter = itk::TractDensityImageFilter< ItkDoubleImgType >::New(); tdiFilter->SetFiberBundle(m_FiberBundleTransformed); tdiFilter->SetBinaryOutput(false); tdiFilter->SetOutputAbsoluteValues(false); tdiFilter->SetInputImage(intraAxonalVolumeImage); tdiFilter->SetUseImageGeometry(true); tdiFilter->Update(); intraAxonalVolumeImage = tdiFilter->GetOutput(); m_StatusText += "0% 10 20 30 40 50 60 70 80 90 100%\n"; m_StatusText += "|----|----|----|----|----|----|----|----|----|----|\n*"; boost::progress_display disp(m_MaskImage->GetLargestPossibleRegion().GetNumberOfPixels()*m_Parameters.m_SignalGen.GetNumVolumes()); for (unsigned int g=0; gSetSeed(signalModelSeed); for (int i=0; iSetSeed(signalModelSeed); if (m_Parameters.m_SignalGen.m_DoAddMotion && g>0) // if fibers have moved we need a new TDI and new directions { fOdfFilter->SetFiberBundle(m_FiberBundleTransformed); fOdfFilter->SetMaskImage(m_MaskImage); fOdfFilter->Update(); directionImageContainer = fOdfFilter->GetDirectionImageContainer(); tdiFilter->SetFiberBundle(m_FiberBundleTransformed); tdiFilter->Update(); intraAxonalVolumeImage = tdiFilter->GetOutput(); } ImageRegionIterator< ItkUcharImgType > it(m_MaskImage, m_MaskImage->GetLargestPossibleRegion()); while(!it.IsAtEnd()) { ++disp; unsigned long newTick = 50*disp.count()/disp.expected_count(); for (unsigned int tick = 0; tick<(newTick-lastTick); tick++) m_StatusText += "*"; lastTick = newTick; if (this->GetAbortGenerateData()) { m_StatusText += "\n"+this->GetTime()+" > Simulation aborted\n"; return; } if (it.Get()>0) { // generate fiber signal for (int c=0; cGetPixel(it.GetIndex()); for (unsigned int i=0; iSize(); i++) { itk::Vector< double, 3> dir; dir.CastFrom(directionImageContainer->GetElement(i)->GetPixel(it.GetIndex())); double norm = dir.GetNorm(); if (norm>0.0001) { m_Parameters.m_FiberModelList.at(c)->SetFiberDirection(dir); pix[g] += m_Parameters.m_FiberModelList.at(c)->SimulateMeasurement(g)*norm; count++; } } if (count>0) pix[g] /= count; pix[g] *= intraAxonalVolumeImage->GetPixel(it.GetIndex())*m_VoxelVolume; m_CompartmentImages.at(c)->SetPixel(it.GetIndex(), pix); } // simulate other compartments SimulateNonFiberSignal(it.GetIndex(), intraAxonalVolumeImage->GetPixel(it.GetIndex())*m_VoxelVolume, g); } ++it; } SimulateMotion(g); } itk::ImageFileWriter< ItkUcharImgType >::Pointer wr = itk::ImageFileWriter< ItkUcharImgType >::New(); wr->SetInput(fOdfFilter->GetNumDirectionsImage()); wr->SetFileName(mitk::IOUtil::GetTempPath()+"/NumDirections_MainFiberDirections.nrrd"); wr->Update(); break; } case (SignalGenerationParameters::RANDOM_DIRECTIONS): { ItkUcharImgType::Pointer numDirectionsImage = ItkUcharImgType::New(); numDirectionsImage->SetSpacing( m_UpsampledSpacing ); numDirectionsImage->SetOrigin( m_UpsampledOrigin ); numDirectionsImage->SetDirection( m_Parameters.m_SignalGen.m_ImageDirection ); numDirectionsImage->SetLargestPossibleRegion( m_UpsampledImageRegion ); numDirectionsImage->SetBufferedRegion( m_UpsampledImageRegion ); numDirectionsImage->SetRequestedRegion( m_UpsampledImageRegion ); numDirectionsImage->Allocate(); numDirectionsImage->FillBuffer(0); double sepAngle = cos(m_Parameters.m_SignalGen.m_FiberSeparationThreshold*M_PI/180.0); m_StatusText += "0% 10 20 30 40 50 60 70 80 90 100%\n"; m_StatusText += "|----|----|----|----|----|----|----|----|----|----|\n*"; boost::progress_display disp(m_MaskImage->GetLargestPossibleRegion().GetNumberOfPixels()); ImageRegionIterator it(m_MaskImage, m_MaskImage->GetLargestPossibleRegion()); while(!it.IsAtEnd()) { ++disp; unsigned long newTick = 50*disp.count()/disp.expected_count(); for (unsigned int tick = 0; tick<(newTick-lastTick); tick++) m_StatusText += "*"; lastTick = newTick; if (this->GetAbortGenerateData()) { m_StatusText += "\n"+this->GetTime()+" > Simulation aborted\n"; return; } if (it.Get()>0) { int numFibs = m_RandGen->GetIntegerVariate(2)+1; DoubleDwiType::PixelType pix = m_CompartmentImages.at(0)->GetPixel(it.GetIndex()); double volume = m_RandGen->GetVariateWithClosedRange(0.3); // double sum = 0; std::vector< double > fractions; for (int i=0; iGetVariateWithClosedRange(0.5)); // sum += fractions.at(i); } // for (int i=0; i > directions; for (int i=0; iGetVariateWithClosedRange(2)-1.0; fib[1] = m_RandGen->GetVariateWithClosedRange(2)-1.0; fib[2] = m_RandGen->GetVariateWithClosedRange(2)-1.0; fib.Normalize(); double min = 0; for (unsigned int d=0; dmin) min = angle; } if (minSetFiberDirection(fib); pix += m_Parameters.m_FiberModelList.at(0)->SimulateMeasurement()*fractions[i]; directions.push_back(fib); } else i--; } pix *= (1-volume); m_CompartmentImages.at(0)->SetPixel(it.GetIndex(), pix); // CSF/GM { pix += volume*m_Parameters.m_NonFiberModelList.at(0)->SimulateMeasurement(); } numDirectionsImage->SetPixel(it.GetIndex(), numFibs); } ++it; } itk::ImageFileWriter< ItkUcharImgType >::Pointer wr = itk::ImageFileWriter< ItkUcharImgType >::New(); wr->SetInput(numDirectionsImage); wr->SetFileName(mitk::IOUtil::GetTempPath()+"/NumDirections_RandomDirections.nrrd"); wr->Update(); } } if (m_Logfile.is_open()) { m_Logfile << "DONE"; m_Logfile.close(); } m_StatusText += "\n\n"; if (this->GetAbortGenerateData()) { m_StatusText += "\n"+this->GetTime()+" > Simulation aborted\n"; return; } DoubleDwiType::Pointer doubleOutImage; if ( m_Parameters.m_SignalGen.m_SimulateKspaceAcquisition ) // do k-space stuff { m_StatusText += this->GetTime()+" > Adjusting complex signal\n"; MITK_INFO << "Adjusting complex signal:"; if (m_Parameters.m_SignalGen.m_DoSimulateRelaxation) m_StatusText += "Simulating signal relaxation\n"; if (m_Parameters.m_SignalGen.m_FrequencyMap.IsNotNull()) m_StatusText += "Simulating distortions\n"; if (m_Parameters.m_SignalGen.m_DoAddGibbsRinging) m_StatusText += "Simulating ringing artifacts\n"; if (m_Parameters.m_SignalGen.m_EddyStrength>0) m_StatusText += "Simulating eddy currents\n"; if (m_Parameters.m_SignalGen.m_Spikes>0) m_StatusText += "Simulating spikes\n"; if (m_Parameters.m_SignalGen.m_CroppingFactor<1.0) m_StatusText += "Simulating aliasing artifacts\n"; if (m_Parameters.m_SignalGen.m_KspaceLineOffset>0) m_StatusText += "Simulating ghosts\n"; doubleOutImage = DoKspaceStuff(m_CompartmentImages); m_Parameters.m_SignalGen.m_SignalScale = 1; // already scaled in DoKspaceStuff } else // don't do k-space stuff, just sum compartments { m_StatusText += this->GetTime()+" > Summing compartments\n"; MITK_INFO << "Summing compartments"; doubleOutImage = m_CompartmentImages.at(0); for (unsigned int i=1; i::Pointer adder = itk::AddImageFilter< DoubleDwiType, DoubleDwiType, DoubleDwiType>::New(); adder->SetInput1(doubleOutImage); adder->SetInput2(m_CompartmentImages.at(i)); adder->Update(); doubleOutImage = adder->GetOutput(); } } if (this->GetAbortGenerateData()) { m_StatusText += "\n"+this->GetTime()+" > Simulation aborted\n"; return; } m_StatusText += this->GetTime()+" > Finalizing image\n"; MITK_INFO << "Finalizing image"; if (m_Parameters.m_SignalGen.m_SignalScale>1) m_StatusText += " Scaling signal\n"; if (m_Parameters.m_NoiseModel!=NULL) m_StatusText += " Adding noise\n"; unsigned int window = 0; unsigned int min = itk::NumericTraits::max(); ImageRegionIterator it4 (outImage, outImage->GetLargestPossibleRegion()); DoubleDwiType::PixelType signal; signal.SetSize(m_Parameters.m_SignalGen.GetNumVolumes()); boost::progress_display disp2(outImage->GetLargestPossibleRegion().GetNumberOfPixels()); m_StatusText += "0% 10 20 30 40 50 60 70 80 90 100%\n"; m_StatusText += "|----|----|----|----|----|----|----|----|----|----|\n*"; lastTick = 0; while(!it4.IsAtEnd()) { if (this->GetAbortGenerateData()) { m_StatusText += "\n"+this->GetTime()+" > Simulation aborted\n"; return; } ++disp2; unsigned long newTick = 50*disp2.count()/disp2.expected_count(); for (unsigned long tick = 0; tick<(newTick-lastTick); tick++) m_StatusText += "*"; lastTick = newTick; typename OutputImageType::IndexType index = it4.GetIndex(); signal = doubleOutImage->GetPixel(index)*m_Parameters.m_SignalGen.m_SignalScale; if (m_Parameters.m_NoiseModel!=NULL) m_Parameters.m_NoiseModel->AddNoise(signal); for (unsigned int i=0; i0) signal[i] = floor(signal[i]+0.5); else signal[i] = ceil(signal[i]-0.5); if ( (!m_Parameters.m_SignalGen.IsBaselineIndex(i) || signal.Size()==1) && signal[i]>window) window = signal[i]; if ( (!m_Parameters.m_SignalGen.IsBaselineIndex(i) || signal.Size()==1) && signal[i]SetNthOutput(0, outImage); m_StatusText += "\n\n"; m_StatusText += "Finished simulation\n"; m_StatusText += "Simulation time: "+GetTime(); m_TimeProbe.Stop(); } template< class PixelType > void TractsToDWIImageFilter< PixelType >::SimulateMotion(int g) { if (m_Parameters.m_SignalGen.m_DoAddMotion && gGetDeepCopy(); m_Rotation[0] = m_RandGen->GetVariateWithClosedRange(m_Parameters.m_SignalGen.m_Rotation[0]*2)-m_Parameters.m_SignalGen.m_Rotation[0]; m_Rotation[1] = m_RandGen->GetVariateWithClosedRange(m_Parameters.m_SignalGen.m_Rotation[1]*2)-m_Parameters.m_SignalGen.m_Rotation[1]; m_Rotation[2] = m_RandGen->GetVariateWithClosedRange(m_Parameters.m_SignalGen.m_Rotation[2]*2)-m_Parameters.m_SignalGen.m_Rotation[2]; m_Translation[0] = m_RandGen->GetVariateWithClosedRange(m_Parameters.m_SignalGen.m_Translation[0]*2)-m_Parameters.m_SignalGen.m_Translation[0]; m_Translation[1] = m_RandGen->GetVariateWithClosedRange(m_Parameters.m_SignalGen.m_Translation[1]*2)-m_Parameters.m_SignalGen.m_Translation[1]; m_Translation[2] = m_RandGen->GetVariateWithClosedRange(m_Parameters.m_SignalGen.m_Translation[2]*2)-m_Parameters.m_SignalGen.m_Translation[2]; } // rotate mask image if (m_MaskImageSet) { ImageRegionIterator maskIt(m_UpsampledMaskImage, m_UpsampledMaskImage->GetLargestPossibleRegion()); m_MaskImage->FillBuffer(0); while(!maskIt.IsAtEnd()) { if (maskIt.Get()<=0) { ++maskIt; continue; } DoubleDwiType::IndexType index = maskIt.GetIndex(); itk::Point point; m_UpsampledMaskImage->TransformIndexToPhysicalPoint(index, point); if (m_Parameters.m_SignalGen.m_DoRandomizeMotion) point = m_FiberBundleWorkingCopy->TransformPoint(point.GetVnlVector(), m_Rotation[0],m_Rotation[1],m_Rotation[2],m_Translation[0],m_Translation[1],m_Translation[2]); else point = m_FiberBundleWorkingCopy->TransformPoint(point.GetVnlVector(), m_Rotation[0]*(g+1),m_Rotation[1]*(g+1),m_Rotation[2]*(g+1),m_Translation[0]*(g+1),m_Translation[1]*(g+1),m_Translation[2]*(g+1)); m_MaskImage->TransformPhysicalPointToIndex(point, index); if (m_MaskImage->GetLargestPossibleRegion().IsInside(index)) m_MaskImage->SetPixel(index,100); ++maskIt; } } // rotate fibers if (m_Logfile.is_open()) { m_Logfile << g+1 << " rotation: " << m_Rotation[0] << "," << m_Rotation[1] << "," << m_Rotation[2] << ";"; m_Logfile << " translation: " << m_Translation[0] << "," << m_Translation[1] << "," << m_Translation[2] << "\n"; } m_FiberBundleTransformed->TransformFibers(m_Rotation[0],m_Rotation[1],m_Rotation[2],m_Translation[0],m_Translation[1],m_Translation[2]); } } template< class PixelType > void TractsToDWIImageFilter< PixelType >::SimulateNonFiberSignal(ItkUcharImgType::IndexType index, double intraAxonalVolume, int g) { int numFiberCompartments = m_Parameters.m_FiberModelList.size(); int numNonFiberCompartments = m_Parameters.m_NonFiberModelList.size(); if (intraAxonalVolume>0.0001 && m_Parameters.m_SignalGen.m_DoDisablePartialVolume) // only fiber in voxel { DoubleDwiType::PixelType pix = m_CompartmentImages.at(0)->GetPixel(index); if (g>=0) pix[g] *= m_VoxelVolume/intraAxonalVolume; else pix *= m_VoxelVolume/intraAxonalVolume; m_CompartmentImages.at(0)->SetPixel(index, pix); m_VolumeFractions.at(0)->SetPixel(index, 1); for (int i=1; iGetPixel(index); if (g>=0) pix[g] = 0.0; else pix.Fill(0.0); m_CompartmentImages.at(i)->SetPixel(index, pix); } } else { m_VolumeFractions.at(0)->SetPixel(index, intraAxonalVolume/m_VoxelVolume); itk::Point point; m_MaskImage->TransformIndexToPhysicalPoint(index, point); if (m_Parameters.m_SignalGen.m_DoAddMotion) { if (m_Parameters.m_SignalGen.m_DoRandomizeMotion && g>0) point = m_FiberBundleWorkingCopy->TransformPoint(point.GetVnlVector(), -m_Rotation[0],-m_Rotation[1],-m_Rotation[2],-m_Translation[0],-m_Translation[1],-m_Translation[2]); else if (g>=0) point = m_FiberBundleWorkingCopy->TransformPoint(point.GetVnlVector(), -m_Rotation[0]*g,-m_Rotation[1]*g,-m_Rotation[2]*g,-m_Translation[0]*g,-m_Translation[1]*g,-m_Translation[2]*g); } if (m_Parameters.m_SignalGen.m_DoDisablePartialVolume) { int maxVolumeIndex = 0; double maxWeight = 0; for (int i=0; i1) { DoubleDwiType::IndexType newIndex; m_Parameters.m_NonFiberModelList[i]->GetVolumeFractionImage()->TransformPhysicalPointToIndex(point, newIndex); if (!m_Parameters.m_NonFiberModelList[i]->GetVolumeFractionImage()->GetLargestPossibleRegion().IsInside(newIndex)) continue; weight = m_Parameters.m_NonFiberModelList[i]->GetVolumeFractionImage()->GetPixel(newIndex); } if (weight>maxWeight) { maxWeight = weight; maxVolumeIndex = i; } } DoubleDwiType::Pointer doubleDwi = m_CompartmentImages.at(maxVolumeIndex+numFiberCompartments); DoubleDwiType::PixelType pix = doubleDwi->GetPixel(index); if (g>=0) pix[g] += m_Parameters.m_NonFiberModelList[maxVolumeIndex]->SimulateMeasurement(g); else pix += m_Parameters.m_NonFiberModelList[maxVolumeIndex]->SimulateMeasurement(); doubleDwi->SetPixel(index, pix); m_VolumeFractions.at(maxVolumeIndex+numFiberCompartments)->SetPixel(index, 1); } else { double extraAxonalVolume = m_VoxelVolume-intraAxonalVolume; // non-fiber volume double interAxonalVolume = 0; if (numFiberCompartments>1) interAxonalVolume = extraAxonalVolume * intraAxonalVolume/m_VoxelVolume; // inter-axonal fraction of non fiber compartment scales linearly with f double other = extraAxonalVolume - interAxonalVolume; // rest of compartment double singleinter = interAxonalVolume/(numFiberCompartments-1); // adjust non-fiber and intra-axonal signal for (int i=1; iGetPixel(index); if (intraAxonalVolume>0) // remove scaling by intra-axonal volume from inter-axonal compartment { if (g>=0) pix[g] /= intraAxonalVolume; else pix /= intraAxonalVolume; } if (g>=0) pix[g] *= singleinter; else pix *= singleinter; m_CompartmentImages.at(i)->SetPixel(index, pix); m_VolumeFractions.at(i)->SetPixel(index, singleinter/m_VoxelVolume); } for (int i=0; i1) { DoubleDwiType::IndexType newIndex; m_Parameters.m_NonFiberModelList[i]->GetVolumeFractionImage()->TransformPhysicalPointToIndex(point, newIndex); if (!m_Parameters.m_NonFiberModelList[i]->GetVolumeFractionImage()->GetLargestPossibleRegion().IsInside(newIndex)) continue; weight = m_Parameters.m_NonFiberModelList[i]->GetVolumeFractionImage()->GetPixel(newIndex); } DoubleDwiType::Pointer doubleDwi = m_CompartmentImages.at(i+numFiberCompartments); DoubleDwiType::PixelType pix = doubleDwi->GetPixel(index); if (g>=0) pix[g] += m_Parameters.m_NonFiberModelList[i]->SimulateMeasurement(g)*other*weight; else pix += m_Parameters.m_NonFiberModelList[i]->SimulateMeasurement()*other*weight; doubleDwi->SetPixel(index, pix); m_VolumeFractions.at(i+numFiberCompartments)->SetPixel(index, other/m_VoxelVolume*weight); } } } } template< class PixelType > itk::Point TractsToDWIImageFilter< PixelType >::GetItkPoint(double point[3]) { itk::Point itkPoint; itkPoint[0] = point[0]; itkPoint[1] = point[1]; itkPoint[2] = point[2]; return itkPoint; } template< class PixelType > itk::Vector TractsToDWIImageFilter< PixelType >::GetItkVector(double point[3]) { itk::Vector itkVector; itkVector[0] = point[0]; itkVector[1] = point[1]; itkVector[2] = point[2]; return itkVector; } template< class PixelType > vnl_vector_fixed TractsToDWIImageFilter< PixelType >::GetVnlVector(double point[3]) { vnl_vector_fixed vnlVector; vnlVector[0] = point[0]; vnlVector[1] = point[1]; vnlVector[2] = point[2]; return vnlVector; } template< class PixelType > vnl_vector_fixed TractsToDWIImageFilter< PixelType >::GetVnlVector(Vector& vector) { vnl_vector_fixed vnlVector; vnlVector[0] = vector[0]; vnlVector[1] = vector[1]; vnlVector[2] = vector[2]; return vnlVector; } template< class PixelType > double TractsToDWIImageFilter< PixelType >::RoundToNearest(double num) { return (num > 0.0) ? floor(num + 0.5) : ceil(num - 0.5); } template< class PixelType > std::string TractsToDWIImageFilter< PixelType >::GetTime() { m_TimeProbe.Stop(); unsigned long total = RoundToNearest(m_TimeProbe.GetTotal()); unsigned long hours = total/3600; unsigned long minutes = (total%3600)/60; unsigned long seconds = total%60; std::string out = ""; out.append(boost::lexical_cast(hours)); out.append(":"); out.append(boost::lexical_cast(minutes)); out.append(":"); out.append(boost::lexical_cast(seconds)); m_TimeProbe.Start(); return out; } } diff --git a/Modules/DiffusionImaging/FiberTracking/IODataStructures/FiberBundleX/mitkFiberBundleX.cpp b/Modules/DiffusionImaging/FiberTracking/IODataStructures/FiberBundleX/mitkFiberBundleX.cpp index 27f97c58ef..5f3ce15dd8 100755 --- a/Modules/DiffusionImaging/FiberTracking/IODataStructures/FiberBundleX/mitkFiberBundleX.cpp +++ b/Modules/DiffusionImaging/FiberTracking/IODataStructures/FiberBundleX/mitkFiberBundleX.cpp @@ -1,1915 +1,1871 @@ /*=================================================================== The Medical Imaging Interaction Toolkit (MITK) Copyright (c) German Cancer Research Center, Division of Medical and Biological Informatics. All rights reserved. This software is distributed WITHOUT ANY WARRANTY; without even the implied warranty of MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See LICENSE.txt or http://www.mitk.org for details. ===================================================================*/ #define _USE_MATH_DEFINES #include "mitkFiberBundleX.h" #include #include #include #include "mitkImagePixelReadAccessor.h" #include #include #include #include #include #include #include #include #include #include #include #include #include #include #include #include #include #include #include +#include +#include +#include -const char* mitk::FiberBundleX::COLORCODING_ORIENTATION_BASED = "Color_Orient"; -//const char* mitk::FiberBundleX::COLORCODING_FA_AS_OPACITY = "Color_Orient_FA_Opacity"; -const char* mitk::FiberBundleX::COLORCODING_FA_BASED = "FA_Values"; -const char* mitk::FiberBundleX::COLORCODING_CUSTOM = "custom"; const char* mitk::FiberBundleX::FIBER_ID_ARRAY = "Fiber_IDs"; using namespace std; mitk::FiberBundleX::FiberBundleX( vtkPolyData* fiberPolyData ) - : m_CurrentColorCoding(NULL) - , m_NumFibers(0) + : m_NumFibers(0) , m_FiberSampling(0) { + m_FiberWeights = vtkSmartPointer::New(); + m_FiberWeights->SetName("FIBER_WEIGHTS"); + m_FiberPolyData = vtkSmartPointer::New(); if (fiberPolyData != NULL) { m_FiberPolyData = fiberPolyData; - //m_FiberPolyData->DeepCopy(fiberPolyData); this->DoColorCodingOrientationBased(); } this->UpdateFiberGeometry(); - this->SetColorCoding(COLORCODING_ORIENTATION_BASED); this->GenerateFiberIds(); } mitk::FiberBundleX::~FiberBundleX() { } mitk::FiberBundleX::Pointer mitk::FiberBundleX::GetDeepCopy() { mitk::FiberBundleX::Pointer newFib = mitk::FiberBundleX::New(m_FiberPolyData); - newFib->SetColorCoding(m_CurrentColorCoding); + newFib->SetFiberColors(this->m_FiberColors); + newFib->SetFiberWeights(this->m_FiberWeights); return newFib; } vtkSmartPointer mitk::FiberBundleX::GeneratePolyDataByIds(std::vector fiberIds) { - MITK_DEBUG << "\n=====FINAL RESULT: fib_id ======\n"; - MITK_DEBUG << "Number of new Fibers: " << fiberIds.size(); - // iterate through the vectorcontainer hosting all desired fiber Ids - vtkSmartPointer newFiberPolyData = vtkSmartPointer::New(); vtkSmartPointer newLineSet = vtkSmartPointer::New(); vtkSmartPointer newPointSet = vtkSmartPointer::New(); - // if FA array available, initialize fa double array - // if color orient array is available init color array - vtkSmartPointer faValueArray; - vtkSmartPointer colorsT; - //colors and alpha value for each single point, RGBA = 4 components - unsigned char rgba[4] = {0,0,0,0}; - int componentSize = sizeof(rgba); - - if (m_FiberIdDataSet->GetPointData()->HasArray(COLORCODING_FA_BASED)){ - MITK_DEBUG << "FA VALUES AVAILABLE, init array for new fiberbundle"; - faValueArray = vtkSmartPointer::New(); - } - - if (m_FiberIdDataSet->GetPointData()->HasArray(COLORCODING_ORIENTATION_BASED)){ - MITK_DEBUG << "colorValues available, init array for new fiberbundle"; - colorsT = vtkUnsignedCharArray::New(); - colorsT->SetNumberOfComponents(componentSize); - colorsT->SetName(COLORCODING_ORIENTATION_BASED); - } - - - std::vector::iterator finIt = fiberIds.begin(); while ( finIt != fiberIds.end() ) { if (*finIt < 0 || *finIt>GetNumFibers()){ MITK_INFO << "FiberID can not be negative or >NumFibers!!! check id Extraction!" << *finIt; break; } vtkSmartPointer fiber = m_FiberIdDataSet->GetCell(*finIt);//->DeepCopy(fiber); - vtkSmartPointer fibPoints = fiber->GetPoints(); - vtkSmartPointer newFiber = vtkSmartPointer::New(); newFiber->GetPointIds()->SetNumberOfIds( fibPoints->GetNumberOfPoints() ); for(int i=0; iGetNumberOfPoints(); i++) { - // MITK_DEBUG << "id: " << fiber->GetPointId(i); - // MITK_DEBUG << fibPoints->GetPoint(i)[0] << " | " << fibPoints->GetPoint(i)[1] << " | " << fibPoints->GetPoint(i)[2]; newFiber->GetPointIds()->SetId(i, newPointSet->GetNumberOfPoints()); newPointSet->InsertNextPoint(fibPoints->GetPoint(i)[0], fibPoints->GetPoint(i)[1], fibPoints->GetPoint(i)[2]); - - - if (m_FiberIdDataSet->GetPointData()->HasArray(COLORCODING_FA_BASED)){ - // MITK_DEBUG << m_FiberIdDataSet->GetPointData()->GetArray(FA_VALUE_ARRAY)->GetTuple(fiber->GetPointId(i)); - } - - if (m_FiberIdDataSet->GetPointData()->HasArray(COLORCODING_ORIENTATION_BASED)){ - // MITK_DEBUG << "ColorValue: " << m_FiberIdDataSet->GetPointData()->GetArray(COLORCODING_ORIENTATION_BASED)->GetTuple(fiber->GetPointId(i))[0]; - } } newLineSet->InsertNextCell(newFiber); ++finIt; } newFiberPolyData->SetPoints(newPointSet); newFiberPolyData->SetLines(newLineSet); - MITK_DEBUG << "new fiberbundle polydata points: " << newFiberPolyData->GetNumberOfPoints(); - MITK_DEBUG << "new fiberbundle polydata lines: " << newFiberPolyData->GetNumberOfLines(); - MITK_DEBUG << "=====================\n"; - - // mitk::FiberBundleX::Pointer newFib = mitk::FiberBundleX::New(newFiberPolyData); return newFiberPolyData; } // merge two fiber bundles mitk::FiberBundleX::Pointer mitk::FiberBundleX::AddBundle(mitk::FiberBundleX* fib) { if (fib==NULL) { MITK_WARN << "trying to call AddBundle with NULL argument"; return NULL; } MITK_INFO << "Adding fibers"; vtkSmartPointer vNewPolyData = vtkSmartPointer::New(); vtkSmartPointer vNewLines = vtkSmartPointer::New(); vtkSmartPointer vNewPoints = vtkSmartPointer::New(); // add current fiber bundle + vtkSmartPointer weights = vtkSmartPointer::New(); + weights->SetNumberOfValues(this->GetNumFibers()+fib->GetNumFibers()); + + unsigned int counter = 0; for (int i=0; iGetNumberOfCells(); i++) { vtkCell* cell = m_FiberPolyData->GetCell(i); int numPoints = cell->GetNumberOfPoints(); vtkPoints* points = cell->GetPoints(); vtkSmartPointer container = vtkSmartPointer::New(); for (int j=0; jGetPoint(j, p); vtkIdType id = vNewPoints->InsertNextPoint(p); container->GetPointIds()->InsertNextId(id); } + weights->InsertValue(counter, this->GetFiberWeight(i)); vNewLines->InsertNextCell(container); + counter++; } // add new fiber bundle for (int i=0; iGetFiberPolyData()->GetNumberOfCells(); i++) { vtkCell* cell = fib->GetFiberPolyData()->GetCell(i); int numPoints = cell->GetNumberOfPoints(); vtkPoints* points = cell->GetPoints(); vtkSmartPointer container = vtkSmartPointer::New(); for (int j=0; jGetPoint(j, p); vtkIdType id = vNewPoints->InsertNextPoint(p); container->GetPointIds()->InsertNextId(id); } + weights->InsertValue(counter, fib->GetFiberWeight(i)); vNewLines->InsertNextCell(container); + counter++; } // initialize polydata vNewPolyData->SetPoints(vNewPoints); vNewPolyData->SetLines(vNewLines); // initialize fiber bundle mitk::FiberBundleX::Pointer newFib = mitk::FiberBundleX::New(vNewPolyData); + newFib->SetFiberWeights(weights); return newFib; } // subtract two fiber bundles mitk::FiberBundleX::Pointer mitk::FiberBundleX::SubtractBundle(mitk::FiberBundleX* fib) { MITK_INFO << "Subtracting fibers"; vtkSmartPointer vNewPolyData = vtkSmartPointer::New(); vtkSmartPointer vNewLines = vtkSmartPointer::New(); vtkSmartPointer vNewPoints = vtkSmartPointer::New(); // iterate over current fibers boost::progress_display disp(m_NumFibers); for( int i=0; iGetCell(i); int numPoints = cell->GetNumberOfPoints(); vtkPoints* points = cell->GetPoints(); if (points==NULL || numPoints<=0) continue; int numFibers2 = fib->GetNumFibers(); bool contained = false; for( int i2=0; i2GetFiberPolyData()->GetCell(i2); int numPoints2 = cell2->GetNumberOfPoints(); vtkPoints* points2 = cell2->GetPoints(); if (points2==NULL)// || numPoints2<=0) continue; // check endpoints if (numPoints2==numPoints) { itk::Point point_start = GetItkPoint(points->GetPoint(0)); itk::Point point_end = GetItkPoint(points->GetPoint(numPoints-1)); itk::Point point2_start = GetItkPoint(points2->GetPoint(0)); itk::Point point2_end = GetItkPoint(points2->GetPoint(numPoints2-1)); if ((point_start.SquaredEuclideanDistanceTo(point2_start)<=mitk::eps && point_end.SquaredEuclideanDistanceTo(point2_end)<=mitk::eps) || (point_start.SquaredEuclideanDistanceTo(point2_end)<=mitk::eps && point_end.SquaredEuclideanDistanceTo(point2_start)<=mitk::eps)) { // further checking ??? contained = true; break; } } } // add to result because fiber is not subtracted if (!contained) { vtkSmartPointer container = vtkSmartPointer::New(); for( int j=0; jInsertNextPoint(points->GetPoint(j)); container->GetPointIds()->InsertNextId(id); } vNewLines->InsertNextCell(container); } } if(vNewLines->GetNumberOfCells()==0) return NULL; // initialize polydata vNewPolyData->SetPoints(vNewPoints); vNewPolyData->SetLines(vNewLines); // initialize fiber bundle return mitk::FiberBundleX::New(vNewPolyData); } itk::Point mitk::FiberBundleX::GetItkPoint(double point[3]) { itk::Point itkPoint; itkPoint[0] = point[0]; itkPoint[1] = point[1]; itkPoint[2] = point[2]; return itkPoint; } /* * set polydata (additional flag to recompute fiber geometry, default = true) */ void mitk::FiberBundleX::SetFiberPolyData(vtkSmartPointer fiberPD, bool updateGeometry) { if (fiberPD == NULL) this->m_FiberPolyData = vtkSmartPointer::New(); else { m_FiberPolyData->DeepCopy(fiberPD); DoColorCodingOrientationBased(); } m_NumFibers = m_FiberPolyData->GetNumberOfLines(); if (updateGeometry) UpdateFiberGeometry(); - SetColorCoding(COLORCODING_ORIENTATION_BASED); GenerateFiberIds(); } /* * return vtkPolyData */ vtkSmartPointer mitk::FiberBundleX::GetFiberPolyData() const { return m_FiberPolyData; } void mitk::FiberBundleX::DoColorCodingOrientationBased() { //===== FOR WRITING A TEST ======================== // colorT size == tupelComponents * tupelElements // compare color results // to cover this code 100% also polydata needed, where colorarray already exists // + one fiber with exactly 1 point // + one fiber with 0 points //================================================= - /* make sure that processing colorcoding is only called when necessary */ - if ( m_FiberPolyData->GetPointData()->HasArray(COLORCODING_ORIENTATION_BASED) && - m_FiberPolyData->GetNumberOfPoints() == - m_FiberPolyData->GetPointData()->GetArray(COLORCODING_ORIENTATION_BASED)->GetNumberOfTuples() ) - { - // fiberstructure is already colorcoded - MITK_DEBUG << " NO NEED TO REGENERATE COLORCODING! " ; - this->ResetFiberOpacity(); - this->SetColorCoding(COLORCODING_ORIENTATION_BASED); - return; - } - - /* Finally, execute color calculation */ vtkPoints* extrPoints = NULL; extrPoints = m_FiberPolyData->GetPoints(); int numOfPoints = 0; if (extrPoints!=NULL) numOfPoints = extrPoints->GetNumberOfPoints(); //colors and alpha value for each single point, RGBA = 4 components unsigned char rgba[4] = {0,0,0,0}; - // int componentSize = sizeof(rgba); int componentSize = 4; + m_FiberColors = vtkSmartPointer::New(); + m_FiberColors->Allocate(numOfPoints * componentSize); + m_FiberColors->SetNumberOfComponents(componentSize); + m_FiberColors->SetName("FIBER_COLORS"); - vtkSmartPointer colorsT = vtkSmartPointer::New(); - colorsT->Allocate(numOfPoints * componentSize); - colorsT->SetNumberOfComponents(componentSize); - colorsT->SetName(COLORCODING_ORIENTATION_BASED); - - /* checkpoint: does polydata contain any fibers */ int numOfFibers = m_FiberPolyData->GetNumberOfLines(); if (numOfFibers < 1) return; /* extract single fibers of fiberBundle */ vtkCellArray* fiberList = m_FiberPolyData->GetLines(); fiberList->InitTraversal(); for (int fi=0; fiGetNextCell(pointsPerFiber, idList); /* single fiber checkpoints: is number of points valid */ if (pointsPerFiber > 1) { /* operate on points of single fiber */ for (int i=0; i 0) { /* The color value of the current point is influenced by the previous point and next point. */ vnl_vector_fixed< double, 3 > currentPntvtk(extrPoints->GetPoint(idList[i])[0], extrPoints->GetPoint(idList[i])[1],extrPoints->GetPoint(idList[i])[2]); vnl_vector_fixed< double, 3 > nextPntvtk(extrPoints->GetPoint(idList[i+1])[0], extrPoints->GetPoint(idList[i+1])[1], extrPoints->GetPoint(idList[i+1])[2]); vnl_vector_fixed< double, 3 > prevPntvtk(extrPoints->GetPoint(idList[i-1])[0], extrPoints->GetPoint(idList[i-1])[1], extrPoints->GetPoint(idList[i-1])[2]); vnl_vector_fixed< double, 3 > diff1; diff1 = currentPntvtk - nextPntvtk; vnl_vector_fixed< double, 3 > diff2; diff2 = currentPntvtk - prevPntvtk; vnl_vector_fixed< double, 3 > diff; diff = (diff1 - diff2) / 2.0; diff.normalize(); rgba[0] = (unsigned char) (255.0 * std::fabs(diff[0])); rgba[1] = (unsigned char) (255.0 * std::fabs(diff[1])); rgba[2] = (unsigned char) (255.0 * std::fabs(diff[2])); rgba[3] = (unsigned char) (255.0); } else if (i==0) { /* First point has no previous point, therefore only diff1 is taken */ vnl_vector_fixed< double, 3 > currentPntvtk(extrPoints->GetPoint(idList[i])[0], extrPoints->GetPoint(idList[i])[1],extrPoints->GetPoint(idList[i])[2]); vnl_vector_fixed< double, 3 > nextPntvtk(extrPoints->GetPoint(idList[i+1])[0], extrPoints->GetPoint(idList[i+1])[1], extrPoints->GetPoint(idList[i+1])[2]); vnl_vector_fixed< double, 3 > diff1; diff1 = currentPntvtk - nextPntvtk; diff1.normalize(); rgba[0] = (unsigned char) (255.0 * std::fabs(diff1[0])); rgba[1] = (unsigned char) (255.0 * std::fabs(diff1[1])); rgba[2] = (unsigned char) (255.0 * std::fabs(diff1[2])); rgba[3] = (unsigned char) (255.0); } else if (i==pointsPerFiber-1) { /* Last point has no next point, therefore only diff2 is taken */ vnl_vector_fixed< double, 3 > currentPntvtk(extrPoints->GetPoint(idList[i])[0], extrPoints->GetPoint(idList[i])[1],extrPoints->GetPoint(idList[i])[2]); vnl_vector_fixed< double, 3 > prevPntvtk(extrPoints->GetPoint(idList[i-1])[0], extrPoints->GetPoint(idList[i-1])[1], extrPoints->GetPoint(idList[i-1])[2]); vnl_vector_fixed< double, 3 > diff2; diff2 = currentPntvtk - prevPntvtk; diff2.normalize(); rgba[0] = (unsigned char) (255.0 * std::fabs(diff2[0])); rgba[1] = (unsigned char) (255.0 * std::fabs(diff2[1])); rgba[2] = (unsigned char) (255.0 * std::fabs(diff2[2])); rgba[3] = (unsigned char) (255.0); - } - colorsT->InsertTupleValue(idList[i], rgba); - } //end for loop + m_FiberColors->InsertTupleValue(idList[i], rgba); + } } else if (pointsPerFiber == 1) { /* a single point does not define a fiber (use vertex mechanisms instead */ continue; } else { MITK_DEBUG << "Fiber with 0 points detected... please check your tractography algorithm!" ; continue; } - }//end for loop - - m_FiberPolyData->GetPointData()->AddArray(colorsT); - - this->SetColorCoding(COLORCODING_ORIENTATION_BASED); - - //mini test, shall be ported to MITK TESTINGS! - if (colorsT->GetSize() != numOfPoints*componentSize) - MITK_DEBUG << "ALLOCATION ERROR IN INITIATING COLOR ARRAY"; -} - -void mitk::FiberBundleX::DoColorCodingFaBased() -{ - if(m_FiberPolyData->GetPointData()->HasArray(COLORCODING_FA_BASED) != 1 ) - return; - - this->SetColorCoding(COLORCODING_FA_BASED); - // this->GenerateFiberIds(); + } + m_UpdateTime3D.Modified(); + m_UpdateTime2D.Modified(); } -void mitk::FiberBundleX::DoUseFaFiberOpacity() +void mitk::FiberBundleX::SetFiberOpacity(vtkDoubleArray* FAValArray) { - if(m_FiberPolyData->GetPointData()->HasArray(COLORCODING_FA_BASED) != 1 ) - return; - - if(m_FiberPolyData->GetPointData()->HasArray(COLORCODING_ORIENTATION_BASED) != 1 ) - return; - - vtkDoubleArray* FAValArray = (vtkDoubleArray*) m_FiberPolyData->GetPointData()->GetArray(COLORCODING_FA_BASED); - vtkUnsignedCharArray* ColorArray = dynamic_cast (m_FiberPolyData->GetPointData()->GetArray(COLORCODING_ORIENTATION_BASED)); - - for(long i=0; iGetNumberOfTuples(); i++) { + for(long i=0; iGetNumberOfTuples(); i++) + { double faValue = FAValArray->GetValue(i); faValue = faValue * 255.0; - ColorArray->SetComponent(i,3, (unsigned char) faValue ); + m_FiberColors->SetComponent(i,3, (unsigned char) faValue ); } - - this->SetColorCoding(COLORCODING_ORIENTATION_BASED); - // this->GenerateFiberIds(); + m_UpdateTime3D.Modified(); + m_UpdateTime2D.Modified(); } -void mitk::FiberBundleX::ResetFiberOpacity() { - vtkUnsignedCharArray* ColorArray = dynamic_cast (m_FiberPolyData->GetPointData()->GetArray(COLORCODING_ORIENTATION_BASED)); - if (ColorArray==NULL) - return; - for(long i=0; iGetNumberOfTuples(); i++) - ColorArray->SetComponent(i,3, 255.0 ); +void mitk::FiberBundleX::ResetFiberOpacity() +{ + for(long i=0; iGetNumberOfTuples(); i++) + m_FiberColors->SetComponent(i,3, 255.0 ); + m_UpdateTime3D.Modified(); + m_UpdateTime2D.Modified(); } -void mitk::FiberBundleX::SetFAMap(mitk::Image::Pointer FAimage) +void mitk::FiberBundleX::ColorFibersByScalarMap(mitk::Image::Pointer FAimage, bool opacity) { - mitkPixelTypeMultiplex1( SetFAMap, FAimage->GetPixelType(), FAimage ); + mitkPixelTypeMultiplex2( ColorFibersByScalarMap, FAimage->GetPixelType(), FAimage, opacity ); + m_UpdateTime3D.Modified(); + m_UpdateTime2D.Modified(); } template -void mitk::FiberBundleX::SetFAMap(const mitk::PixelType, mitk::Image::Pointer FAimage) +void mitk::FiberBundleX::ColorFibersByScalarMap(const mitk::PixelType, mitk::Image::Pointer image, bool opacity) { - MITK_DEBUG << "SetFAMap"; - vtkSmartPointer faValues = vtkSmartPointer::New(); - faValues->SetName(COLORCODING_FA_BASED); - faValues->Allocate(m_FiberPolyData->GetNumberOfPoints()); - faValues->SetNumberOfValues(m_FiberPolyData->GetNumberOfPoints()); + m_FiberColors = vtkSmartPointer::New(); + m_FiberColors->Allocate(m_FiberPolyData->GetNumberOfPoints() * 4); + m_FiberColors->SetNumberOfComponents(4); + m_FiberColors->SetName("FIBER_COLORS"); - mitk::ImagePixelReadAccessor readFAimage (FAimage, FAimage->GetVolumeData(0)); + mitk::ImagePixelReadAccessor readimage(image, image->GetVolumeData(0)); + unsigned char rgba[4] = {0,0,0,0}; vtkPoints* pointSet = m_FiberPolyData->GetPoints(); + + mitk::LookupTable::Pointer mitkLookup = mitk::LookupTable::New(); + vtkSmartPointer lookupTable = vtkSmartPointer::New(); + lookupTable->SetTableRange(0.0, 0.8); + lookupTable->Build(); + mitkLookup->SetVtkLookupTable(lookupTable); + mitkLookup->SetType(mitk::LookupTable::JET); + for(long i=0; iGetNumberOfPoints(); ++i) { Point3D px; px[0] = pointSet->GetPoint(i)[0]; px[1] = pointSet->GetPoint(i)[1]; px[2] = pointSet->GetPoint(i)[2]; - double faPixelValue = 1-readFAimage.GetPixelByWorldCoordinates(px); - faValues->InsertValue(i, faPixelValue); - } + double pixelValue = readimage.GetPixelByWorldCoordinates(px); - m_FiberPolyData->GetPointData()->AddArray(faValues); - this->GenerateFiberIds(); - - if(m_FiberPolyData->GetPointData()->HasArray(COLORCODING_FA_BASED)) - MITK_DEBUG << "FA VALUE ARRAY SET"; + double color[3]; + lookupTable->GetColor(pixelValue, color); + rgba[0] = (unsigned char) (255.0 * color[0]); + rgba[1] = (unsigned char) (255.0 * color[1]); + rgba[2] = (unsigned char) (255.0 * color[2]); + if (opacity) + rgba[3] = (unsigned char) (255.0 * pixelValue); + else + rgba[3] = (unsigned char) (255.0); + m_FiberColors->InsertTupleValue(i, rgba); + } + m_UpdateTime3D.Modified(); + m_UpdateTime2D.Modified(); } +void mitk::FiberBundleX::SetFiberColors(float r, float g, float b, float alpha) +{ + m_FiberColors = vtkSmartPointer::New(); + m_FiberColors->Allocate(m_FiberPolyData->GetNumberOfPoints() * 4); + m_FiberColors->SetNumberOfComponents(4); + m_FiberColors->SetName("FIBER_COLORS"); + + unsigned char rgba[4] = {0,0,0,0}; + for(long i=0; iGetNumberOfPoints(); ++i) + { + rgba[0] = (unsigned char) r; + rgba[1] = (unsigned char) g; + rgba[2] = (unsigned char) b; + rgba[3] = (unsigned char) alpha; + m_FiberColors->InsertTupleValue(i, rgba); + } + m_UpdateTime3D.Modified(); + m_UpdateTime2D.Modified(); +} void mitk::FiberBundleX::GenerateFiberIds() { if (m_FiberPolyData == NULL) return; vtkSmartPointer idFiberFilter = vtkSmartPointer::New(); idFiberFilter->SetInputData(m_FiberPolyData); idFiberFilter->CellIdsOn(); // idFiberFilter->PointIdsOn(); // point id's are not needed idFiberFilter->SetIdsArrayName(FIBER_ID_ARRAY); idFiberFilter->FieldDataOn(); idFiberFilter->Update(); m_FiberIdDataSet = idFiberFilter->GetOutput(); - MITK_DEBUG << "Generating Fiber Ids...[done] | " << m_FiberIdDataSet->GetNumberOfCells(); - } mitk::FiberBundleX::Pointer mitk::FiberBundleX::ExtractFiberSubset(ItkUcharImgType* mask, bool anyPoint, bool invert) { vtkSmartPointer polyData = m_FiberPolyData; if (anyPoint) { float minSpacing = 1; if(mask->GetSpacing()[0]GetSpacing()[1] && mask->GetSpacing()[0]GetSpacing()[2]) minSpacing = mask->GetSpacing()[0]; else if (mask->GetSpacing()[1] < mask->GetSpacing()[2]) minSpacing = mask->GetSpacing()[1]; else minSpacing = mask->GetSpacing()[2]; mitk::FiberBundleX::Pointer fibCopy = this->GetDeepCopy(); fibCopy->ResampleSpline(minSpacing/5); polyData = fibCopy->GetFiberPolyData(); } vtkSmartPointer vtkNewPoints = vtkSmartPointer::New(); vtkSmartPointer vtkNewCells = vtkSmartPointer::New(); MITK_INFO << "Extracting fibers"; boost::progress_display disp(m_NumFibers); for (int i=0; iGetCell(i); int numPoints = cell->GetNumberOfPoints(); vtkPoints* points = cell->GetPoints(); vtkCell* cellOriginal = m_FiberPolyData->GetCell(i); int numPointsOriginal = cellOriginal->GetNumberOfPoints(); vtkPoints* pointsOriginal = cellOriginal->GetPoints(); vtkSmartPointer container = vtkSmartPointer::New(); if (numPoints>1 && numPointsOriginal) { if (anyPoint) { if (!invert) { for (int j=0; jGetPoint(j); itk::Point itkP; itkP[0] = p[0]; itkP[1] = p[1]; itkP[2] = p[2]; itk::Index<3> idx; mask->TransformPhysicalPointToIndex(itkP, idx); if ( mask->GetPixel(idx)>0 && mask->GetLargestPossibleRegion().IsInside(idx) ) { for (int k=0; kGetPoint(k); vtkIdType id = vtkNewPoints->InsertNextPoint(p); container->GetPointIds()->InsertNextId(id); } break; } } } else { bool includeFiber = true; for (int j=0; jGetPoint(j); itk::Point itkP; itkP[0] = p[0]; itkP[1] = p[1]; itkP[2] = p[2]; itk::Index<3> idx; mask->TransformPhysicalPointToIndex(itkP, idx); if ( mask->GetPixel(idx)>0 && mask->GetLargestPossibleRegion().IsInside(idx) ) { includeFiber = false; break; } } if (includeFiber) { for (int k=0; kGetPoint(k); vtkIdType id = vtkNewPoints->InsertNextPoint(p); container->GetPointIds()->InsertNextId(id); } } } } else { double* start = pointsOriginal->GetPoint(0); itk::Point itkStart; itkStart[0] = start[0]; itkStart[1] = start[1]; itkStart[2] = start[2]; itk::Index<3> idxStart; mask->TransformPhysicalPointToIndex(itkStart, idxStart); double* end = pointsOriginal->GetPoint(numPointsOriginal-1); itk::Point itkEnd; itkEnd[0] = end[0]; itkEnd[1] = end[1]; itkEnd[2] = end[2]; itk::Index<3> idxEnd; mask->TransformPhysicalPointToIndex(itkEnd, idxEnd); if ( mask->GetPixel(idxStart)>0 && mask->GetPixel(idxEnd)>0 && mask->GetLargestPossibleRegion().IsInside(idxStart) && mask->GetLargestPossibleRegion().IsInside(idxEnd) ) { for (int j=0; jGetPoint(j); vtkIdType id = vtkNewPoints->InsertNextPoint(p); container->GetPointIds()->InsertNextId(id); } } } } vtkNewCells->InsertNextCell(container); } if (vtkNewCells->GetNumberOfCells()<=0) return NULL; vtkSmartPointer newPolyData = vtkSmartPointer::New(); newPolyData->SetPoints(vtkNewPoints); newPolyData->SetLines(vtkNewCells); return mitk::FiberBundleX::New(newPolyData); } mitk::FiberBundleX::Pointer mitk::FiberBundleX::RemoveFibersOutside(ItkUcharImgType* mask, bool invert) { float minSpacing = 1; if(mask->GetSpacing()[0]GetSpacing()[1] && mask->GetSpacing()[0]GetSpacing()[2]) minSpacing = mask->GetSpacing()[0]; else if (mask->GetSpacing()[1] < mask->GetSpacing()[2]) minSpacing = mask->GetSpacing()[1]; else minSpacing = mask->GetSpacing()[2]; mitk::FiberBundleX::Pointer fibCopy = this->GetDeepCopy(); fibCopy->ResampleSpline(minSpacing/10); vtkSmartPointer polyData =fibCopy->GetFiberPolyData(); vtkSmartPointer vtkNewPoints = vtkSmartPointer::New(); vtkSmartPointer vtkNewCells = vtkSmartPointer::New(); MITK_INFO << "Cutting fibers"; boost::progress_display disp(m_NumFibers); for (int i=0; iGetCell(i); int numPoints = cell->GetNumberOfPoints(); vtkPoints* points = cell->GetPoints(); vtkSmartPointer container = vtkSmartPointer::New(); if (numPoints>1) { int newNumPoints = 0; for (int j=0; jGetPoint(j); itk::Point itkP; itkP[0] = p[0]; itkP[1] = p[1]; itkP[2] = p[2]; itk::Index<3> idx; mask->TransformPhysicalPointToIndex(itkP, idx); if ( mask->GetPixel(idx)>0 && mask->GetLargestPossibleRegion().IsInside(idx) && !invert ) { vtkIdType id = vtkNewPoints->InsertNextPoint(p); container->GetPointIds()->InsertNextId(id); newNumPoints++; } else if ( (mask->GetPixel(idx)<=0 || !mask->GetLargestPossibleRegion().IsInside(idx)) && invert ) { vtkIdType id = vtkNewPoints->InsertNextPoint(p); container->GetPointIds()->InsertNextId(id); newNumPoints++; } else if (newNumPoints>0) { vtkNewCells->InsertNextCell(container); newNumPoints = 0; container = vtkSmartPointer::New(); } } if (newNumPoints>0) vtkNewCells->InsertNextCell(container); } } if (vtkNewCells->GetNumberOfCells()<=0) return NULL; vtkSmartPointer newPolyData = vtkSmartPointer::New(); newPolyData->SetPoints(vtkNewPoints); newPolyData->SetLines(vtkNewCells); mitk::FiberBundleX::Pointer newFib = mitk::FiberBundleX::New(newPolyData); newFib->ResampleSpline(minSpacing/2); return newFib; } mitk::FiberBundleX::Pointer mitk::FiberBundleX::ExtractFiberSubset(BaseData* roi) { if (roi==NULL || !(dynamic_cast(roi) || dynamic_cast(roi)) ) return NULL; std::vector tmp = ExtractFiberIdSubset(roi); if (tmp.size()<=0) return mitk::FiberBundleX::New(); vtkSmartPointer pTmp = GeneratePolyDataByIds(tmp); return mitk::FiberBundleX::New(pTmp); } std::vector mitk::FiberBundleX::ExtractFiberIdSubset(BaseData* roi) { std::vector result; if (roi==NULL) return result; mitk::PlanarFigureComposite::Pointer pfc = dynamic_cast(roi); if (!pfc.IsNull()) // handle composite { switch (pfc->getOperationType()) { case 0: // AND { result = this->ExtractFiberIdSubset(pfc->getChildAt(0)); std::vector::iterator it; for (int i=1; igetNumberOfChildren(); ++i) { std::vector inRoi = this->ExtractFiberIdSubset(pfc->getChildAt(i)); std::vector rest(std::min(result.size(),inRoi.size())); it = std::set_intersection(result.begin(), result.end(), inRoi.begin(), inRoi.end(), rest.begin() ); rest.resize( it - rest.begin() ); result = rest; } break; } case 1: // OR { result = ExtractFiberIdSubset(pfc->getChildAt(0)); std::vector::iterator it; for (int i=1; igetNumberOfChildren(); ++i) { it = result.end(); std::vector inRoi = ExtractFiberIdSubset(pfc->getChildAt(i)); result.insert(it, inRoi.begin(), inRoi.end()); } // remove duplicates sort(result.begin(), result.end()); it = unique(result.begin(), result.end()); result.resize( it - result.begin() ); break; } case 2: // NOT { for(long i=0; iGetNumFibers(); i++) result.push_back(i); std::vector::iterator it; for (long i=0; igetNumberOfChildren(); ++i) { std::vector inRoi = ExtractFiberIdSubset(pfc->getChildAt(i)); std::vector rest(result.size()-inRoi.size()); it = std::set_difference(result.begin(), result.end(), inRoi.begin(), inRoi.end(), rest.begin() ); rest.resize( it - rest.begin() ); result = rest; } break; } } } else if ( dynamic_cast(roi) ) // actual extraction { mitk::PlanarFigure::Pointer planarFigure = dynamic_cast(roi); Vector3D planeNormal = planarFigure->GetPlaneGeometry()->GetNormal(); planeNormal.Normalize(); Point3D planeOrigin = planarFigure->GetPlaneGeometry()->GetOrigin(); // define cutting plane by ROI geometry (PlanarFigure) vtkSmartPointer plane = vtkSmartPointer::New(); plane->SetOrigin(planeOrigin[0],planeOrigin[1],planeOrigin[2]); plane->SetNormal(planeNormal[0],planeNormal[1],planeNormal[2]); // get all fiber/plane intersection points vtkSmartPointer clipper = vtkSmartPointer::New(); clipper->SetInputData(m_FiberIdDataSet); clipper->SetClipFunction(plane); clipper->GenerateClipScalarsOn(); clipper->GenerateClippedOutputOn(); clipper->Update(); vtkSmartPointer clipperout = clipper->GetClippedOutput(); if (!clipperout->GetCellData()->HasArray(FIBER_ID_ARRAY)) return result; vtkSmartPointer distanceList = clipperout->GetPointData()->GetScalars(); vtkIdType numPoints = distanceList->GetNumberOfTuples(); std::vector pointsOnPlane; pointsOnPlane.reserve(numPoints); for (int i=0; iGetTuple(i)[0]; // check if point is on plane if (distance >= -0.01 && distance <= 0.01) pointsOnPlane.push_back(i); } if (pointsOnPlane.empty()) return result; // get all point IDs inside the ROI std::vector pointsInROI; pointsInROI.reserve(pointsOnPlane.size()); mitk::PlanarCircle::Pointer circleName = mitk::PlanarCircle::New(); mitk::PlanarPolygon::Pointer polyName = mitk::PlanarPolygon::New(); if ( planarFigure->GetNameOfClass() == circleName->GetNameOfClass() ) { //calculate circle radius mitk::Point3D V1w = planarFigure->GetWorldControlPoint(0); //centerPoint mitk::Point3D V2w = planarFigure->GetWorldControlPoint(1); //radiusPoint double radius = V1w.EuclideanDistanceTo(V2w); radius *= radius; for (unsigned int i=0; iGetPoint(pointsOnPlane[i], p); double dist = (p[0]-V1w[0])*(p[0]-V1w[0])+(p[1]-V1w[1])*(p[1]-V1w[1])+(p[2]-V1w[2])*(p[2]-V1w[2]); if( dist <= radius) pointsInROI.push_back(pointsOnPlane[i]); } } else if ( planarFigure->GetNameOfClass() == polyName->GetNameOfClass() ) { //create vtkPolygon using controlpoints from planarFigure polygon vtkSmartPointer polygonVtk = vtkSmartPointer::New(); for (unsigned int i=0; iGetNumberOfControlPoints(); ++i) { itk::Point p = planarFigure->GetWorldControlPoint(i); polygonVtk->GetPoints()->InsertNextPoint(p[0], p[1], p[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); for (unsigned int i=0; iGetPoint(pointsOnPlane[i], p); int isInPolygon = polygonVtk->PointInPolygon(p, polygonVtk->GetPoints()->GetNumberOfPoints(), static_cast(polygonVtk->GetPoints()->GetData()->GetVoidPointer(0)), bounds, n); if( isInPolygon ) pointsInROI.push_back(pointsOnPlane[i]); } } if (pointsInROI.empty()) return result; // get the fiber IDs corresponding to all clipped points std::vector< long > pointToFiberMap; // pointToFiberMap[PointID] = FiberIndex pointToFiberMap.resize(clipperout->GetNumberOfPoints()); vtkCellArray* clipperlines = clipperout->GetLines(); clipperlines->InitTraversal(); for (int i=0, ic=0 ; iGetNumberOfCells(); i++, ic+=3) { // ic is the index counter for the cells hosting the desired information. each cell consits of 3 items. long fiberID = clipperout->GetCellData()->GetArray(FIBER_ID_ARRAY)->GetTuple(i)[0]; vtkIdType numPoints; vtkIdType* pointIDs; clipperlines->GetCell(ic, numPoints, pointIDs); for (long j=0; j=0) result.push_back( pointToFiberMap[pointsInROI[k]] ); else MITK_INFO << "ERROR in ExtractFiberIdSubset; impossible fiber id detected"; } // remove duplicates std::vector::iterator it; sort(result.begin(), result.end()); it = unique (result.begin(), result.end()); result.resize( it - result.begin() ); } return result; } void mitk::FiberBundleX::UpdateFiberGeometry() { vtkSmartPointer cleaner = vtkSmartPointer::New(); cleaner->SetInputData(m_FiberPolyData); cleaner->PointMergingOff(); cleaner->Update(); m_FiberPolyData = cleaner->GetOutput(); m_FiberLengths.clear(); m_MeanFiberLength = 0; m_MedianFiberLength = 0; m_LengthStDev = 0; m_NumFibers = m_FiberPolyData->GetNumberOfCells(); + if (m_FiberColors==NULL || m_FiberColors->GetNumberOfTuples()!=m_FiberPolyData->GetNumberOfPoints()) + this->DoColorCodingOrientationBased(); + + if (m_FiberWeights->GetSize()!=m_NumFibers) + { + m_FiberWeights = vtkSmartPointer::New(); + m_FiberWeights->SetName("FIBER_WEIGHTS"); + m_FiberWeights->SetNumberOfValues(m_NumFibers); + this->SetFiberWeights(1); + } + if (m_NumFibers<=0) // no fibers present; apply default geometry { m_MinFiberLength = 0; m_MaxFiberLength = 0; mitk::Geometry3D::Pointer geometry = mitk::Geometry3D::New(); geometry->SetImageGeometry(false); float b[] = {0, 1, 0, 1, 0, 1}; geometry->SetFloatBounds(b); SetGeometry(geometry); return; } double b[6]; m_FiberPolyData->GetBounds(b); // calculate statistics for (int i=0; iGetNumberOfCells(); i++) { vtkCell* cell = m_FiberPolyData->GetCell(i); int p = cell->GetNumberOfPoints(); vtkPoints* points = cell->GetPoints(); float length = 0; for (int j=0; jGetPoint(j, p1); double p2[3]; points->GetPoint(j+1, p2); float dist = std::sqrt((p1[0]-p2[0])*(p1[0]-p2[0])+(p1[1]-p2[1])*(p1[1]-p2[1])+(p1[2]-p2[2])*(p1[2]-p2[2])); length += dist; } m_FiberLengths.push_back(length); m_MeanFiberLength += length; if (i==0) { m_MinFiberLength = length; m_MaxFiberLength = length; } else { if (lengthm_MaxFiberLength) m_MaxFiberLength = length; } } m_MeanFiberLength /= m_NumFibers; std::vector< float > sortedLengths = m_FiberLengths; std::sort(sortedLengths.begin(), sortedLengths.end()); for (int i=0; i1) m_LengthStDev /= (m_NumFibers-1); else m_LengthStDev = 0; m_LengthStDev = std::sqrt(m_LengthStDev); m_MedianFiberLength = sortedLengths.at(m_NumFibers/2); mitk::Geometry3D::Pointer geometry = mitk::Geometry3D::New(); geometry->SetFloatBounds(b); this->SetGeometry(geometry); m_UpdateTime3D.Modified(); m_UpdateTime2D.Modified(); } -std::vector mitk::FiberBundleX::GetAvailableColorCodings() +float mitk::FiberBundleX::GetFiberWeight(unsigned int fiber) { - std::vector availableColorCodings; - int numColors = m_FiberPolyData->GetPointData()->GetNumberOfArrays(); - for(int i=0; iGetPointData()->GetArrayName(i)); - } - - //this controlstructure shall be implemented by the calling method - if (availableColorCodings.empty()) - MITK_DEBUG << "no colorcodings available in fiberbundleX"; - - return availableColorCodings; + return m_FiberWeights->GetValue(fiber); } - -char* mitk::FiberBundleX::GetCurrentColorCoding() +void mitk::FiberBundleX::SetFiberWeights(float newWeight) { - return m_CurrentColorCoding; + for (int i=0; iGetSize(); i++) + m_FiberWeights->SetValue(i, newWeight); } -void mitk::FiberBundleX::SetColorCoding(const char* requestedColorCoding) +void mitk::FiberBundleX::SetFiberWeights(vtkSmartPointer weights) { - if (requestedColorCoding==NULL) + if (m_NumFibers!=weights->GetSize()) return; - if( strcmp (COLORCODING_ORIENTATION_BASED,requestedColorCoding) == 0 ) { - this->m_CurrentColorCoding = (char*) COLORCODING_ORIENTATION_BASED; + for (int i=0; iGetSize(); i++) + m_FiberWeights->SetValue(i, weights->GetValue(i)); - } else if( strcmp (COLORCODING_FA_BASED,requestedColorCoding) == 0 ) { - this->m_CurrentColorCoding = (char*) COLORCODING_FA_BASED; + m_FiberWeights->SetName("FIBER_WEIGHTS"); +} - } else if( strcmp (COLORCODING_CUSTOM,requestedColorCoding) == 0 ) { - this->m_CurrentColorCoding = (char*) COLORCODING_CUSTOM; +void mitk::FiberBundleX::SetFiberWeight(unsigned int fiber, float weight) +{ + m_FiberWeights->SetValue(fiber, weight); +} - } else { - MITK_DEBUG << "FIBERBUNDLE X: UNKNOWN COLORCODING in FIBERBUNDLEX Datastructure"; - this->m_CurrentColorCoding = (char*) COLORCODING_CUSTOM; //will cause blank colorcoding of fibers +void mitk::FiberBundleX::SetFiberColors(vtkSmartPointer fiberColors) +{ + for(long i=0; iGetNumberOfPoints(); ++i) + { + unsigned char source[4] = {0,0,0,0}; + fiberColors->GetTupleValue(i, source); + + unsigned char target[4] = {0,0,0,0}; + target[0] = source[0]; + target[1] = source[1]; + target[2] = source[2]; + target[3] = source[3]; + m_FiberColors->InsertTupleValue(i, target); } - m_UpdateTime3D.Modified(); m_UpdateTime2D.Modified(); } itk::Matrix< double, 3, 3 > mitk::FiberBundleX::TransformMatrix(itk::Matrix< double, 3, 3 > m, double rx, double ry, double rz) { rx = rx*M_PI/180; ry = ry*M_PI/180; rz = rz*M_PI/180; itk::Matrix< double, 3, 3 > rotX; rotX.SetIdentity(); rotX[1][1] = cos(rx); rotX[2][2] = rotX[1][1]; rotX[1][2] = -sin(rx); rotX[2][1] = -rotX[1][2]; itk::Matrix< double, 3, 3 > rotY; rotY.SetIdentity(); rotY[0][0] = cos(ry); rotY[2][2] = rotY[0][0]; rotY[0][2] = sin(ry); rotY[2][0] = -rotY[0][2]; itk::Matrix< double, 3, 3 > rotZ; rotZ.SetIdentity(); rotZ[0][0] = cos(rz); rotZ[1][1] = rotZ[0][0]; rotZ[0][1] = -sin(rz); rotZ[1][0] = -rotZ[0][1]; itk::Matrix< double, 3, 3 > rot = rotZ*rotY*rotX; m = rot*m; return m; } itk::Point mitk::FiberBundleX::TransformPoint(vnl_vector_fixed< double, 3 > point, double rx, double ry, double rz, double tx, double ty, double tz) { rx = rx*M_PI/180; ry = ry*M_PI/180; rz = rz*M_PI/180; vnl_matrix_fixed< double, 3, 3 > rotX; rotX.set_identity(); rotX[1][1] = cos(rx); rotX[2][2] = rotX[1][1]; rotX[1][2] = -sin(rx); rotX[2][1] = -rotX[1][2]; vnl_matrix_fixed< double, 3, 3 > rotY; rotY.set_identity(); rotY[0][0] = cos(ry); rotY[2][2] = rotY[0][0]; rotY[0][2] = sin(ry); rotY[2][0] = -rotY[0][2]; vnl_matrix_fixed< double, 3, 3 > rotZ; rotZ.set_identity(); rotZ[0][0] = cos(rz); rotZ[1][1] = rotZ[0][0]; rotZ[0][1] = -sin(rz); rotZ[1][0] = -rotZ[0][1]; vnl_matrix_fixed< double, 3, 3 > rot = rotZ*rotY*rotX; mitk::BaseGeometry::Pointer geom = this->GetGeometry(); mitk::Point3D center = geom->GetCenter(); point[0] -= center[0]; point[1] -= center[1]; point[2] -= center[2]; point = rot*point; point[0] += center[0]+tx; point[1] += center[1]+ty; point[2] += center[2]+tz; itk::Point out; out[0] = point[0]; out[1] = point[1]; out[2] = point[2]; return out; } void mitk::FiberBundleX::TransformFibers(double rx, double ry, double rz, double tx, double ty, double tz) { rx = rx*M_PI/180; ry = ry*M_PI/180; rz = rz*M_PI/180; vnl_matrix_fixed< double, 3, 3 > rotX; rotX.set_identity(); rotX[1][1] = cos(rx); rotX[2][2] = rotX[1][1]; rotX[1][2] = -sin(rx); rotX[2][1] = -rotX[1][2]; vnl_matrix_fixed< double, 3, 3 > rotY; rotY.set_identity(); rotY[0][0] = cos(ry); rotY[2][2] = rotY[0][0]; rotY[0][2] = sin(ry); rotY[2][0] = -rotY[0][2]; vnl_matrix_fixed< double, 3, 3 > rotZ; rotZ.set_identity(); rotZ[0][0] = cos(rz); rotZ[1][1] = rotZ[0][0]; rotZ[0][1] = -sin(rz); rotZ[1][0] = -rotZ[0][1]; vnl_matrix_fixed< double, 3, 3 > rot = rotZ*rotY*rotX; mitk::BaseGeometry::Pointer geom = this->GetGeometry(); mitk::Point3D center = geom->GetCenter(); vtkSmartPointer vtkNewPoints = vtkSmartPointer::New(); vtkSmartPointer vtkNewCells = vtkSmartPointer::New(); for (int i=0; iGetCell(i); int numPoints = cell->GetNumberOfPoints(); vtkPoints* points = cell->GetPoints(); vtkSmartPointer container = vtkSmartPointer::New(); for (int j=0; jGetPoint(j); vnl_vector_fixed< double, 3 > dir; dir[0] = p[0]-center[0]; dir[1] = p[1]-center[1]; dir[2] = p[2]-center[2]; dir = rot*dir; dir[0] += center[0]+tx; dir[1] += center[1]+ty; dir[2] += center[2]+tz; vtkIdType id = vtkNewPoints->InsertNextPoint(dir.data_block()); container->GetPointIds()->InsertNextId(id); } vtkNewCells->InsertNextCell(container); } m_FiberPolyData = vtkSmartPointer::New(); m_FiberPolyData->SetPoints(vtkNewPoints); m_FiberPolyData->SetLines(vtkNewCells); this->SetFiberPolyData(m_FiberPolyData, true); } void mitk::FiberBundleX::RotateAroundAxis(double x, double y, double z) { x = x*M_PI/180; y = y*M_PI/180; z = z*M_PI/180; vnl_matrix_fixed< double, 3, 3 > rotX; rotX.set_identity(); rotX[1][1] = cos(x); rotX[2][2] = rotX[1][1]; rotX[1][2] = -sin(x); rotX[2][1] = -rotX[1][2]; vnl_matrix_fixed< double, 3, 3 > rotY; rotY.set_identity(); rotY[0][0] = cos(y); rotY[2][2] = rotY[0][0]; rotY[0][2] = sin(y); rotY[2][0] = -rotY[0][2]; vnl_matrix_fixed< double, 3, 3 > rotZ; rotZ.set_identity(); rotZ[0][0] = cos(z); rotZ[1][1] = rotZ[0][0]; rotZ[0][1] = -sin(z); rotZ[1][0] = -rotZ[0][1]; mitk::BaseGeometry::Pointer geom = this->GetGeometry(); mitk::Point3D center = geom->GetCenter(); vtkSmartPointer vtkNewPoints = vtkSmartPointer::New(); vtkSmartPointer vtkNewCells = vtkSmartPointer::New(); for (int i=0; iGetCell(i); int numPoints = cell->GetNumberOfPoints(); vtkPoints* points = cell->GetPoints(); vtkSmartPointer container = vtkSmartPointer::New(); for (int j=0; jGetPoint(j); vnl_vector_fixed< double, 3 > dir; dir[0] = p[0]-center[0]; dir[1] = p[1]-center[1]; dir[2] = p[2]-center[2]; dir = rotZ*rotY*rotX*dir; dir[0] += center[0]; dir[1] += center[1]; dir[2] += center[2]; vtkIdType id = vtkNewPoints->InsertNextPoint(dir.data_block()); container->GetPointIds()->InsertNextId(id); } vtkNewCells->InsertNextCell(container); } m_FiberPolyData = vtkSmartPointer::New(); m_FiberPolyData->SetPoints(vtkNewPoints); m_FiberPolyData->SetLines(vtkNewCells); this->SetFiberPolyData(m_FiberPolyData, true); } void mitk::FiberBundleX::ScaleFibers(double x, double y, double z, bool subtractCenter) { MITK_INFO << "Scaling fibers"; boost::progress_display disp(m_NumFibers); mitk::BaseGeometry* geom = this->GetGeometry(); mitk::Point3D c = geom->GetCenter(); vtkSmartPointer vtkNewPoints = vtkSmartPointer::New(); vtkSmartPointer vtkNewCells = vtkSmartPointer::New(); for (int i=0; iGetCell(i); int numPoints = cell->GetNumberOfPoints(); vtkPoints* points = cell->GetPoints(); vtkSmartPointer container = vtkSmartPointer::New(); for (int j=0; jGetPoint(j); if (subtractCenter) { p[0] -= c[0]; p[1] -= c[1]; p[2] -= c[2]; } p[0] *= x; p[1] *= y; p[2] *= z; if (subtractCenter) { p[0] += c[0]; p[1] += c[1]; p[2] += c[2]; } vtkIdType id = vtkNewPoints->InsertNextPoint(p); container->GetPointIds()->InsertNextId(id); } vtkNewCells->InsertNextCell(container); } m_FiberPolyData = vtkSmartPointer::New(); m_FiberPolyData->SetPoints(vtkNewPoints); m_FiberPolyData->SetLines(vtkNewCells); this->SetFiberPolyData(m_FiberPolyData, true); } void mitk::FiberBundleX::TranslateFibers(double x, double y, double z) { vtkSmartPointer vtkNewPoints = vtkSmartPointer::New(); vtkSmartPointer vtkNewCells = vtkSmartPointer::New(); for (int i=0; iGetCell(i); int numPoints = cell->GetNumberOfPoints(); vtkPoints* points = cell->GetPoints(); vtkSmartPointer container = vtkSmartPointer::New(); for (int j=0; jGetPoint(j); p[0] += x; p[1] += y; p[2] += z; vtkIdType id = vtkNewPoints->InsertNextPoint(p); container->GetPointIds()->InsertNextId(id); } vtkNewCells->InsertNextCell(container); } m_FiberPolyData = vtkSmartPointer::New(); m_FiberPolyData->SetPoints(vtkNewPoints); m_FiberPolyData->SetLines(vtkNewCells); this->SetFiberPolyData(m_FiberPolyData, true); } void mitk::FiberBundleX::MirrorFibers(unsigned int axis) { if (axis>2) return; MITK_INFO << "Mirroring fibers"; boost::progress_display disp(m_NumFibers); vtkSmartPointer vtkNewPoints = vtkSmartPointer::New(); vtkSmartPointer vtkNewCells = vtkSmartPointer::New(); for (int i=0; iGetCell(i); int numPoints = cell->GetNumberOfPoints(); vtkPoints* points = cell->GetPoints(); vtkSmartPointer container = vtkSmartPointer::New(); for (int j=0; jGetPoint(j); p[axis] = -p[axis]; vtkIdType id = vtkNewPoints->InsertNextPoint(p); container->GetPointIds()->InsertNextId(id); } vtkNewCells->InsertNextCell(container); } m_FiberPolyData = vtkSmartPointer::New(); m_FiberPolyData->SetPoints(vtkNewPoints); m_FiberPolyData->SetLines(vtkNewCells); this->SetFiberPolyData(m_FiberPolyData, true); } void mitk::FiberBundleX::RemoveDir(vnl_vector_fixed dir, double threshold) { dir.normalize(); vtkSmartPointer vtkNewPoints = vtkSmartPointer::New(); vtkSmartPointer vtkNewCells = vtkSmartPointer::New(); boost::progress_display disp(m_FiberPolyData->GetNumberOfCells()); for (int i=0; iGetNumberOfCells(); i++) { ++disp ; vtkCell* cell = m_FiberPolyData->GetCell(i); int numPoints = cell->GetNumberOfPoints(); vtkPoints* points = cell->GetPoints(); // calculate curvatures vtkSmartPointer container = vtkSmartPointer::New(); bool discard = false; for (int j=0; jGetPoint(j, p1); double p2[3]; points->GetPoint(j+1, p2); vnl_vector_fixed< double, 3 > v1; v1[0] = p2[0]-p1[0]; v1[1] = p2[1]-p1[1]; v1[2] = p2[2]-p1[2]; if (v1.magnitude()>0.001) { v1.normalize(); if (fabs(dot_product(v1,dir))>threshold) { discard = true; break; } } } if (!discard) { for (int j=0; jGetPoint(j, p1); vtkIdType id = vtkNewPoints->InsertNextPoint(p1); container->GetPointIds()->InsertNextId(id); } vtkNewCells->InsertNextCell(container); } } m_FiberPolyData = vtkSmartPointer::New(); m_FiberPolyData->SetPoints(vtkNewPoints); m_FiberPolyData->SetLines(vtkNewCells); this->SetFiberPolyData(m_FiberPolyData, true); -// UpdateColorCoding(); -// UpdateFiberGeometry(); + // UpdateColorCoding(); + // UpdateFiberGeometry(); } bool mitk::FiberBundleX::ApplyCurvatureThreshold(float minRadius, bool deleteFibers) { if (minRadius<0) return true; vtkSmartPointer vtkNewPoints = vtkSmartPointer::New(); vtkSmartPointer vtkNewCells = vtkSmartPointer::New(); MITK_INFO << "Applying curvature threshold"; boost::progress_display disp(m_FiberPolyData->GetNumberOfCells()); for (int i=0; iGetNumberOfCells(); i++) { ++disp ; vtkCell* cell = m_FiberPolyData->GetCell(i); int numPoints = cell->GetNumberOfPoints(); vtkPoints* points = cell->GetPoints(); // calculate curvatures vtkSmartPointer container = vtkSmartPointer::New(); for (int j=0; jGetPoint(j, p1); double p2[3]; points->GetPoint(j+1, p2); double p3[3]; points->GetPoint(j+2, p3); vnl_vector_fixed< float, 3 > v1, v2, v3; v1[0] = p2[0]-p1[0]; v1[1] = p2[1]-p1[1]; v1[2] = p2[2]-p1[2]; v2[0] = p3[0]-p2[0]; v2[1] = p3[1]-p2[1]; v2[2] = p3[2]-p2[2]; v3[0] = p1[0]-p3[0]; v3[1] = p1[1]-p3[1]; v3[2] = p1[2]-p3[2]; float a = v1.magnitude(); float b = v2.magnitude(); float c = v3.magnitude(); float r = a*b*c/std::sqrt((a+b+c)*(a+b-c)*(b+c-a)*(a-b+c)); // radius of triangle via Heron's formula (area of triangle) vtkIdType id = vtkNewPoints->InsertNextPoint(p1); container->GetPointIds()->InsertNextId(id); if (deleteFibers && rInsertNextCell(container); container = vtkSmartPointer::New(); } else if (j==numPoints-3) { id = vtkNewPoints->InsertNextPoint(p2); container->GetPointIds()->InsertNextId(id); id = vtkNewPoints->InsertNextPoint(p3); container->GetPointIds()->InsertNextId(id); vtkNewCells->InsertNextCell(container); } } } if (vtkNewCells->GetNumberOfCells()<=0) return false; m_FiberPolyData = vtkSmartPointer::New(); m_FiberPolyData->SetPoints(vtkNewPoints); m_FiberPolyData->SetLines(vtkNewCells); this->SetFiberPolyData(m_FiberPolyData, true); return true; } bool mitk::FiberBundleX::RemoveShortFibers(float lengthInMM) { MITK_INFO << "Removing short fibers"; if (lengthInMM<=0 || lengthInMMm_MaxFiberLength) // can't remove all fibers { MITK_WARN << "Process aborted. No fibers would be left!"; return false; } vtkSmartPointer vtkNewPoints = vtkSmartPointer::New(); vtkSmartPointer vtkNewCells = vtkSmartPointer::New(); float min = m_MaxFiberLength; boost::progress_display disp(m_NumFibers); for (int i=0; iGetCell(i); int numPoints = cell->GetNumberOfPoints(); vtkPoints* points = cell->GetPoints(); if (m_FiberLengths.at(i)>=lengthInMM) { vtkSmartPointer container = vtkSmartPointer::New(); for (int j=0; jGetPoint(j); vtkIdType id = vtkNewPoints->InsertNextPoint(p); container->GetPointIds()->InsertNextId(id); } vtkNewCells->InsertNextCell(container); if (m_FiberLengths.at(i)GetNumberOfCells()<=0) return false; m_FiberPolyData = vtkSmartPointer::New(); m_FiberPolyData->SetPoints(vtkNewPoints); m_FiberPolyData->SetLines(vtkNewCells); this->SetFiberPolyData(m_FiberPolyData, true); return true; } bool mitk::FiberBundleX::RemoveLongFibers(float lengthInMM) { if (lengthInMM<=0 || lengthInMM>m_MaxFiberLength) return true; if (lengthInMM vtkNewPoints = vtkSmartPointer::New(); vtkSmartPointer vtkNewCells = vtkSmartPointer::New(); MITK_INFO << "Removing long fibers"; boost::progress_display disp(m_NumFibers); for (int i=0; iGetCell(i); int numPoints = cell->GetNumberOfPoints(); vtkPoints* points = cell->GetPoints(); if (m_FiberLengths.at(i)<=lengthInMM) { vtkSmartPointer container = vtkSmartPointer::New(); for (int j=0; jGetPoint(j); vtkIdType id = vtkNewPoints->InsertNextPoint(p); container->GetPointIds()->InsertNextId(id); } vtkNewCells->InsertNextCell(container); } } if (vtkNewCells->GetNumberOfCells()<=0) return false; m_FiberPolyData = vtkSmartPointer::New(); m_FiberPolyData->SetPoints(vtkNewPoints); m_FiberPolyData->SetLines(vtkNewCells); this->SetFiberPolyData(m_FiberPolyData, true); return true; } void mitk::FiberBundleX::ResampleSpline(float pointDistance, double tension, double continuity, double bias ) { if (pointDistance<=0) return; vtkSmartPointer vtkSmoothPoints = vtkSmartPointer::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 vtkSmartPointer vtkSmoothCells = vtkSmartPointer::New(); //cellcontainer for smoothed lines vtkIdType pointHelperCnt = 0; MITK_INFO << "Smoothing fibers"; boost::progress_display disp(m_NumFibers); for (int i=0; iGetCell(i); int numPoints = cell->GetNumberOfPoints(); vtkPoints* points = cell->GetPoints(); vtkSmartPointer newPoints = vtkSmartPointer::New(); for (int j=0; jInsertNextPoint(points->GetPoint(j)); float length = m_FiberLengths.at(i); int sampling = std::ceil(length/pointDistance); vtkSmartPointer xSpline = vtkSmartPointer::New(); vtkSmartPointer ySpline = vtkSmartPointer::New(); vtkSmartPointer zSpline = vtkSmartPointer::New(); xSpline->SetDefaultBias(bias); xSpline->SetDefaultTension(tension); xSpline->SetDefaultContinuity(continuity); ySpline->SetDefaultBias(bias); ySpline->SetDefaultTension(tension); ySpline->SetDefaultContinuity(continuity); zSpline->SetDefaultBias(bias); zSpline->SetDefaultTension(tension); zSpline->SetDefaultContinuity(continuity); vtkSmartPointer spline = vtkSmartPointer::New(); spline->SetXSpline(xSpline); spline->SetYSpline(ySpline); spline->SetZSpline(zSpline); spline->SetPoints(newPoints); vtkSmartPointer functionSource = vtkSmartPointer::New(); functionSource->SetParametricFunction(spline); functionSource->SetUResolution(sampling); functionSource->SetVResolution(sampling); functionSource->SetWResolution(sampling); functionSource->Update(); vtkPolyData* outputFunction = functionSource->GetOutput(); vtkPoints* tmpSmoothPnts = outputFunction->GetPoints(); //smoothPoints of current fiber vtkSmartPointer smoothLine = vtkSmartPointer::New(); smoothLine->GetPointIds()->SetNumberOfIds(tmpSmoothPnts->GetNumberOfPoints()); for (int j=0; jGetNumberOfPoints(); j++) { smoothLine->GetPointIds()->SetId(j, j+pointHelperCnt); vtkSmoothPoints->InsertNextPoint(tmpSmoothPnts->GetPoint(j)); } vtkSmoothCells->InsertNextCell(smoothLine); pointHelperCnt += tmpSmoothPnts->GetNumberOfPoints(); } m_FiberPolyData = vtkSmartPointer::New(); m_FiberPolyData->SetPoints(vtkSmoothPoints); m_FiberPolyData->SetLines(vtkSmoothCells); this->SetFiberPolyData(m_FiberPolyData, true); m_FiberSampling = 10/pointDistance; } void mitk::FiberBundleX::ResampleSpline(float pointDistance) { ResampleSpline(pointDistance, 0, 0, 0 ); } unsigned long mitk::FiberBundleX::GetNumberOfPoints() { unsigned long points = 0; for (int i=0; iGetNumberOfCells(); i++) { vtkCell* cell = m_FiberPolyData->GetCell(i); points += cell->GetNumberOfPoints(); } return points; } void mitk::FiberBundleX::Compress(float error) { vtkSmartPointer vtkNewPoints = vtkSmartPointer::New(); vtkSmartPointer vtkNewCells = vtkSmartPointer::New(); MITK_INFO << "Compressing fibers"; unsigned long numRemovedPoints = 0; boost::progress_display disp(m_FiberPolyData->GetNumberOfCells()); for (int i=0; iGetNumberOfCells(); i++) { ++disp; vtkCell* cell = m_FiberPolyData->GetCell(i); int numPoints = cell->GetNumberOfPoints(); vtkPoints* points = cell->GetPoints(); // calculate curvatures std::vector< int > removedPoints; removedPoints.resize(numPoints, 0); removedPoints[0]=-1; removedPoints[numPoints-1]=-1; vtkSmartPointer container = vtkSmartPointer::New(); bool pointFound = true; while (pointFound) { pointFound = false; double minError = error; int removeIndex = -1; for (int j=0; jGetPoint(j, cand); vnl_vector_fixed< double, 3 > candV; candV[0]=cand[0]; candV[1]=cand[1]; candV[2]=cand[2]; int validP = -1; vnl_vector_fixed< double, 3 > pred; for (int k=j-1; k>=0; k--) if (removedPoints[k]<=0) { double ref[3]; points->GetPoint(k, ref); pred[0]=ref[0]; pred[1]=ref[1]; pred[2]=ref[2]; validP = k; break; } int validS = -1; vnl_vector_fixed< double, 3 > succ; for (int k=j+1; kGetPoint(k, ref); succ[0]=ref[0]; succ[1]=ref[1]; succ[2]=ref[2]; validS = k; break; } if (validP>=0 && validS>=0) { double a = (candV-pred).magnitude(); double b = (candV-succ).magnitude(); double c = (pred-succ).magnitude(); double s=0.5*(a+b+c); double hc=(2.0/c)*sqrt(fabs(s*(s-a)*(s-b)*(s-c))); if (hcGetPoint(j, cand); vtkIdType id = vtkNewPoints->InsertNextPoint(cand); container->GetPointIds()->InsertNextId(id); } } vtkNewCells->InsertNextCell(container); } if (vtkNewCells->GetNumberOfCells()>0) { MITK_INFO << "Removed points: " << numRemovedPoints; m_FiberPolyData = vtkSmartPointer::New(); m_FiberPolyData->SetPoints(vtkNewPoints); m_FiberPolyData->SetLines(vtkNewCells); this->SetFiberPolyData(m_FiberPolyData, true); } } -// reapply selected colorcoding in case polydata structure has changed -void mitk::FiberBundleX::UpdateColorCoding() -{ - char* cc = GetCurrentColorCoding(); - - if( strcmp (COLORCODING_ORIENTATION_BASED,cc) == 0 ) - DoColorCodingOrientationBased(); - else if( strcmp (COLORCODING_FA_BASED,cc) == 0 ) - DoColorCodingFaBased(); -} - // reapply selected colorcoding in case polydata structure has changed bool mitk::FiberBundleX::Equals(mitk::FiberBundleX* fib, double eps) { if (fib==NULL) { MITK_INFO << "Reference bundle is NULL!"; return false; } if (m_NumFibers!=fib->GetNumFibers()) { MITK_INFO << "Unequal number of fibers!"; MITK_INFO << m_NumFibers << " vs. " << fib->GetNumFibers(); return false; } for (int i=0; iGetCell(i); int numPoints = cell->GetNumberOfPoints(); vtkPoints* points = cell->GetPoints(); vtkCell* cell2 = fib->GetFiberPolyData()->GetCell(i); int numPoints2 = cell2->GetNumberOfPoints(); vtkPoints* points2 = cell2->GetPoints(); if (numPoints2!=numPoints) { MITK_INFO << "Unequal number of points in fiber " << i << "!"; MITK_INFO << numPoints2 << " vs. " << numPoints; return false; } for (int j=0; jGetPoint(j); double* p2 = points2->GetPoint(j); if (fabs(p1[0]-p2[0])>eps || fabs(p1[1]-p2[1])>eps || fabs(p1[2]-p2[2])>eps) { MITK_INFO << "Unequal points in fiber " << i << " at position " << j << "!"; MITK_INFO << "p1: " << p1[0] << ", " << p1[1] << ", " << p1[2]; MITK_INFO << "p2: " << p2[0] << ", " << p2[1] << ", " << p2[2]; return false; } } } return true; } /* ESSENTIAL IMPLEMENTATION OF SUPERCLASS METHODS */ void mitk::FiberBundleX::UpdateOutputInformation() { } void mitk::FiberBundleX::SetRequestedRegionToLargestPossibleRegion() { } bool mitk::FiberBundleX::RequestedRegionIsOutsideOfTheBufferedRegion() { return false; } bool mitk::FiberBundleX::VerifyRequestedRegion() { return true; } void mitk::FiberBundleX::SetRequestedRegion(const itk::DataObject* ) { } diff --git a/Modules/DiffusionImaging/FiberTracking/IODataStructures/FiberBundleX/mitkFiberBundleX.h b/Modules/DiffusionImaging/FiberTracking/IODataStructures/FiberBundleX/mitkFiberBundleX.h index 5cd056a4b6..37d44ad5f2 100644 --- a/Modules/DiffusionImaging/FiberTracking/IODataStructures/FiberBundleX/mitkFiberBundleX.h +++ b/Modules/DiffusionImaging/FiberTracking/IODataStructures/FiberBundleX/mitkFiberBundleX.h @@ -1,177 +1,178 @@ /*=================================================================== The Medical Imaging Interaction Toolkit (MITK) Copyright (c) German Cancer Research Center, Division of Medical and Biological Informatics. All rights reserved. This software is distributed WITHOUT ANY WARRANTY; without even the implied warranty of MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See LICENSE.txt or http://www.mitk.org for details. ===================================================================*/ #ifndef _MITK_FiberBundleX_H #define _MITK_FiberBundleX_H //includes for MITK datastructure #include #include #include //includes storing fiberdata #include #include #include #include #include +#include //#include #include #include #include namespace mitk { /** * \brief Base Class for Fiber Bundles; */ class MitkFiberTracking_EXPORT FiberBundleX : public BaseData { public: typedef itk::Image ItkUcharImgType; // fiber colorcodings - static const char* COLORCODING_ORIENTATION_BASED; - static const char* COLORCODING_FA_BASED; - static const char* COLORCODING_CUSTOM; static const char* FIBER_ID_ARRAY; virtual void UpdateOutputInformation(); virtual void SetRequestedRegionToLargestPossibleRegion(); virtual bool RequestedRegionIsOutsideOfTheBufferedRegion(); virtual bool VerifyRequestedRegion(); virtual void SetRequestedRegion(const itk::DataObject*); mitkClassMacro( FiberBundleX, BaseData ) itkFactorylessNewMacro(Self) itkCloneMacro(Self) mitkNewMacro1Param(Self, vtkSmartPointer) // custom constructor // colorcoding related methods - void SetColorCoding(const char*); - void SetFAMap(mitk::Image::Pointer); + void ColorFibersByScalarMap(mitk::Image::Pointer, bool opacity); template - void SetFAMap(const mitk::PixelType pixelType, mitk::Image::Pointer); + void ColorFibersByScalarMap(const mitk::PixelType pixelType, mitk::Image::Pointer, bool opacity); void DoColorCodingOrientationBased(); - void DoColorCodingFaBased(); - void DoUseFaFiberOpacity(); + void SetFiberOpacity(vtkDoubleArray *FAValArray); void ResetFiberOpacity(); + void SetFiberColors(vtkSmartPointer fiberColors); + void SetFiberColors(float r, float g, float b, float alpha=255); + vtkSmartPointer GetFiberColors() const { return m_FiberColors; } // fiber compression void Compress(float error = 0.0); // fiber resampling void ResampleSpline(float pointDistance=1); void ResampleSpline(float pointDistance, double tension, double continuity, double bias ); bool RemoveShortFibers(float lengthInMM); bool RemoveLongFibers(float lengthInMM); bool ApplyCurvatureThreshold(float minRadius, bool deleteFibers); void MirrorFibers(unsigned int axis); void RotateAroundAxis(double x, double y, double z); void TranslateFibers(double x, double y, double z); void ScaleFibers(double x, double y, double z, bool subtractCenter=true); void TransformFibers(double rx, double ry, double rz, double tx, double ty, double tz); void RemoveDir(vnl_vector_fixed dir, double threshold); itk::Point TransformPoint(vnl_vector_fixed< double, 3 > point, double rx, double ry, double rz, double tx, double ty, double tz); itk::Matrix< double, 3, 3 > TransformMatrix(itk::Matrix< double, 3, 3 > m, double rx, double ry, double rz); // add/subtract fibers FiberBundleX::Pointer AddBundle(FiberBundleX* fib); FiberBundleX::Pointer SubtractBundle(FiberBundleX* fib); // fiber subset extraction FiberBundleX::Pointer ExtractFiberSubset(BaseData* roi); std::vector ExtractFiberIdSubset(BaseData* roi); FiberBundleX::Pointer ExtractFiberSubset(ItkUcharImgType* mask, bool anyPoint, bool invert=false); FiberBundleX::Pointer RemoveFibersOutside(ItkUcharImgType* mask, bool invert=false); vtkSmartPointer GeneratePolyDataByIds( std::vector ); // TODO: make protected void GenerateFiberIds(); // TODO: make protected // get/set data + vtkSmartPointer GetFiberWeights() const { return m_FiberWeights; } + float GetFiberWeight(unsigned int fiber); + void SetFiberWeights(float newWeight); + void SetFiberWeight(unsigned int fiber, float weight); + void SetFiberWeights(vtkSmartPointer weights); void SetFiberPolyData(vtkSmartPointer, bool updateGeometry = true); vtkSmartPointer GetFiberPolyData() const; - std::vector< std::string > GetAvailableColorCodings(); - char* GetCurrentColorCoding(); itkGetMacro( NumFibers, int) //itkGetMacro( FiberSampling, int) int GetNumFibers() const {return m_NumFibers;} itkGetMacro( MinFiberLength, float ) itkGetMacro( MaxFiberLength, float ) itkGetMacro( MeanFiberLength, float ) itkGetMacro( MedianFiberLength, float ) itkGetMacro( LengthStDev, float ) itkGetMacro( UpdateTime2D, itk::TimeStamp ) itkGetMacro( UpdateTime3D, itk::TimeStamp ) void RequestUpdate2D(){ m_UpdateTime2D.Modified(); } void RequestUpdate3D(){ m_UpdateTime3D.Modified(); } + void RequestUpdate(){ m_UpdateTime2D.Modified(); m_UpdateTime3D.Modified(); } unsigned long GetNumberOfPoints(); // copy fiber bundle mitk::FiberBundleX::Pointer GetDeepCopy(); // compare fiber bundles bool Equals(FiberBundleX* fib, double eps=0.0001); itkSetMacro( ReferenceGeometry, mitk::BaseGeometry::Pointer ) itkGetConstMacro( ReferenceGeometry, mitk::BaseGeometry::Pointer ) protected: FiberBundleX( vtkPolyData* fiberPolyData = NULL ); virtual ~FiberBundleX(); itk::Point GetItkPoint(double point[3]); // calculate geometry from fiber extent void UpdateFiberGeometry(); - // calculate colorcoding values according to m_CurrentColorCoding - void UpdateColorCoding(); - private: // actual fiber container vtkSmartPointer m_FiberPolyData; // contains fiber ids vtkSmartPointer m_FiberIdDataSet; - char* m_CurrentColorCoding; int m_NumFibers; + vtkSmartPointer m_FiberColors; + vtkSmartPointer m_FiberWeights; std::vector< float > m_FiberLengths; float m_MinFiberLength; float m_MaxFiberLength; float m_MeanFiberLength; float m_MedianFiberLength; float m_LengthStDev; int m_FiberSampling; itk::TimeStamp m_UpdateTime2D; itk::TimeStamp m_UpdateTime3D; mitk::BaseGeometry::Pointer m_ReferenceGeometry; }; } // namespace mitk #endif /* _MITK_FiberBundleX_H */ diff --git a/Plugins/org.mitk.gui.qt.diffusionimaging/src/internal/QmitkControlVisualizationPropertiesView.cpp b/Plugins/org.mitk.gui.qt.diffusionimaging/src/internal/QmitkControlVisualizationPropertiesView.cpp index 50cfe086bc..5519f43796 100644 --- a/Plugins/org.mitk.gui.qt.diffusionimaging/src/internal/QmitkControlVisualizationPropertiesView.cpp +++ b/Plugins/org.mitk.gui.qt.diffusionimaging/src/internal/QmitkControlVisualizationPropertiesView.cpp @@ -1,1839 +1,1022 @@ /*=================================================================== The Medical Imaging Interaction Toolkit (MITK) Copyright (c) German Cancer Research Center, Division of Medical and Biological Informatics. All rights reserved. This software is distributed WITHOUT ANY WARRANTY; without even the implied warranty of MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See LICENSE.txt or http://www.mitk.org for details. ===================================================================*/ #include "QmitkControlVisualizationPropertiesView.h" #include "mitkNodePredicateDataType.h" #include "mitkDataNodeObject.h" #include "mitkOdfNormalizationMethodProperty.h" #include "mitkOdfScaleByProperty.h" #include "mitkResliceMethodProperty.h" #include "mitkRenderingManager.h" #include "mitkTbssImage.h" #include "mitkPlanarFigure.h" #include "mitkFiberBundleX.h" #include "QmitkDataStorageComboBox.h" #include "QmitkStdMultiWidget.h" #include "mitkFiberBundleInteractor.h" #include "mitkPlanarFigureInteractor.h" #include #include #include #include #include #include "mitkGlobalInteraction.h" #include "usModuleRegistry.h" #include "mitkPlaneGeometry.h" #include "berryIWorkbenchWindow.h" #include "berryIWorkbenchPage.h" #include "berryISelectionService.h" #include "berryConstants.h" #include "berryPlatformUI.h" #include "itkRGBAPixel.h" #include #include "qwidgetaction.h" #include "qcolordialog.h" +#include #include #define ROUND(a) ((a)>0 ? (int)((a)+0.5) : -(int)(0.5-(a))) -static bool DetermineAffectedImageSlice( const mitk::Image* image, const mitk::PlaneGeometry* plane, int& affectedDimension, int& affectedSlice ) -{ - assert(image); - assert(plane); - - // compare normal of plane to the three axis vectors of the image - mitk::Vector3D normal = plane->GetNormal(); - mitk::Vector3D imageNormal0 = image->GetSlicedGeometry()->GetAxisVector(0); - mitk::Vector3D imageNormal1 = image->GetSlicedGeometry()->GetAxisVector(1); - mitk::Vector3D imageNormal2 = image->GetSlicedGeometry()->GetAxisVector(2); - - normal.Normalize(); - imageNormal0.Normalize(); - imageNormal1.Normalize(); - imageNormal2.Normalize(); - - imageNormal0.SetVnlVector( vnl_cross_3d(normal.GetVnlVector(),imageNormal0.GetVnlVector()) ); - imageNormal1.SetVnlVector( vnl_cross_3d(normal.GetVnlVector(),imageNormal1.GetVnlVector()) ); - imageNormal2.SetVnlVector( vnl_cross_3d(normal.GetVnlVector(),imageNormal2.GetVnlVector()) ); - - double eps( 0.00001 ); - // axial - if ( imageNormal2.GetNorm() <= eps ) - { - affectedDimension = 2; - } - // sagittal - else if ( imageNormal1.GetNorm() <= eps ) - { - affectedDimension = 1; - } - // frontal - else if ( imageNormal0.GetNorm() <= eps ) - { - affectedDimension = 0; - } - else - { - affectedDimension = -1; // no idea - return false; - } - - // determine slice number in image - mitk::BaseGeometry* imageGeometry = image->GetGeometry(0); - mitk::Point3D testPoint = imageGeometry->GetCenter(); - mitk::Point3D projectedPoint; - plane->Project( testPoint, projectedPoint ); - - mitk::Point3D indexPoint; - - imageGeometry->WorldToIndex( projectedPoint, indexPoint ); - affectedSlice = ROUND( indexPoint[affectedDimension] ); - MITK_DEBUG << "indexPoint " << indexPoint << " affectedDimension " << affectedDimension << " affectedSlice " << affectedSlice; - - // check if this index is still within the image - if ( affectedSlice < 0 || affectedSlice >= static_cast(image->GetDimension(affectedDimension)) ) return false; - - return true; -} - const std::string QmitkControlVisualizationPropertiesView::VIEW_ID = "org.mitk.views.controlvisualizationpropertiesview"; using namespace berry; -struct CvpSelListener : ISelectionListener -{ - - berryObjectMacro(CvpSelListener); +QmitkControlVisualizationPropertiesView::QmitkControlVisualizationPropertiesView() + : QmitkFunctionality(), + m_Controls(NULL), + m_MultiWidget(NULL), + m_NodeUsedForOdfVisualization(NULL), + m_IconTexOFF(new QIcon(":/QmitkDiffusionImaging/texIntOFFIcon.png")), + m_IconTexON(new QIcon(":/QmitkDiffusionImaging/texIntONIcon.png")), + m_IconGlyOFF_T(new QIcon(":/QmitkDiffusionImaging/glyphsoff_T.png")), + m_IconGlyON_T(new QIcon(":/QmitkDiffusionImaging/glyphson_T.png")), + m_IconGlyOFF_C(new QIcon(":/QmitkDiffusionImaging/glyphsoff_C.png")), + m_IconGlyON_C(new QIcon(":/QmitkDiffusionImaging/glyphson_C.png")), + m_IconGlyOFF_S(new QIcon(":/QmitkDiffusionImaging/glyphsoff_S.png")), + m_IconGlyON_S(new QIcon(":/QmitkDiffusionImaging/glyphson_S.png")), + m_CurrentSelection(0), + m_CurrentPickingNode(0), + m_GlyIsOn_S(false), + m_GlyIsOn_C(false), + m_GlyIsOn_T(false), + m_FiberBundleObserverTag(0), + m_FiberBundleObserveOpacityTag(0), + m_Color(NULL) +{ + currentThickSlicesMode = 1; + m_MyMenu = NULL; + int numThread = itk::MultiThreader::GetGlobalMaximumNumberOfThreads(); + if (numThread > 12) + numThread = 12; + itk::MultiThreader::SetGlobalDefaultNumberOfThreads(numThread); +} - CvpSelListener(QmitkControlVisualizationPropertiesView* view) - { - m_View = view; - } +QmitkControlVisualizationPropertiesView::QmitkControlVisualizationPropertiesView(const QmitkControlVisualizationPropertiesView& other) +{ + Q_UNUSED(other) + throw std::runtime_error("Copy constructor not implemented"); +} - void ApplySettings(mitk::DataNode::Pointer node) - { - bool tex_int; - node->GetBoolProperty("texture interpolation", tex_int); - if(tex_int) +QmitkControlVisualizationPropertiesView::~QmitkControlVisualizationPropertiesView() +{ + if(m_SlicesRotationObserverTag1 ) { - m_View->m_Controls->m_TextureIntON->setIcon(*m_View->m_IconTexON); - m_View->m_Controls->m_TextureIntON->setChecked(true); - m_View->m_TexIsOn = true; + mitk::SlicesCoordinator::Pointer coordinator = m_MultiWidget->GetSlicesRotator(); + if( coordinator.IsNotNull() ) + coordinator->RemoveObserver(m_SlicesRotationObserverTag1); } - else + if( m_SlicesRotationObserverTag2) { - m_View->m_Controls->m_TextureIntON->setIcon(*m_View->m_IconTexOFF); - m_View->m_Controls->m_TextureIntON->setChecked(false); - m_View->m_TexIsOn = false; + mitk::SlicesCoordinator::Pointer coordinator = m_MultiWidget->GetSlicesRotator(); + if( coordinator.IsNotNull() ) + coordinator->RemoveObserver(m_SlicesRotationObserverTag1); } - int val; - node->GetIntProperty("ShowMaxNumber", val); - m_View->m_Controls->m_ShowMaxNumber->setValue(val); - - m_View->m_Controls->m_NormalizationDropdown->setCurrentIndex(dynamic_cast(node->GetProperty("Normalization"))->GetValueAsId()); - - float fval; - node->GetFloatProperty("Scaling",fval); - m_View->m_Controls->m_ScalingFactor->setValue(fval); - - m_View->m_Controls->m_AdditionalScaling->setCurrentIndex(dynamic_cast(node->GetProperty("ScaleBy"))->GetValueAsId()); - - node->GetFloatProperty("IndexParam1",fval); - m_View->m_Controls->m_IndexParam1->setValue(fval); - - node->GetFloatProperty("IndexParam2",fval); - m_View->m_Controls->m_IndexParam2->setValue(fval); - } - - void DoSelectionChanged(ISelection::ConstPointer selection) - { - // save current selection in member variable - m_View->m_CurrentSelection = selection.Cast(); - - m_View->m_Controls->m_VisibleOdfsON_T->setVisible(false); - m_View->m_Controls->m_VisibleOdfsON_S->setVisible(false); - m_View->m_Controls->m_VisibleOdfsON_C->setVisible(false); - m_View->m_Controls->m_TextureIntON->setVisible(false); - - m_View->m_Controls->m_ImageControlsFrame->setVisible(false); - m_View->m_Controls->m_PlanarFigureControlsFrame->setVisible(false); - m_View->m_Controls->m_BundleControlsFrame->setVisible(false); - m_View->m_SelectedNode = 0; + this->GetSite()->GetWorkbenchWindow()->GetSelectionService()->RemovePostSelectionListener(/*"org.mitk.views.datamanager",*/ m_SelListener); +} - if(m_View->m_CurrentSelection.IsNull()) - return; +void QmitkControlVisualizationPropertiesView::OnThickSlicesModeSelected( QAction* action ) +{ + currentThickSlicesMode = action->data().toInt(); - if(m_View->m_CurrentSelection->Size() == 1) + switch(currentThickSlicesMode) { - mitk::DataNodeObject::Pointer nodeObj = m_View->m_CurrentSelection->Begin()->Cast(); - if(nodeObj.IsNotNull()) - { - mitk::DataNode::Pointer node = nodeObj->GetDataNode(); - - // check if node has data, - // if some helper nodes are shown in the DataManager, the GetData() returns 0x0 which would lead to SIGSEV - mitk::BaseData* nodeData = node->GetData(); - - if(nodeData != NULL ) - { - if(dynamic_cast(nodeData) != 0) - { - m_View->m_Controls->m_PlanarFigureControlsFrame->setVisible(true); - m_View->m_SelectedNode = node; - - float val; - node->GetFloatProperty("planarfigure.line.width", val); - m_View->m_Controls->m_PFWidth->setValue((int)(val*10.0)); - - QString label = "Width %1"; - label = label.arg(val); - m_View->m_Controls->label_pfwidth->setText(label); - - float color[3]; - node->GetColor( color, NULL, "planarfigure.default.line.color"); - QString styleSheet = "background-color:rgb("; - styleSheet.append(QString::number(color[0]*255.0)); - styleSheet.append(","); - styleSheet.append(QString::number(color[1]*255.0)); - styleSheet.append(","); - styleSheet.append(QString::number(color[2]*255.0)); - styleSheet.append(")"); - m_View->m_Controls->m_PFColor->setAutoFillBackground(true); - m_View->m_Controls->m_PFColor->setStyleSheet(styleSheet); - - node->GetColor( color, NULL, "color"); - styleSheet = "background-color:rgb("; - styleSheet.append(QString::number(color[0]*255.0)); - styleSheet.append(","); - styleSheet.append(QString::number(color[1]*255.0)); - styleSheet.append(","); - styleSheet.append(QString::number(color[2]*255.0)); - styleSheet.append(")"); - - m_View->PlanarFigureFocus(); - } - - if(dynamic_cast(nodeData) != 0) - { - m_View->m_Controls->m_BundleControlsFrame->setVisible(true); - m_View->m_SelectedNode = node; - - if(m_View->m_CurrentPickingNode != 0 && node.GetPointer() != m_View->m_CurrentPickingNode) - { - m_View->m_Controls->m_Crosshair->setEnabled(false); - } - else - { - m_View->m_Controls->m_Crosshair->setEnabled(true); - } - - int width; - node->GetIntProperty("LineWidth", width); - m_View->m_Controls->m_LineWidth->setValue(width); - - float range; - node->GetFloatProperty("Fiber2DSliceThickness",range); - mitk::FiberBundleX::Pointer fib = dynamic_cast(node->GetData()); - mitk::BaseGeometry::Pointer geo = fib->GetGeometry(); - mitk::ScalarType max = geo->GetExtentInMM(0); - max = std::max(max, geo->GetExtentInMM(1)); - max = std::max(max, geo->GetExtentInMM(2)); - - m_View->m_Controls->m_FiberThicknessSlider->setMaximum(max * 10); - - m_View->m_Controls->m_FiberThicknessSlider->setValue(range * 10); + default: + case 1: + this->m_Controls->m_TSMenu->setText("MIP"); + break; + case 2: + this->m_Controls->m_TSMenu->setText("SUM"); + break; + case 3: + this->m_Controls->m_TSMenu->setText("WEIGH"); + break; + } - } + mitk::DataNode* n; + n = this->m_MultiWidget->GetWidgetPlane1(); if(n) n->SetProperty( "reslice.thickslices", mitk::ResliceMethodProperty::New( currentThickSlicesMode ) ); + n = this->m_MultiWidget->GetWidgetPlane2(); if(n) n->SetProperty( "reslice.thickslices", mitk::ResliceMethodProperty::New( currentThickSlicesMode ) ); + n = this->m_MultiWidget->GetWidgetPlane3(); if(n) n->SetProperty( "reslice.thickslices", mitk::ResliceMethodProperty::New( currentThickSlicesMode ) ); - } // check node data != NULL - } + mitk::BaseRenderer::Pointer renderer = + this->GetActiveStdMultiWidget()->GetRenderWindow1()->GetRenderer(); + if(renderer.IsNotNull()) + { + renderer->SendUpdateSlice(); } - - if(m_View->m_CurrentSelection->Size() > 0 && m_View->m_SelectedNode == 0) + renderer = this->GetActiveStdMultiWidget()->GetRenderWindow2()->GetRenderer(); + if(renderer.IsNotNull()) { - m_View->m_Controls->m_ImageControlsFrame->setVisible(true); - - bool foundDiffusionImage = false; - bool foundQBIVolume = false; - bool foundTensorVolume = false; - bool foundImage = false; - bool foundMultipleOdfImages = false; - bool foundRGBAImage = false; - bool foundTbssImage = false; - - // do something with the selected items - if(m_View->m_CurrentSelection) - { - // iterate selection - for (IStructuredSelection::iterator i = m_View->m_CurrentSelection->Begin(); - i != m_View->m_CurrentSelection->End(); ++i) - { - - // extract datatree node - if (mitk::DataNodeObject::Pointer nodeObj = i->Cast()) - { - mitk::DataNode::Pointer node = nodeObj->GetDataNode(); - - mitk::BaseData* nodeData = node->GetData(); - - if(nodeData != NULL ) - { - // only look at interesting types - if(QString("DiffusionImage").compare(nodeData->GetNameOfClass())==0) - { - foundDiffusionImage = true; - bool tex_int; - node->GetBoolProperty("texture interpolation", tex_int); - if(tex_int) - { - m_View->m_Controls->m_TextureIntON->setIcon(*m_View->m_IconTexON); - m_View->m_Controls->m_TextureIntON->setChecked(true); - m_View->m_TexIsOn = true; - } - else - { - m_View->m_Controls->m_TextureIntON->setIcon(*m_View->m_IconTexOFF); - m_View->m_Controls->m_TextureIntON->setChecked(false); - m_View->m_TexIsOn = false; - } - int val; - node->GetIntProperty("DisplayChannel", val); - m_View->m_Controls->m_DisplayIndex->setValue(val); - m_View->m_Controls->m_DisplayIndexSpinBox->setValue(val); - - QString label = "Channel %1"; - label = label.arg(val); - m_View->m_Controls->label_channel->setText(label); - - mitk::DiffusionPropertyHelper::ImageType::Pointer itkVectorImagePointer = mitk::DiffusionPropertyHelper::ImageType::New(); - mitk::CastToItkImage(dynamic_cast(nodeData), itkVectorImagePointer); - - int maxVal = itkVectorImagePointer->GetVectorLength(); - m_View->m_Controls->m_DisplayIndex->setMaximum(maxVal-1); - m_View->m_Controls->m_DisplayIndexSpinBox->setMaximum(maxVal-1); - } - - if(QString("TbssImage").compare(nodeData->GetNameOfClass())==0) - { - foundTbssImage = true; - bool tex_int; - node->GetBoolProperty("texture interpolation", tex_int); - if(tex_int) - { - m_View->m_Controls->m_TextureIntON->setIcon(*m_View->m_IconTexON); - m_View->m_Controls->m_TextureIntON->setChecked(true); - m_View->m_TexIsOn = true; - } - else - { - m_View->m_Controls->m_TextureIntON->setIcon(*m_View->m_IconTexOFF); - m_View->m_Controls->m_TextureIntON->setChecked(false); - m_View->m_TexIsOn = false; - } - int val; - node->GetIntProperty("DisplayChannel", val); - m_View->m_Controls->m_DisplayIndex->setValue(val); - m_View->m_Controls->m_DisplayIndexSpinBox->setValue(val); - - QString label = "Channel %1"; - label = label.arg(val); - m_View->m_Controls->label_channel->setText(label); - - int maxVal = (dynamic_cast(nodeData))->GetImage()->GetVectorLength(); - m_View->m_Controls->m_DisplayIndex->setMaximum(maxVal-1); - m_View->m_Controls->m_DisplayIndexSpinBox->setMaximum(maxVal-1); - } - - - else if(QString("QBallImage").compare(nodeData->GetNameOfClass())==0) - { - foundMultipleOdfImages = foundQBIVolume || foundTensorVolume; - foundQBIVolume = true; - ApplySettings(node); - } - - else if(QString("TensorImage").compare(nodeData->GetNameOfClass())==0) - { - foundMultipleOdfImages = foundQBIVolume || foundTensorVolume; - foundTensorVolume = true; - ApplySettings(node); - } - - else if(QString("Image").compare(nodeData->GetNameOfClass())==0) - { - foundImage = true; - mitk::Image::Pointer img = dynamic_cast(nodeData); - if(img.IsNotNull() - && img->GetPixelType().GetPixelType() == itk::ImageIOBase::RGBA - && img->GetPixelType().GetComponentType() == itk::ImageIOBase::UCHAR ) - { - foundRGBAImage = true; - } - - bool tex_int; - node->GetBoolProperty("texture interpolation", tex_int); - if(tex_int) - { - m_View->m_Controls->m_TextureIntON->setIcon(*m_View->m_IconTexON); - m_View->m_Controls->m_TextureIntON->setChecked(true); - m_View->m_TexIsOn = true; - } - else - { - m_View->m_Controls->m_TextureIntON->setIcon(*m_View->m_IconTexOFF); - m_View->m_Controls->m_TextureIntON->setChecked(false); - m_View->m_TexIsOn = false; - } - } - - } // END CHECK node != NULL - } - } - } - - m_View->m_FoundSingleOdfImage = (foundQBIVolume || foundTensorVolume) - && !foundMultipleOdfImages; - m_View->m_Controls->m_NumberGlyphsFrame->setVisible(m_View->m_FoundSingleOdfImage); - - m_View->m_Controls->m_NormalizationDropdown->setVisible(m_View->m_FoundSingleOdfImage); - m_View->m_Controls->label->setVisible(m_View->m_FoundSingleOdfImage); - m_View->m_Controls->m_ScalingFactor->setVisible(m_View->m_FoundSingleOdfImage); - m_View->m_Controls->m_AdditionalScaling->setVisible(m_View->m_FoundSingleOdfImage); - m_View->m_Controls->m_NormalizationScalingFrame->setVisible(m_View->m_FoundSingleOdfImage); - - m_View->m_Controls->OpacMinFrame->setVisible(foundRGBAImage || m_View->m_FoundSingleOdfImage); - - // changed for SPIE paper, Principle curvature scaling - //m_View->m_Controls->params_frame->setVisible(m_View->m_FoundSingleOdfImage); - m_View->m_Controls->params_frame->setVisible(false); - - m_View->m_Controls->m_VisibleOdfsON_T->setVisible(m_View->m_FoundSingleOdfImage); - m_View->m_Controls->m_VisibleOdfsON_S->setVisible(m_View->m_FoundSingleOdfImage); - m_View->m_Controls->m_VisibleOdfsON_C->setVisible(m_View->m_FoundSingleOdfImage); - - bool foundAnyImage = foundDiffusionImage || - foundQBIVolume || foundTensorVolume || foundImage || foundTbssImage; - - m_View->m_Controls->m_Reinit->setVisible(foundAnyImage); - m_View->m_Controls->m_TextureIntON->setVisible(foundAnyImage); - m_View->m_Controls->m_TSMenu->setVisible(foundAnyImage); - + renderer->SendUpdateSlice(); } - } - - void SelectionChanged(IWorkbenchPart::Pointer part, ISelection::ConstPointer selection) - { - // check, if selection comes from datamanager - if (part) + renderer = this->GetActiveStdMultiWidget()->GetRenderWindow3()->GetRenderer(); + if(renderer.IsNotNull()) { - QString partname(part->GetPartName().c_str()); - if(partname.compare("Data Manager")==0) - { - - // apply selection - DoSelectionChanged(selection); - - } + renderer->SendUpdateSlice(); } - } - - QmitkControlVisualizationPropertiesView* m_View; -}; - -QmitkControlVisualizationPropertiesView::QmitkControlVisualizationPropertiesView() - : QmitkFunctionality(), - m_Controls(NULL), - m_MultiWidget(NULL), - m_NodeUsedForOdfVisualization(NULL), - m_IconTexOFF(new QIcon(":/QmitkDiffusionImaging/texIntOFFIcon.png")), - m_IconTexON(new QIcon(":/QmitkDiffusionImaging/texIntONIcon.png")), - m_IconGlyOFF_T(new QIcon(":/QmitkDiffusionImaging/glyphsoff_T.png")), - m_IconGlyON_T(new QIcon(":/QmitkDiffusionImaging/glyphson_T.png")), - m_IconGlyOFF_C(new QIcon(":/QmitkDiffusionImaging/glyphsoff_C.png")), - m_IconGlyON_C(new QIcon(":/QmitkDiffusionImaging/glyphson_C.png")), - m_IconGlyOFF_S(new QIcon(":/QmitkDiffusionImaging/glyphsoff_S.png")), - m_IconGlyON_S(new QIcon(":/QmitkDiffusionImaging/glyphson_S.png")), - m_CurrentSelection(0), - m_CurrentPickingNode(0), - m_GlyIsOn_S(false), - m_GlyIsOn_C(false), - m_GlyIsOn_T(false), - m_FiberBundleObserverTag(0), - m_Color(NULL) -{ - currentThickSlicesMode = 1; - m_MyMenu = NULL; - int numThread = itk::MultiThreader::GetGlobalMaximumNumberOfThreads(); - if (numThread > 12) - numThread = 12; - itk::MultiThreader::SetGlobalDefaultNumberOfThreads(numThread); -} - -QmitkControlVisualizationPropertiesView::QmitkControlVisualizationPropertiesView(const QmitkControlVisualizationPropertiesView& other) -{ - Q_UNUSED(other) - throw std::runtime_error("Copy constructor not implemented"); -} - -QmitkControlVisualizationPropertiesView::~QmitkControlVisualizationPropertiesView() -{ - if(m_SlicesRotationObserverTag1 ) - { - mitk::SlicesCoordinator::Pointer coordinator = m_MultiWidget->GetSlicesRotator(); - if( coordinator.IsNotNull() ) - coordinator->RemoveObserver(m_SlicesRotationObserverTag1); - } - if( m_SlicesRotationObserverTag2) - { - mitk::SlicesCoordinator::Pointer coordinator = m_MultiWidget->GetSlicesRotator(); - if( coordinator.IsNotNull() ) - coordinator->RemoveObserver(m_SlicesRotationObserverTag1); - } - - this->GetSite()->GetWorkbenchWindow()->GetSelectionService()->RemovePostSelectionListener(/*"org.mitk.views.datamanager",*/ m_SelListener); -} - -void QmitkControlVisualizationPropertiesView::OnThickSlicesModeSelected( QAction* action ) -{ - currentThickSlicesMode = action->data().toInt(); - - switch(currentThickSlicesMode) - { - default: - case 1: - this->m_Controls->m_TSMenu->setText("MIP"); - break; - case 2: - this->m_Controls->m_TSMenu->setText("SUM"); - break; - case 3: - this->m_Controls->m_TSMenu->setText("WEIGH"); - break; - } - - mitk::DataNode* n; - n = this->m_MultiWidget->GetWidgetPlane1(); if(n) n->SetProperty( "reslice.thickslices", mitk::ResliceMethodProperty::New( currentThickSlicesMode ) ); - n = this->m_MultiWidget->GetWidgetPlane2(); if(n) n->SetProperty( "reslice.thickslices", mitk::ResliceMethodProperty::New( currentThickSlicesMode ) ); - n = this->m_MultiWidget->GetWidgetPlane3(); if(n) n->SetProperty( "reslice.thickslices", mitk::ResliceMethodProperty::New( currentThickSlicesMode ) ); - - mitk::BaseRenderer::Pointer renderer = - this->GetActiveStdMultiWidget()->GetRenderWindow1()->GetRenderer(); - if(renderer.IsNotNull()) - { - renderer->SendUpdateSlice(); - } - renderer = this->GetActiveStdMultiWidget()->GetRenderWindow2()->GetRenderer(); - if(renderer.IsNotNull()) - { - renderer->SendUpdateSlice(); - } - renderer = this->GetActiveStdMultiWidget()->GetRenderWindow3()->GetRenderer(); - if(renderer.IsNotNull()) - { - renderer->SendUpdateSlice(); - } - renderer->GetRenderingManager()->RequestUpdateAll(); + renderer->GetRenderingManager()->RequestUpdateAll(); } void QmitkControlVisualizationPropertiesView::OnTSNumChanged(int num) { - if(num==0) - { - mitk::DataNode* n; - n = this->m_MultiWidget->GetWidgetPlane1(); - if(n) n->SetProperty( "reslice.thickslices", mitk::ResliceMethodProperty::New( 0 ) ); - if(n) n->SetProperty( "reslice.thickslices.num", mitk::IntProperty::New( num ) ); - if(n) n->SetProperty( "reslice.thickslices.showarea", mitk::BoolProperty::New( false ) ); - - n = this->m_MultiWidget->GetWidgetPlane2(); - if(n) n->SetProperty( "reslice.thickslices", mitk::ResliceMethodProperty::New( 0 ) ); - if(n) n->SetProperty( "reslice.thickslices.num", mitk::IntProperty::New( num ) ); - if(n) n->SetProperty( "reslice.thickslices.showarea", mitk::BoolProperty::New( false ) ); - - n = this->m_MultiWidget->GetWidgetPlane3(); - if(n) n->SetProperty( "reslice.thickslices", mitk::ResliceMethodProperty::New( 0 ) ); - if(n) n->SetProperty( "reslice.thickslices.num", mitk::IntProperty::New( num ) ); - if(n) n->SetProperty( "reslice.thickslices.showarea", mitk::BoolProperty::New( false ) ); - } - else - { - mitk::DataNode* n; - n = this->m_MultiWidget->GetWidgetPlane1(); - if(n) n->SetProperty( "reslice.thickslices", mitk::ResliceMethodProperty::New( currentThickSlicesMode ) ); - if(n) n->SetProperty( "reslice.thickslices.num", mitk::IntProperty::New( num ) ); - if(n) n->SetProperty( "reslice.thickslices.showarea", mitk::BoolProperty::New( (num>0) ) ); - - n = this->m_MultiWidget->GetWidgetPlane2(); - if(n) n->SetProperty( "reslice.thickslices", mitk::ResliceMethodProperty::New( currentThickSlicesMode ) ); - if(n) n->SetProperty( "reslice.thickslices.num", mitk::IntProperty::New( num ) ); - if(n) n->SetProperty( "reslice.thickslices.showarea", mitk::BoolProperty::New( (num>0) ) ); - - n = this->m_MultiWidget->GetWidgetPlane3(); - if(n) n->SetProperty( "reslice.thickslices", mitk::ResliceMethodProperty::New( currentThickSlicesMode ) ); - if(n) n->SetProperty( "reslice.thickslices.num", mitk::IntProperty::New( num ) ); - if(n) n->SetProperty( "reslice.thickslices.showarea", mitk::BoolProperty::New( (num>0) ) ); - } + if(num==0) + { + mitk::DataNode* n; + n = this->m_MultiWidget->GetWidgetPlane1(); + if(n) n->SetProperty( "reslice.thickslices", mitk::ResliceMethodProperty::New( 0 ) ); + if(n) n->SetProperty( "reslice.thickslices.num", mitk::IntProperty::New( num ) ); + if(n) n->SetProperty( "reslice.thickslices.showarea", mitk::BoolProperty::New( false ) ); + + n = this->m_MultiWidget->GetWidgetPlane2(); + if(n) n->SetProperty( "reslice.thickslices", mitk::ResliceMethodProperty::New( 0 ) ); + if(n) n->SetProperty( "reslice.thickslices.num", mitk::IntProperty::New( num ) ); + if(n) n->SetProperty( "reslice.thickslices.showarea", mitk::BoolProperty::New( false ) ); + + n = this->m_MultiWidget->GetWidgetPlane3(); + if(n) n->SetProperty( "reslice.thickslices", mitk::ResliceMethodProperty::New( 0 ) ); + if(n) n->SetProperty( "reslice.thickslices.num", mitk::IntProperty::New( num ) ); + if(n) n->SetProperty( "reslice.thickslices.showarea", mitk::BoolProperty::New( false ) ); + } + else + { + mitk::DataNode* n; + n = this->m_MultiWidget->GetWidgetPlane1(); + if(n) n->SetProperty( "reslice.thickslices", mitk::ResliceMethodProperty::New( currentThickSlicesMode ) ); + if(n) n->SetProperty( "reslice.thickslices.num", mitk::IntProperty::New( num ) ); + if(n) n->SetProperty( "reslice.thickslices.showarea", mitk::BoolProperty::New( (num>0) ) ); + + n = this->m_MultiWidget->GetWidgetPlane2(); + if(n) n->SetProperty( "reslice.thickslices", mitk::ResliceMethodProperty::New( currentThickSlicesMode ) ); + if(n) n->SetProperty( "reslice.thickslices.num", mitk::IntProperty::New( num ) ); + if(n) n->SetProperty( "reslice.thickslices.showarea", mitk::BoolProperty::New( (num>0) ) ); + + n = this->m_MultiWidget->GetWidgetPlane3(); + if(n) n->SetProperty( "reslice.thickslices", mitk::ResliceMethodProperty::New( currentThickSlicesMode ) ); + if(n) n->SetProperty( "reslice.thickslices.num", mitk::IntProperty::New( num ) ); + if(n) n->SetProperty( "reslice.thickslices.showarea", mitk::BoolProperty::New( (num>0) ) ); + } - m_TSLabel->setText(QString::number(num*2+1)); + m_TSLabel->setText(QString::number(num*2+1)); - mitk::BaseRenderer::Pointer renderer = this->GetActiveStdMultiWidget()->GetRenderWindow1()->GetRenderer(); - if(renderer.IsNotNull()) - renderer->SendUpdateSlice(); + mitk::BaseRenderer::Pointer renderer = this->GetActiveStdMultiWidget()->GetRenderWindow1()->GetRenderer(); + if(renderer.IsNotNull()) + renderer->SendUpdateSlice(); - renderer = this->GetActiveStdMultiWidget()->GetRenderWindow2()->GetRenderer(); - if(renderer.IsNotNull()) - renderer->SendUpdateSlice(); + renderer = this->GetActiveStdMultiWidget()->GetRenderWindow2()->GetRenderer(); + if(renderer.IsNotNull()) + renderer->SendUpdateSlice(); - renderer = this->GetActiveStdMultiWidget()->GetRenderWindow3()->GetRenderer(); - if(renderer.IsNotNull()) - renderer->SendUpdateSlice(); + renderer = this->GetActiveStdMultiWidget()->GetRenderWindow3()->GetRenderer(); + if(renderer.IsNotNull()) + renderer->SendUpdateSlice(); - renderer->GetRenderingManager()->RequestUpdateAll(mitk::RenderingManager::REQUEST_UPDATE_2DWINDOWS); + renderer->GetRenderingManager()->RequestUpdateAll(mitk::RenderingManager::REQUEST_UPDATE_2DWINDOWS); } void QmitkControlVisualizationPropertiesView::CreateQtPartControl(QWidget *parent) { - if (!m_Controls) - { - // create GUI widgets - m_Controls = new Ui::QmitkControlVisualizationPropertiesViewControls; - m_Controls->setupUi(parent); - this->CreateConnections(); - - // hide warning (ODFs in rotated planes) - m_Controls->m_lblRotatedPlanesWarning->hide(); - - m_MyMenu = new QMenu(parent); - - // button for changing rotation mode - m_Controls->m_TSMenu->setMenu( m_MyMenu ); - //m_CrosshairModeButton->setIcon( QIcon( iconCrosshairMode_xpm ) ); - - m_Controls->params_frame->setVisible(false); - - QIcon icon5(":/QmitkDiffusionImaging/Refresh_48.png"); - m_Controls->m_Reinit->setIcon(icon5); - m_Controls->m_Focus->setIcon(icon5); - - QIcon iconColor(":/QmitkDiffusionImaging/color24.gif"); - m_Controls->m_PFColor->setIcon(iconColor); - m_Controls->m_Color->setIcon(iconColor); - - QIcon iconReset(":/QmitkDiffusionImaging/reset.png"); - m_Controls->m_ResetColoring->setIcon(iconReset); - - m_Controls->m_PFColor->setToolButtonStyle(Qt::ToolButtonTextBesideIcon); + if (!m_Controls) + { + // create GUI widgets + m_Controls = new Ui::QmitkControlVisualizationPropertiesViewControls; + m_Controls->setupUi(parent); + this->CreateConnections(); - QIcon iconCrosshair(":/QmitkDiffusionImaging/crosshair.png"); - m_Controls->m_Crosshair->setIcon(iconCrosshair); - // was is los - QIcon iconPaint(":/QmitkDiffusionImaging/paint2.png"); - m_Controls->m_TDI->setIcon(iconPaint); + // hide warning (ODFs in rotated planes) + m_Controls->m_lblRotatedPlanesWarning->hide(); - QIcon iconFiberFade(":/QmitkDiffusionImaging/MapperEfx2D.png"); - m_Controls->m_FiberFading2D->setIcon(iconFiberFade); + m_MyMenu = new QMenu(parent); + m_Controls->m_TSMenu->setMenu( m_MyMenu ); - m_Controls->m_TextureIntON->setCheckable(true); + QIcon iconFiberFade(":/QmitkDiffusionImaging/MapperEfx2D.png"); + m_Controls->m_FiberFading2D->setIcon(iconFiberFade); #ifndef DIFFUSION_IMAGING_EXTENDED - int size = m_Controls->m_AdditionalScaling->count(); - for(int t=0; tm_AdditionalScaling->itemText(t).toStdString() == "Scale by ASR") - { - m_Controls->m_AdditionalScaling->removeItem(t); - } - } + int size = m_Controls->m_AdditionalScaling->count(); + for(int t=0; tm_AdditionalScaling->itemText(t).toStdString() == "Scale by ASR") + { + m_Controls->m_AdditionalScaling->removeItem(t); + } + } #endif - m_Controls->m_OpacitySlider->setRange(0.0,1.0); - m_Controls->m_OpacitySlider->setMinimumValue(0.0); - m_Controls->m_OpacitySlider->setMaximumValue(0.0); - - m_Controls->m_ScalingFrame->setVisible(false); - m_Controls->m_NormalizationFrame->setVisible(false); - } - - m_IsInitialized = false; - m_SelListener = berry::ISelectionListener::Pointer(new CvpSelListener(this)); - this->GetSite()->GetWorkbenchWindow()->GetSelectionService()->AddPostSelectionListener(/*"org.mitk.views.datamanager",*/ m_SelListener); - berry::ISelection::ConstPointer sel( - this->GetSite()->GetWorkbenchWindow()->GetSelectionService()->GetSelection("org.mitk.views.datamanager")); - m_CurrentSelection = sel.Cast(); - m_SelListener.Cast()->DoSelectionChanged(sel); - m_IsInitialized = true; + m_Controls->m_ScalingFrame->setVisible(false); + m_Controls->m_NormalizationFrame->setVisible(false); + } } void QmitkControlVisualizationPropertiesView::StdMultiWidgetAvailable (QmitkStdMultiWidget &stdMultiWidget) { - m_MultiWidget = &stdMultiWidget; + m_MultiWidget = &stdMultiWidget; - if (m_MultiWidget) - { - mitk::SlicesCoordinator* coordinator = m_MultiWidget->GetSlicesRotator(); - if (coordinator) + if (m_MultiWidget) { - itk::ReceptorMemberCommand::Pointer command2 = itk::ReceptorMemberCommand::New(); - command2->SetCallbackFunction( this, &QmitkControlVisualizationPropertiesView::SliceRotation ); - m_SlicesRotationObserverTag1 = coordinator->AddObserver( mitk::SliceRotationEvent(), command2 ); - } + mitk::SlicesCoordinator* coordinator = m_MultiWidget->GetSlicesRotator(); + if (coordinator) + { + itk::ReceptorMemberCommand::Pointer command2 = itk::ReceptorMemberCommand::New(); + command2->SetCallbackFunction( this, &QmitkControlVisualizationPropertiesView::SliceRotation ); + m_SlicesRotationObserverTag1 = coordinator->AddObserver( mitk::SliceRotationEvent(), command2 ); + } - coordinator = m_MultiWidget->GetSlicesSwiveller(); - if (coordinator) - { - itk::ReceptorMemberCommand::Pointer command2 = itk::ReceptorMemberCommand::New(); - command2->SetCallbackFunction( this, &QmitkControlVisualizationPropertiesView::SliceRotation ); - m_SlicesRotationObserverTag2 = coordinator->AddObserver( mitk::SliceRotationEvent(), command2 ); + coordinator = m_MultiWidget->GetSlicesSwiveller(); + if (coordinator) + { + itk::ReceptorMemberCommand::Pointer command2 = itk::ReceptorMemberCommand::New(); + command2->SetCallbackFunction( this, &QmitkControlVisualizationPropertiesView::SliceRotation ); + m_SlicesRotationObserverTag2 = coordinator->AddObserver( mitk::SliceRotationEvent(), command2 ); + } } - } } void QmitkControlVisualizationPropertiesView::SliceRotation(const itk::EventObject&) { - // test if plane rotated - if( m_GlyIsOn_T || m_GlyIsOn_C || m_GlyIsOn_S ) - { - if( this->IsPlaneRotated() ) + // test if plane rotated + if( m_GlyIsOn_T || m_GlyIsOn_C || m_GlyIsOn_S ) { - // show label - m_Controls->m_lblRotatedPlanesWarning->show(); - } - else - { - //hide label - m_Controls->m_lblRotatedPlanesWarning->hide(); + if( this->IsPlaneRotated() ) + { + // show label + m_Controls->m_lblRotatedPlanesWarning->show(); + } + else + { + //hide label + m_Controls->m_lblRotatedPlanesWarning->hide(); + } } - } } - void QmitkControlVisualizationPropertiesView::StdMultiWidgetNotAvailable() { - m_MultiWidget = NULL; + m_MultiWidget = NULL; } void QmitkControlVisualizationPropertiesView::NodeRemoved(const mitk::DataNode* node) { } #include void QmitkControlVisualizationPropertiesView::CreateConnections() { - if ( m_Controls ) - { - connect( (QObject*)(m_Controls->m_DisplayIndex), SIGNAL(valueChanged(int)), this, SLOT(DisplayIndexChanged(int)) ); - connect( (QObject*)(m_Controls->m_DisplayIndexSpinBox), SIGNAL(valueChanged(int)), this, SLOT(DisplayIndexChanged(int)) ); - connect( (QObject*)(m_Controls->m_TextureIntON), SIGNAL(clicked()), this, SLOT(TextIntON()) ); - connect( (QObject*)(m_Controls->m_Reinit), SIGNAL(clicked()), this, SLOT(Reinit()) ); - connect( (QObject*)(m_Controls->m_VisibleOdfsON_T), SIGNAL(clicked()), this, SLOT(VisibleOdfsON_T()) ); - connect( (QObject*)(m_Controls->m_VisibleOdfsON_S), SIGNAL(clicked()), this, SLOT(VisibleOdfsON_S()) ); - connect( (QObject*)(m_Controls->m_VisibleOdfsON_C), SIGNAL(clicked()), this, SLOT(VisibleOdfsON_C()) ); - connect( (QObject*)(m_Controls->m_ShowMaxNumber), SIGNAL(editingFinished()), this, SLOT(ShowMaxNumberChanged()) ); - connect( (QObject*)(m_Controls->m_NormalizationDropdown), SIGNAL(currentIndexChanged(int)), this, SLOT(NormalizationDropdownChanged(int)) ); - connect( (QObject*)(m_Controls->m_ScalingFactor), SIGNAL(valueChanged(double)), this, SLOT(ScalingFactorChanged(double)) ); - connect( (QObject*)(m_Controls->m_AdditionalScaling), SIGNAL(currentIndexChanged(int)), this, SLOT(AdditionalScaling(int)) ); - connect( (QObject*)(m_Controls->m_IndexParam1), SIGNAL(valueChanged(double)), this, SLOT(IndexParam1Changed(double)) ); - connect( (QObject*)(m_Controls->m_IndexParam2), SIGNAL(valueChanged(double)), this, SLOT(IndexParam2Changed(double)) ); - connect( (QObject*)(m_Controls->m_ScalingCheckbox), SIGNAL(clicked()), this, SLOT(ScalingCheckbox()) ); - connect( (QObject*)(m_Controls->m_OpacitySlider), SIGNAL(spanChanged(double,double)), this, SLOT(OpacityChanged(double,double)) ); - connect((QObject*) m_Controls->m_Color, SIGNAL(clicked()), (QObject*) this, SLOT(BundleRepresentationColor())); - connect((QObject*) m_Controls->m_ResetColoring, SIGNAL(clicked()), (QObject*) this, SLOT(BundleRepresentationResetColoring())); - connect((QObject*) m_Controls->m_Focus, SIGNAL(clicked()), (QObject*) this, SLOT(PlanarFigureFocus())); - connect((QObject*) m_Controls->m_FiberFading2D, SIGNAL(clicked()), (QObject*) this, SLOT( Fiber2DfadingEFX() ) ); - connect((QObject*) m_Controls->m_FiberThicknessSlider, SIGNAL(sliderReleased()), (QObject*) this, SLOT( FiberSlicingThickness2D() ) ); - connect((QObject*) m_Controls->m_FiberThicknessSlider, SIGNAL(valueChanged(int)), (QObject*) this, SLOT( FiberSlicingUpdateLabel(int) )); - connect((QObject*) m_Controls->m_Crosshair, SIGNAL(clicked()), (QObject*) this, SLOT(SetInteractor())); - connect((QObject*) m_Controls->m_PFWidth, SIGNAL(valueChanged(int)), (QObject*) this, SLOT(PFWidth(int))); - connect((QObject*) m_Controls->m_PFColor, SIGNAL(clicked()), (QObject*) this, SLOT(PFColor())); - connect((QObject*) m_Controls->m_TDI, SIGNAL(clicked()), (QObject*) this, SLOT(GenerateTdi())); - connect((QObject*) m_Controls->m_LineWidth, SIGNAL(editingFinished()), (QObject*) this, SLOT(LineWidthChanged())); - } + if ( m_Controls ) + { + connect( (QObject*)(m_Controls->m_VisibleOdfsON_T), SIGNAL(clicked()), this, SLOT(VisibleOdfsON_T()) ); + connect( (QObject*)(m_Controls->m_VisibleOdfsON_S), SIGNAL(clicked()), this, SLOT(VisibleOdfsON_S()) ); + connect( (QObject*)(m_Controls->m_VisibleOdfsON_C), SIGNAL(clicked()), this, SLOT(VisibleOdfsON_C()) ); + connect( (QObject*)(m_Controls->m_ShowMaxNumber), SIGNAL(editingFinished()), this, SLOT(ShowMaxNumberChanged()) ); + connect( (QObject*)(m_Controls->m_NormalizationDropdown), SIGNAL(currentIndexChanged(int)), this, SLOT(NormalizationDropdownChanged(int)) ); + connect( (QObject*)(m_Controls->m_ScalingFactor), SIGNAL(valueChanged(double)), this, SLOT(ScalingFactorChanged(double)) ); + connect( (QObject*)(m_Controls->m_AdditionalScaling), SIGNAL(currentIndexChanged(int)), this, SLOT(AdditionalScaling(int)) ); + connect( (QObject*)(m_Controls->m_ScalingCheckbox), SIGNAL(clicked()), this, SLOT(ScalingCheckbox()) ); + connect((QObject*) m_Controls->m_ResetColoring, SIGNAL(clicked()), (QObject*) this, SLOT(BundleRepresentationResetColoring())); + connect((QObject*) m_Controls->m_FiberFading2D, SIGNAL(clicked()), (QObject*) this, SLOT( Fiber2DfadingEFX() ) ); + connect((QObject*) m_Controls->m_FiberThicknessSlider, SIGNAL(sliderReleased()), (QObject*) this, SLOT( FiberSlicingThickness2D() ) ); + connect((QObject*) m_Controls->m_FiberThicknessSlider, SIGNAL(valueChanged(int)), (QObject*) this, SLOT( FiberSlicingUpdateLabel(int) )); + connect((QObject*) m_Controls->m_Crosshair, SIGNAL(clicked()), (QObject*) this, SLOT(SetInteractor())); + connect((QObject*) m_Controls->m_LineWidth, SIGNAL(editingFinished()), (QObject*) this, SLOT(LineWidthChanged())); + } } void QmitkControlVisualizationPropertiesView::Activated() { - berry::ISelection::ConstPointer sel( - this->GetSite()->GetWorkbenchWindow()->GetSelectionService()->GetSelection("org.mitk.views.datamanager")); - m_CurrentSelection = sel.Cast(); - m_SelListener.Cast()->DoSelectionChanged(sel); - QmitkFunctionality::Activated(); -} -void QmitkControlVisualizationPropertiesView::Deactivated() -{ - QmitkFunctionality::Deactivated(); } -int QmitkControlVisualizationPropertiesView::GetSizeFlags(bool width) +void QmitkControlVisualizationPropertiesView::Deactivated() { - if(!width) - { - return berry::Constants::MIN | berry::Constants::MAX | berry::Constants::FILL; - } - else - { - return 0; - } -} -int QmitkControlVisualizationPropertiesView::ComputePreferredSize(bool width, int /*availableParallel*/, int /*availablePerpendicular*/, int preferredResult) -{ - if(width==false) - { - return m_FoundSingleOdfImage ? 120 : 80; - } - else - { - return preferredResult; - } } // set diffusion image channel to b0 volume void QmitkControlVisualizationPropertiesView::NodeAdded(const mitk::DataNode *node) { - mitk::DataNode* notConst = const_cast(node); + mitk::DataNode* notConst = const_cast(node); - bool isDiffusionImage( mitk::DiffusionPropertyHelper::IsDiffusionWeightedImage( dynamic_cast(node->GetData())) ); + bool isDiffusionImage( mitk::DiffusionPropertyHelper::IsDiffusionWeightedImage( dynamic_cast(node->GetData())) ); - if (isDiffusionImage) - { - mitk::Image::Pointer dimg = dynamic_cast(notConst->GetData()); + if (isDiffusionImage) + { + mitk::Image::Pointer dimg = dynamic_cast(notConst->GetData()); - // if there is no b0 image in the dataset, the GetB0Indices() returns a vector of size 0 - // and hence we cannot set the Property directly to .front() - int displayChannelPropertyValue = 0; - mitk::BValueMapProperty* bmapproperty = static_cast(dimg->GetProperty(mitk::DiffusionPropertyHelper::BVALUEMAPPROPERTYNAME.c_str()).GetPointer() ); - mitk::DiffusionPropertyHelper::BValueMapType map = bmapproperty->GetBValueMap(); - if( map[0].size() > 0) - displayChannelPropertyValue = map[0].front(); + // if there is no b0 image in the dataset, the GetB0Indices() returns a vector of size 0 + // and hence we cannot set the Property directly to .front() + int displayChannelPropertyValue = 0; + mitk::BValueMapProperty* bmapproperty = static_cast(dimg->GetProperty(mitk::DiffusionPropertyHelper::BVALUEMAPPROPERTYNAME.c_str()).GetPointer() ); + mitk::DiffusionPropertyHelper::BValueMapType map = bmapproperty->GetBValueMap(); + if( map[0].size() > 0) + displayChannelPropertyValue = map[0].front(); - notConst->SetIntProperty("DisplayChannel", displayChannelPropertyValue ); - } + notConst->SetIntProperty("DisplayChannel", displayChannelPropertyValue ); + } } /* OnSelectionChanged is registered to SelectionService, therefore no need to implement SelectionService Listener explicitly */ void QmitkControlVisualizationPropertiesView::OnSelectionChanged( std::vector nodes ) { + m_Controls->m_BundleControlsFrame->setVisible(false); + m_Controls->m_ImageControlsFrame->setVisible(false); - // deactivate channel slider if no diffusion weighted image or tbss image is selected - m_Controls->m_DisplayIndex->setVisible(false); - m_Controls->m_DisplayIndexSpinBox->setVisible(false); - m_Controls->label_channel->setVisible(false); + if (nodes.size()>1) // only do stuff if one node is selected + return; - for( std::vector::iterator it = nodes.begin(); it != nodes.end(); ++it ) - { - mitk::DataNode::Pointer node = *it; + m_Controls->m_NumberGlyphsFrame->setVisible(false); + m_Controls->m_GlyphFrame->setVisible(false); + m_Controls->m_TSMenu->setVisible(false); - // check if node has data, - // if some helper nodes are shown in the DataManager, the GetData() returns 0x0 which would lead to SIGSEV - mitk::BaseData* nodeData = node->GetData(); - if(nodeData == NULL) - continue; + m_SelectedNode = NULL; - bool isDiffusionImage( mitk::DiffusionPropertyHelper::IsDiffusionWeightedImage( dynamic_cast(node->GetData())) ); + int numOdfImages = 0; + for( std::vector::iterator it = nodes.begin(); it != nodes.end(); ++it ) + { + mitk::DataNode::Pointer node = *it; + if(node.IsNull()) + continue; + + mitk::BaseData* nodeData = node->GetData(); + if(nodeData == NULL) + continue; + m_SelectedNode = node; - if (node.IsNotNull() && (dynamic_cast(nodeData) || - isDiffusionImage)) - { - m_Controls->m_DisplayIndex->setVisible(true); - m_Controls->m_DisplayIndexSpinBox->setVisible(true); - m_Controls->label_channel->setVisible(true); - } - else if (node.IsNotNull() && dynamic_cast(node->GetData())) - { - if (m_Color.IsNotNull()) - m_Color->RemoveObserver(m_FiberBundleObserverTag); - - itk::ReceptorMemberCommand::Pointer command = itk::ReceptorMemberCommand::New(); - command->SetCallbackFunction( this, &QmitkControlVisualizationPropertiesView::SetFiberBundleCustomColor ); - m_Color = dynamic_cast(node->GetProperty("color", NULL)); - if (m_Color.IsNotNull()) - m_FiberBundleObserverTag = m_Color->AddObserver( itk::ModifiedEvent(), command ); - } - } + if (dynamic_cast(nodeData)) + { + // handle fiber bundle property observers + if (m_Color.IsNotNull()) + m_Color->RemoveObserver(m_FiberBundleObserverTag); + itk::ReceptorMemberCommand::Pointer command = itk::ReceptorMemberCommand::New(); + command->SetCallbackFunction( this, &QmitkControlVisualizationPropertiesView::SetFiberBundleCustomColor ); + m_Color = dynamic_cast(node->GetProperty("color", NULL)); + if (m_Color.IsNotNull()) + m_FiberBundleObserverTag = m_Color->AddObserver( itk::ModifiedEvent(), command ); + + if (m_Opacity.IsNotNull()) + m_Opacity->RemoveObserver(m_FiberBundleObserveOpacityTag); + itk::ReceptorMemberCommand::Pointer command2 = itk::ReceptorMemberCommand::New(); + command2->SetCallbackFunction( this, &QmitkControlVisualizationPropertiesView::SetFiberBundleOpacity ); + m_Opacity = dynamic_cast(node->GetProperty("opacity", NULL)); + if (m_Opacity.IsNotNull()) + m_FiberBundleObserveOpacityTag = m_Opacity->AddObserver( itk::ModifiedEvent(), command2 ); + + m_Controls->m_BundleControlsFrame->setVisible(true); + + // ??? + if(m_CurrentPickingNode != 0 && node.GetPointer() != m_CurrentPickingNode) + m_Controls->m_Crosshair->setEnabled(false); + else + m_Controls->m_Crosshair->setEnabled(true); - for( std::vector::iterator it = nodes.begin(); it != nodes.end(); ++it ) - { - mitk::DataNode::Pointer node = *it; + int width; + node->GetIntProperty("LineWidth", width); + m_Controls->m_LineWidth->setValue(width); - // check if node has data, - // if some helper nodes are shown in the DataManager, the GetData() returns 0x0 which would lead to SIGSEV - mitk::BaseData* nodeData = node->GetData(); - if(nodeData == NULL) - continue; + float range; + node->GetFloatProperty("Fiber2DSliceThickness",range); + mitk::FiberBundleX::Pointer fib = dynamic_cast(node->GetData()); + mitk::BaseGeometry::Pointer geo = fib->GetGeometry(); + mitk::ScalarType max = geo->GetExtentInMM(0); + max = std::max(max, geo->GetExtentInMM(1)); + max = std::max(max, geo->GetExtentInMM(2)); - if( node.IsNotNull() && (dynamic_cast(nodeData) || dynamic_cast(nodeData)) ) - { - if(m_NodeUsedForOdfVisualization.IsNotNull()) - { - m_NodeUsedForOdfVisualization->SetBoolProperty("VisibleOdfs_S", false); - m_NodeUsedForOdfVisualization->SetBoolProperty("VisibleOdfs_C", false); - m_NodeUsedForOdfVisualization->SetBoolProperty("VisibleOdfs_T", false); - } - m_NodeUsedForOdfVisualization = node; - m_NodeUsedForOdfVisualization->SetBoolProperty("VisibleOdfs_S", m_GlyIsOn_S); - m_NodeUsedForOdfVisualization->SetBoolProperty("VisibleOdfs_C", m_GlyIsOn_C); - m_NodeUsedForOdfVisualization->SetBoolProperty("VisibleOdfs_T", m_GlyIsOn_T); - if(m_MultiWidget) - m_MultiWidget->RequestUpdate(); + m_Controls->m_FiberThicknessSlider->setMaximum(max * 10); + m_Controls->m_FiberThicknessSlider->setValue(range * 10); + m_Controls->m_FiberThicknessSlider->setFocus(); + } + else if(dynamic_cast(nodeData) || dynamic_cast(nodeData)) + { + m_Controls->m_ImageControlsFrame->setVisible(true); + m_Controls->m_NumberGlyphsFrame->setVisible(true); + m_Controls->m_GlyphFrame->setVisible(true); - m_Controls->m_TSMenu->setVisible(false); // deactivate mip etc. for tensor and q-ball images - break; - } - else if( node.IsNotNull() && dynamic_cast(nodeData) ) - m_Controls->m_TSMenu->setVisible(false); - else - m_Controls->m_TSMenu->setVisible(true); - } + if(m_NodeUsedForOdfVisualization.IsNotNull()) + { + m_NodeUsedForOdfVisualization->SetBoolProperty("VisibleOdfs_S", false); + m_NodeUsedForOdfVisualization->SetBoolProperty("VisibleOdfs_C", false); + m_NodeUsedForOdfVisualization->SetBoolProperty("VisibleOdfs_T", false); + } + m_NodeUsedForOdfVisualization = node; + m_NodeUsedForOdfVisualization->SetBoolProperty("VisibleOdfs_S", m_GlyIsOn_S); + m_NodeUsedForOdfVisualization->SetBoolProperty("VisibleOdfs_C", m_GlyIsOn_C); + m_NodeUsedForOdfVisualization->SetBoolProperty("VisibleOdfs_T", m_GlyIsOn_T); - // if selection changes, set the current selction member and call SellListener::DoSelectionChanged - berry::ISelection::ConstPointer sel( - this->GetSite()->GetWorkbenchWindow()->GetSelectionService()->GetSelection("org.mitk.views.datamanager")); - m_CurrentSelection = sel.Cast(); - m_SelListener.Cast()->DoSelectionChanged(sel); + int val; + node->GetIntProperty("ShowMaxNumber", val); + m_Controls->m_ShowMaxNumber->setValue(val); - // adapt thick slice controls - // THICK SLICE SUPPORT + m_Controls->m_NormalizationDropdown->setCurrentIndex(dynamic_cast(node->GetProperty("Normalization"))->GetValueAsId()); - if( nodes.size() < 1) - return; + float fval; + node->GetFloatProperty("Scaling",fval); + m_Controls->m_ScalingFactor->setValue(fval); - mitk::DataNode::Pointer node = nodes.at(0); + m_Controls->m_AdditionalScaling->setCurrentIndex(dynamic_cast(node->GetProperty("ScaleBy"))->GetValueAsId()); - if( node.IsNull() ) - return; + numOdfImages++; + } + else if(dynamic_cast(nodeData)) + { + PlanarFigureFocus(); + } + else if( dynamic_cast(nodeData) ) + { + m_Controls->m_ImageControlsFrame->setVisible(true); + m_Controls->m_TSMenu->setVisible(true); + } + } - QMenu *myMenu = m_MyMenu; - myMenu->clear(); + if( nodes.empty() ) + return; - QActionGroup* thickSlicesActionGroup = new QActionGroup(myMenu); - thickSlicesActionGroup->setExclusive(true); + mitk::DataNode::Pointer node = nodes.at(0); - int currentTSMode = 0; - { - mitk::ResliceMethodProperty::Pointer m = dynamic_cast(node->GetProperty( "reslice.thickslices" )); - if( m.IsNotNull() ) - currentTSMode = m->GetValueAsId(); - } + if( node.IsNull() ) + return; - int maxTS = 30; + QMenu *myMenu = m_MyMenu; + myMenu->clear(); - for( std::vector::iterator it = nodes.begin(); it != nodes.end(); ++it ) - { - mitk::Image* image = dynamic_cast((*it)->GetData()); - if (image) + QActionGroup* thickSlicesActionGroup = new QActionGroup(myMenu); + thickSlicesActionGroup->setExclusive(true); + + int currentTSMode = 0; { - int size = std::max(image->GetDimension(0), std::max(image->GetDimension(1), image->GetDimension(2))); - if (size>maxTS) - maxTS=size; + mitk::ResliceMethodProperty::Pointer m = dynamic_cast(node->GetProperty( "reslice.thickslices" )); + if( m.IsNotNull() ) + currentTSMode = m->GetValueAsId(); } - } - maxTS /= 2; - int currentNum = 0; - { - mitk::IntProperty::Pointer m = dynamic_cast(node->GetProperty( "reslice.thickslices.num" )); - if( m.IsNotNull() ) + int maxTS = 30; + + for( std::vector::iterator it = nodes.begin(); it != nodes.end(); ++it ) { - currentNum = m->GetValue(); - if(currentNum < 0) currentNum = 0; - if(currentNum > maxTS) currentNum = maxTS; + mitk::Image* image = dynamic_cast((*it)->GetData()); + if (image) + { + int size = std::max(image->GetDimension(0), std::max(image->GetDimension(1), image->GetDimension(2))); + if (size>maxTS) + maxTS=size; + } } - } + maxTS /= 2; - if(currentTSMode==0) - currentNum=0; + int currentNum = 0; + { + mitk::IntProperty::Pointer m = dynamic_cast(node->GetProperty( "reslice.thickslices.num" )); + if( m.IsNotNull() ) + { + currentNum = m->GetValue(); + if(currentNum < 0) currentNum = 0; + if(currentNum > maxTS) currentNum = maxTS; + } + } - QSlider *m_TSSlider = new QSlider(myMenu); - m_TSSlider->setMinimum(0); - m_TSSlider->setMaximum(maxTS-1); - m_TSSlider->setValue(currentNum); + if(currentTSMode==0) + currentNum=0; - m_TSSlider->setOrientation(Qt::Horizontal); + QSlider *m_TSSlider = new QSlider(myMenu); + m_TSSlider->setMinimum(0); + m_TSSlider->setMaximum(maxTS-1); + m_TSSlider->setValue(currentNum); - connect( m_TSSlider, SIGNAL( valueChanged(int) ), this, SLOT( OnTSNumChanged(int) ) ); + m_TSSlider->setOrientation(Qt::Horizontal); - QHBoxLayout* _TSLayout = new QHBoxLayout; - _TSLayout->setContentsMargins(4,4,4,4); - _TSLayout->addWidget(m_TSSlider); - _TSLayout->addWidget(m_TSLabel=new QLabel(QString::number(currentNum*2+1),myMenu)); + connect( m_TSSlider, SIGNAL( valueChanged(int) ), this, SLOT( OnTSNumChanged(int) ) ); - QWidget* _TSWidget = new QWidget; - _TSWidget->setLayout(_TSLayout); + QHBoxLayout* _TSLayout = new QHBoxLayout; + _TSLayout->setContentsMargins(4,4,4,4); + _TSLayout->addWidget(m_TSSlider); + _TSLayout->addWidget(m_TSLabel=new QLabel(QString::number(currentNum*2+1),myMenu)); - QActionGroup* thickSliceModeActionGroup = new QActionGroup(myMenu); - thickSliceModeActionGroup->setExclusive(true); + QWidget* _TSWidget = new QWidget; + _TSWidget->setLayout(_TSLayout); - QWidgetAction *m_TSSliderAction = new QWidgetAction(myMenu); - m_TSSliderAction->setDefaultWidget(_TSWidget); - myMenu->addAction(m_TSSliderAction); + QActionGroup* thickSliceModeActionGroup = new QActionGroup(myMenu); + thickSliceModeActionGroup->setExclusive(true); - QAction* mipThickSlicesAction = new QAction(myMenu); - mipThickSlicesAction->setActionGroup(thickSliceModeActionGroup); - mipThickSlicesAction->setText("MIP (max. intensity proj.)"); - mipThickSlicesAction->setCheckable(true); - mipThickSlicesAction->setChecked(currentThickSlicesMode==1); - mipThickSlicesAction->setData(1); - myMenu->addAction( mipThickSlicesAction ); + QWidgetAction *m_TSSliderAction = new QWidgetAction(myMenu); + m_TSSliderAction->setDefaultWidget(_TSWidget); + myMenu->addAction(m_TSSliderAction); - QAction* sumThickSlicesAction = new QAction(myMenu); - sumThickSlicesAction->setActionGroup(thickSliceModeActionGroup); - sumThickSlicesAction->setText("SUM (sum intensity proj.)"); - sumThickSlicesAction->setCheckable(true); - sumThickSlicesAction->setChecked(currentThickSlicesMode==2); - sumThickSlicesAction->setData(2); - myMenu->addAction( sumThickSlicesAction ); + QAction* mipThickSlicesAction = new QAction(myMenu); + mipThickSlicesAction->setActionGroup(thickSliceModeActionGroup); + mipThickSlicesAction->setText("MIP (max. intensity proj.)"); + mipThickSlicesAction->setCheckable(true); + mipThickSlicesAction->setChecked(currentThickSlicesMode==1); + mipThickSlicesAction->setData(1); + myMenu->addAction( mipThickSlicesAction ); - QAction* weightedThickSlicesAction = new QAction(myMenu); - weightedThickSlicesAction->setActionGroup(thickSliceModeActionGroup); - weightedThickSlicesAction->setText("WEIGHTED (gaussian proj.)"); - weightedThickSlicesAction->setCheckable(true); - weightedThickSlicesAction->setChecked(currentThickSlicesMode==3); - weightedThickSlicesAction->setData(3); - myMenu->addAction( weightedThickSlicesAction ); + QAction* sumThickSlicesAction = new QAction(myMenu); + sumThickSlicesAction->setActionGroup(thickSliceModeActionGroup); + sumThickSlicesAction->setText("SUM (sum intensity proj.)"); + sumThickSlicesAction->setCheckable(true); + sumThickSlicesAction->setChecked(currentThickSlicesMode==2); + sumThickSlicesAction->setData(2); + myMenu->addAction( sumThickSlicesAction ); - connect( thickSliceModeActionGroup, SIGNAL(triggered(QAction*)), this, SLOT(OnThickSlicesModeSelected(QAction*)) ); + QAction* weightedThickSlicesAction = new QAction(myMenu); + weightedThickSlicesAction->setActionGroup(thickSliceModeActionGroup); + weightedThickSlicesAction->setText("WEIGHTED (gaussian proj.)"); + weightedThickSlicesAction->setCheckable(true); + weightedThickSlicesAction->setChecked(currentThickSlicesMode==3); + weightedThickSlicesAction->setData(3); + myMenu->addAction( weightedThickSlicesAction ); + connect( thickSliceModeActionGroup, SIGNAL(triggered(QAction*)), this, SLOT(OnThickSlicesModeSelected(QAction*)) ); } -mitk::DataStorage::SetOfObjects::Pointer - QmitkControlVisualizationPropertiesView::ActiveSet(std::string classname) +void QmitkControlVisualizationPropertiesView::VisibleOdfsON_S() { - if (m_CurrentSelection) - { - mitk::DataStorage::SetOfObjects::Pointer set = - mitk::DataStorage::SetOfObjects::New(); - - int at = 0; - for (IStructuredSelection::iterator i = m_CurrentSelection->Begin(); - i != m_CurrentSelection->End(); - ++i) + m_GlyIsOn_S = m_Controls->m_VisibleOdfsON_S->isChecked(); + if (m_NodeUsedForOdfVisualization.IsNull()) { - - if (mitk::DataNodeObject::Pointer nodeObj = i->Cast()) - { - mitk::DataNode::Pointer node = nodeObj->GetDataNode(); - - // check if node has data, - // if some helper nodes are shown in the DataManager, the GetData() returns 0x0 which would lead to SIGSEV - const mitk::BaseData* nodeData = node->GetData(); - if(nodeData == NULL) - continue; - - if(QString(classname.c_str()).compare(nodeData->GetNameOfClass())==0) - { - set->InsertElement(at++, node); - } - } + MITK_WARN << "ODF visualization activated but m_NodeUsedForOdfVisualization is NULL"; + return; } - - return set; - } - - return 0; + m_NodeUsedForOdfVisualization->SetBoolProperty("VisibleOdfs_S", m_GlyIsOn_S); + mitk::RenderingManager::GetInstance()->RequestUpdateAll(); } -void QmitkControlVisualizationPropertiesView::SetBoolProp( - mitk::DataStorage::SetOfObjects::Pointer set, - std::string name, bool value) +void QmitkControlVisualizationPropertiesView::VisibleOdfsON_T() { - if(set.IsNotNull()) - { - - mitk::DataStorage::SetOfObjects::const_iterator itemiter( set->begin() ); - mitk::DataStorage::SetOfObjects::const_iterator itemiterend( set->end() ); - while ( itemiter != itemiterend ) + m_GlyIsOn_T = m_Controls->m_VisibleOdfsON_T->isChecked(); + if (m_NodeUsedForOdfVisualization.IsNull()) { - (*itemiter)->SetBoolProperty(name.c_str(), value); - ++itemiter; + MITK_WARN << "ODF visualization activated but m_NodeUsedForOdfVisualization is NULL"; + return; } - } + m_NodeUsedForOdfVisualization->SetBoolProperty("VisibleOdfs_T", m_GlyIsOn_T); + mitk::RenderingManager::GetInstance()->RequestUpdateAll(); } -void QmitkControlVisualizationPropertiesView::SetIntProp( - mitk::DataStorage::SetOfObjects::Pointer set, - std::string name, int value) +void QmitkControlVisualizationPropertiesView::VisibleOdfsON_C() { - if(set.IsNotNull()) - { - - mitk::DataStorage::SetOfObjects::const_iterator itemiter( set->begin() ); - mitk::DataStorage::SetOfObjects::const_iterator itemiterend( set->end() ); - while ( itemiter != itemiterend ) + m_GlyIsOn_C = m_Controls->m_VisibleOdfsON_C->isChecked(); + if (m_NodeUsedForOdfVisualization.IsNull()) { - (*itemiter)->SetIntProperty(name.c_str(), value); - ++itemiter; + MITK_WARN << "ODF visualization activated but m_NodeUsedForOdfVisualization is NULL"; + return; } - } + m_NodeUsedForOdfVisualization->SetBoolProperty("VisibleOdfs_C", m_GlyIsOn_C); + mitk::RenderingManager::GetInstance()->RequestUpdateAll(); } -void QmitkControlVisualizationPropertiesView::SetFloatProp( - mitk::DataStorage::SetOfObjects::Pointer set, - std::string name, float value) +bool QmitkControlVisualizationPropertiesView::IsPlaneRotated() { - if(set.IsNotNull()) - { - - mitk::DataStorage::SetOfObjects::const_iterator itemiter( set->begin() ); - mitk::DataStorage::SetOfObjects::const_iterator itemiterend( set->end() ); - while ( itemiter != itemiterend ) + mitk::Image* currentImage = dynamic_cast( m_NodeUsedForOdfVisualization->GetData() ); + if( currentImage == NULL ) { - (*itemiter)->SetFloatProperty(name.c_str(), value); - ++itemiter; + MITK_ERROR << " Casting problems. Returning false"; + return false; } - } -} -void QmitkControlVisualizationPropertiesView::SetLevelWindowProp( - mitk::DataStorage::SetOfObjects::Pointer set, - std::string name, mitk::LevelWindow value) -{ - if(set.IsNotNull()) - { + mitk::Vector3D imageNormal0 = currentImage->GetSlicedGeometry()->GetAxisVector(0); + mitk::Vector3D imageNormal1 = currentImage->GetSlicedGeometry()->GetAxisVector(1); + mitk::Vector3D imageNormal2 = currentImage->GetSlicedGeometry()->GetAxisVector(2); + imageNormal0.Normalize(); + imageNormal1.Normalize(); + imageNormal2.Normalize(); - mitk::LevelWindowProperty::Pointer prop = mitk::LevelWindowProperty::New(value); - - mitk::DataStorage::SetOfObjects::const_iterator itemiter( set->begin() ); - mitk::DataStorage::SetOfObjects::const_iterator itemiterend( set->end() ); - while ( itemiter != itemiterend ) + double eps = 0.000001; + // for all 2D renderwindows of m_MultiWidget check alignment { - (*itemiter)->SetProperty(name.c_str(), prop); - ++itemiter; + mitk::PlaneGeometry::ConstPointer displayPlane = dynamic_cast( m_MultiWidget->GetRenderWindow1()->GetRenderer()->GetCurrentWorldGeometry2D() ); + if (displayPlane.IsNull()) return false; + mitk::Vector3D normal = displayPlane->GetNormal(); + normal.Normalize(); + int test = 0; + if( fabs(fabs(dot_product(normal.GetVnlVector(),imageNormal0.GetVnlVector()))-1) > eps ) + test++; + if( fabs(fabs(dot_product(normal.GetVnlVector(),imageNormal1.GetVnlVector()))-1) > eps ) + test++; + if( fabs(fabs(dot_product(normal.GetVnlVector(),imageNormal2.GetVnlVector()))-1) > eps ) + test++; + if (test==3) + return true; } - } -} - -void QmitkControlVisualizationPropertiesView::SetEnumProp( - mitk::DataStorage::SetOfObjects::Pointer set, - std::string name, mitk::EnumerationProperty::Pointer value) -{ - if(set.IsNotNull()) - { - mitk::DataStorage::SetOfObjects::const_iterator itemiter( set->begin() ); - mitk::DataStorage::SetOfObjects::const_iterator itemiterend( set->end() ); - while ( itemiter != itemiterend ) { - (*itemiter)->SetProperty(name.c_str(), value); - ++itemiter; + mitk::PlaneGeometry::ConstPointer displayPlane = dynamic_cast( m_MultiWidget->GetRenderWindow2()->GetRenderer()->GetCurrentWorldGeometry2D() ); + if (displayPlane.IsNull()) return false; + mitk::Vector3D normal = displayPlane->GetNormal(); + normal.Normalize(); + int test = 0; + if( fabs(fabs(dot_product(normal.GetVnlVector(),imageNormal0.GetVnlVector()))-1) > eps ) + test++; + if( fabs(fabs(dot_product(normal.GetVnlVector(),imageNormal1.GetVnlVector()))-1) > eps ) + test++; + if( fabs(fabs(dot_product(normal.GetVnlVector(),imageNormal2.GetVnlVector()))-1) > eps ) + test++; + if (test==3) + return true; } - } -} - - - -void QmitkControlVisualizationPropertiesView::DisplayIndexChanged(int dispIndex) -{ - - m_Controls->m_DisplayIndex->setValue(dispIndex); - m_Controls->m_DisplayIndexSpinBox->setValue(dispIndex); - - QString label = "Channel %1"; - label = label.arg(dispIndex); - m_Controls->label_channel->setText(label); - - std::vector sets; - sets.push_back("TbssImage"); - - std::vector::iterator it = sets.begin(); - while(it != sets.end()) - { - std::string s = *it; - mitk::DataStorage::SetOfObjects::Pointer set = - ActiveSet(s); - - if(set.IsNotNull()) { - - mitk::DataStorage::SetOfObjects::const_iterator itemiter( set->begin() ); - mitk::DataStorage::SetOfObjects::const_iterator itemiterend( set->end() ); - while ( itemiter != itemiterend ) - { - (*itemiter)->SetIntProperty("DisplayChannel", dispIndex); - ++itemiter; - } - - //m_MultiWidget->RequestUpdate(); - mitk::RenderingManager::GetInstance()->RequestUpdateAll(); + mitk::PlaneGeometry::ConstPointer displayPlane = dynamic_cast( m_MultiWidget->GetRenderWindow3()->GetRenderer()->GetCurrentWorldGeometry2D() ); + if (displayPlane.IsNull()) return false; + mitk::Vector3D normal = displayPlane->GetNormal(); + normal.Normalize(); + int test = 0; + if( fabs(fabs(dot_product(normal.GetVnlVector(),imageNormal0.GetVnlVector()))-1) > eps ) + test++; + if( fabs(fabs(dot_product(normal.GetVnlVector(),imageNormal1.GetVnlVector()))-1) > eps ) + test++; + if( fabs(fabs(dot_product(normal.GetVnlVector(),imageNormal2.GetVnlVector()))-1) > eps ) + test++; + if (test==3) + return true; } - it++; - } - - + return false; } -void QmitkControlVisualizationPropertiesView::Reinit() +void QmitkControlVisualizationPropertiesView::ShowMaxNumberChanged() { - if (m_CurrentSelection) - { - mitk::DataNodeObject::Pointer nodeObj = - m_CurrentSelection->Begin()->Cast(); - mitk::DataNode::Pointer node = nodeObj->GetDataNode(); - mitk::BaseData::Pointer basedata = node->GetData(); - if (basedata.IsNotNull()) + int maxNr = m_Controls->m_ShowMaxNumber->value(); + if ( maxNr < 1 ) { - mitk::RenderingManager::GetInstance()->InitializeViews( - basedata->GetTimeGeometry(), mitk::RenderingManager::REQUEST_UPDATE_ALL, true ); - mitk::RenderingManager::GetInstance()->RequestUpdateAll(); + m_Controls->m_ShowMaxNumber->setValue( 1 ); + maxNr = 1; } - } -} - -void QmitkControlVisualizationPropertiesView::TextIntON() -{ - if(m_TexIsOn) - { - m_Controls->m_TextureIntON->setIcon(*m_IconTexOFF); - } - else - { - m_Controls->m_TextureIntON->setIcon(*m_IconTexON); - } - - mitk::DataStorage::SetOfObjects::Pointer set = - ActiveSet("DiffusionImage"); - SetBoolProp(set,"texture interpolation", !m_TexIsOn); - set = ActiveSet("TensorImage"); - SetBoolProp(set,"texture interpolation", !m_TexIsOn); + if (dynamic_cast(m_SelectedNode->GetData()) || dynamic_cast(m_SelectedNode->GetData())) + m_SelectedNode->SetIntProperty("ShowMaxNumber", maxNr); - set = ActiveSet("QBallImage"); - SetBoolProp(set,"texture interpolation", !m_TexIsOn); - - set = ActiveSet("Image"); - SetBoolProp(set,"texture interpolation", !m_TexIsOn); + mitk::RenderingManager::GetInstance()->RequestUpdateAll(); +} - m_TexIsOn = !m_TexIsOn; +void QmitkControlVisualizationPropertiesView::NormalizationDropdownChanged(int normDropdown) +{ + typedef mitk::OdfNormalizationMethodProperty PropType; + PropType::Pointer normMeth = PropType::New(); - if(m_MultiWidget) - m_MultiWidget->RequestUpdate(); + switch(normDropdown) + { + case 0: + normMeth->SetNormalizationToMinMax(); + break; + case 1: + normMeth->SetNormalizationToMax(); + break; + case 2: + normMeth->SetNormalizationToNone(); + break; + case 3: + normMeth->SetNormalizationToGlobalMax(); + break; + default: + normMeth->SetNormalizationToMinMax(); + } -} + if (dynamic_cast(m_SelectedNode->GetData()) || dynamic_cast(m_SelectedNode->GetData())) + m_SelectedNode->SetProperty("Normalization", normMeth.GetPointer()); -void QmitkControlVisualizationPropertiesView::VisibleOdfsON_S() -{ - m_GlyIsOn_S = m_Controls->m_VisibleOdfsON_S->isChecked(); - if (m_NodeUsedForOdfVisualization.IsNull()) - { - MITK_WARN << "ODF visualization activated but m_NodeUsedForOdfVisualization is NULL"; - return; - } - m_NodeUsedForOdfVisualization->SetBoolProperty("VisibleOdfs_S", m_GlyIsOn_S); - VisibleOdfsON(0); + mitk::RenderingManager::GetInstance()->RequestUpdateAll(); } -void QmitkControlVisualizationPropertiesView::VisibleOdfsON_T() +void QmitkControlVisualizationPropertiesView::ScalingFactorChanged(double scalingFactor) { - m_GlyIsOn_T = m_Controls->m_VisibleOdfsON_T->isChecked(); - if (m_NodeUsedForOdfVisualization.IsNull()) - { - MITK_WARN << "ODF visualization activated but m_NodeUsedForOdfVisualization is NULL"; - return; - } - m_NodeUsedForOdfVisualization->SetBoolProperty("VisibleOdfs_T", m_GlyIsOn_T); - VisibleOdfsON(1); -} + if (dynamic_cast(m_SelectedNode->GetData()) || dynamic_cast(m_SelectedNode->GetData())) + m_SelectedNode->SetFloatProperty("Scaling", scalingFactor); -void QmitkControlVisualizationPropertiesView::VisibleOdfsON_C() -{ - m_GlyIsOn_C = m_Controls->m_VisibleOdfsON_C->isChecked(); - if (m_NodeUsedForOdfVisualization.IsNull()) - { - MITK_WARN << "ODF visualization activated but m_NodeUsedForOdfVisualization is NULL"; - return; - } - m_NodeUsedForOdfVisualization->SetBoolProperty("VisibleOdfs_C", m_GlyIsOn_C); - VisibleOdfsON(2); + if(m_MultiWidget) + m_MultiWidget->RequestUpdate(); } -bool QmitkControlVisualizationPropertiesView::IsPlaneRotated() +void QmitkControlVisualizationPropertiesView::AdditionalScaling(int additionalScaling) { - // for all 2D renderwindows of m_MultiWidget check alignment - mitk::PlaneGeometry::ConstPointer displayPlane = dynamic_cast( m_MultiWidget->GetRenderWindow1()->GetRenderer()->GetCurrentWorldGeometry2D() ); - if (displayPlane.IsNull()) return false; + typedef mitk::OdfScaleByProperty PropType; + PropType::Pointer scaleBy = PropType::New(); - mitk::Image* currentImage = dynamic_cast( m_NodeUsedForOdfVisualization->GetData() ); - if( currentImage == NULL ) - { - MITK_ERROR << " Casting problems. Returning false"; - return false; - } + switch(additionalScaling) + { + case 0: + scaleBy->SetScaleByNothing(); + break; + case 1: + scaleBy->SetScaleByGFA(); + //m_Controls->params_frame->setVisible(true); + break; +#ifdef DIFFUSION_IMAGING_EXTENDED + case 2: + scaleBy->SetScaleByPrincipalCurvature(); + // commented in for SPIE paper, Principle curvature scaling + //m_Controls->params_frame->setVisible(true); + break; +#endif + default: + scaleBy->SetScaleByNothing(); + } - int affectedDimension(-1); - int affectedSlice(-1); - return !(DetermineAffectedImageSlice( currentImage, displayPlane, affectedDimension, affectedSlice )); + if (dynamic_cast(m_SelectedNode->GetData()) || dynamic_cast(m_SelectedNode->GetData())) + m_SelectedNode->SetProperty("Normalization", scaleBy.GetPointer()); + mitk::RenderingManager::GetInstance()->RequestUpdateAll(); } -void QmitkControlVisualizationPropertiesView::VisibleOdfsON(int view) +void QmitkControlVisualizationPropertiesView::ScalingCheckbox() { + m_Controls->m_ScalingFrame->setVisible( + m_Controls->m_ScalingCheckbox->isChecked()); - if(m_MultiWidget) - m_MultiWidget->RequestUpdate(); - + if(!m_Controls->m_ScalingCheckbox->isChecked()) + { + m_Controls->m_AdditionalScaling->setCurrentIndex(0); + m_Controls->m_ScalingFactor->setValue(1.0); + } } -void QmitkControlVisualizationPropertiesView::ShowMaxNumberChanged() +void QmitkControlVisualizationPropertiesView::Fiber2DfadingEFX() { - int maxNr = m_Controls->m_ShowMaxNumber->value(); - if ( maxNr < 1 ) - { - m_Controls->m_ShowMaxNumber->setValue( 1 ); - maxNr = 1; - } - - mitk::DataStorage::SetOfObjects::Pointer set = - ActiveSet("QBallImage"); - SetIntProp(set,"ShowMaxNumber", maxNr); - - set = ActiveSet("TensorImage"); - SetIntProp(set,"ShowMaxNumber", maxNr); - - if(m_MultiWidget) - m_MultiWidget->RequestUpdate(); - + if (m_SelectedNode && dynamic_cast(m_SelectedNode->GetData()) ) + { + bool currentMode; + m_SelectedNode->GetBoolProperty("Fiber2DfadeEFX", currentMode); + m_SelectedNode->SetProperty("Fiber2DfadeEFX", mitk::BoolProperty::New(!currentMode)); + dynamic_cast(m_SelectedNode->GetData())->RequestUpdate2D(); + mitk::RenderingManager::GetInstance()->RequestUpdateAll(); + } } -void QmitkControlVisualizationPropertiesView::NormalizationDropdownChanged(int normDropdown) +void QmitkControlVisualizationPropertiesView::FiberSlicingThickness2D() { - typedef mitk::OdfNormalizationMethodProperty PropType; - PropType::Pointer normMeth = PropType::New(); - - switch(normDropdown) - { - case 0: - normMeth->SetNormalizationToMinMax(); - break; - case 1: - normMeth->SetNormalizationToMax(); - break; - case 2: - normMeth->SetNormalizationToNone(); - break; - case 3: - normMeth->SetNormalizationToGlobalMax(); - break; - default: - normMeth->SetNormalizationToMinMax(); - } - - mitk::DataStorage::SetOfObjects::Pointer set = - ActiveSet("QBallImage"); - SetEnumProp(set,"Normalization", normMeth.GetPointer()); - - set = ActiveSet("TensorImage"); - SetEnumProp(set,"Normalization", normMeth.GetPointer()); - - // if(m_MultiWidget) - // m_MultiWidget->RequestUpdate(); - mitk::RenderingManager::GetInstance()->RequestUpdateAll(); + if (m_SelectedNode && dynamic_cast(m_SelectedNode->GetData())) + { + float fibThickness = m_Controls->m_FiberThicknessSlider->value() * 0.1; + float currentThickness = 0; + m_SelectedNode->GetFloatProperty("Fiber2DSliceThickness", currentThickness); + if (fabs(fibThickness-currentThickness)<0.001) + return; + m_SelectedNode->SetProperty("Fiber2DSliceThickness", mitk::FloatProperty::New(fibThickness)); + dynamic_cast(m_SelectedNode->GetData())->RequestUpdate2D(); + mitk::RenderingManager::GetInstance()->RequestUpdateAll(); + } } -void QmitkControlVisualizationPropertiesView::ScalingFactorChanged(double scalingFactor) +void QmitkControlVisualizationPropertiesView::FiberSlicingUpdateLabel(int value) { - - mitk::DataStorage::SetOfObjects::Pointer set = - ActiveSet("QBallImage"); - SetFloatProp(set,"Scaling", scalingFactor); - - set = ActiveSet("TensorImage"); - SetFloatProp(set,"Scaling", scalingFactor); - - if(m_MultiWidget) - m_MultiWidget->RequestUpdate(); - + QString label = "Range %1 mm"; + label = label.arg(value * 0.1); + m_Controls->label_range->setText(label); + FiberSlicingThickness2D(); } -void QmitkControlVisualizationPropertiesView::AdditionalScaling(int additionalScaling) +void QmitkControlVisualizationPropertiesView::SetFiberBundleOpacity(const itk::EventObject& /*e*/) { - - typedef mitk::OdfScaleByProperty PropType; - PropType::Pointer scaleBy = PropType::New(); - - switch(additionalScaling) - { - case 0: - scaleBy->SetScaleByNothing(); - break; - case 1: - scaleBy->SetScaleByGFA(); - //m_Controls->params_frame->setVisible(true); - break; -#ifdef DIFFUSION_IMAGING_EXTENDED - case 2: - scaleBy->SetScaleByPrincipalCurvature(); - // commented in for SPIE paper, Principle curvature scaling - //m_Controls->params_frame->setVisible(true); - break; -#endif - default: - scaleBy->SetScaleByNothing(); - } - - mitk::DataStorage::SetOfObjects::Pointer set = - ActiveSet("QBallImage"); - SetEnumProp(set,"ScaleBy", scaleBy.GetPointer()); - - set = ActiveSet("TensorImage"); - SetEnumProp(set,"ScaleBy", scaleBy.GetPointer()); - - if(m_MultiWidget) - m_MultiWidget->RequestUpdate(); - + if(m_SelectedNode) + { + mitk::FiberBundleX::Pointer fib = dynamic_cast(m_SelectedNode->GetData()); + fib->RequestUpdate(); + mitk::RenderingManager::GetInstance()->RequestUpdateAll(); + } } -void QmitkControlVisualizationPropertiesView::IndexParam1Changed(double param1) +void QmitkControlVisualizationPropertiesView::SetFiberBundleCustomColor(const itk::EventObject& /*e*/) { - mitk::DataStorage::SetOfObjects::Pointer set = - ActiveSet("QBallImage"); - SetFloatProp(set,"IndexParam1", param1); - - set = ActiveSet("TensorImage"); - SetFloatProp(set,"IndexParam1", param1); - - if(m_MultiWidget) - m_MultiWidget->RequestUpdate(); + if(m_SelectedNode && dynamic_cast(m_SelectedNode->GetData())) + { + float color[3]; + m_SelectedNode->GetColor(color); + mitk::FiberBundleX::Pointer fib = dynamic_cast(m_SelectedNode->GetData()); + fib->SetFiberColors(color[0]*255, color[1]*255, color[2]*255); + mitk::RenderingManager::GetInstance()->RequestUpdateAll(); + } } -void QmitkControlVisualizationPropertiesView::IndexParam2Changed(double param2) +void QmitkControlVisualizationPropertiesView::BundleRepresentationResetColoring() { - mitk::DataStorage::SetOfObjects::Pointer set = - ActiveSet("QBallImage"); - SetFloatProp(set,"IndexParam2", param2); - - set = ActiveSet("TensorImage"); - SetFloatProp(set,"IndexParam2", param2); - - if(m_MultiWidget) - m_MultiWidget->RequestUpdate(); + if(m_SelectedNode && dynamic_cast(m_SelectedNode->GetData())) + { + mitk::FiberBundleX::Pointer fib = dynamic_cast(m_SelectedNode->GetData()); + fib->DoColorCodingOrientationBased(); + mitk::RenderingManager::GetInstance()->RequestUpdateAll(); + } } -void QmitkControlVisualizationPropertiesView::OpacityChanged(double l, double u) +void QmitkControlVisualizationPropertiesView::PlanarFigureFocus() { - mitk::LevelWindow olw; - olw.SetRangeMinMax(l*255, u*255); + if(m_SelectedNode) + { + mitk::PlanarFigure* _PlanarFigure = 0; + _PlanarFigure = dynamic_cast (m_SelectedNode->GetData()); - mitk::DataStorage::SetOfObjects::Pointer set = - ActiveSet("QBallImage"); - SetLevelWindowProp(set,"opaclevelwindow", olw); + if (_PlanarFigure && _PlanarFigure->GetPlaneGeometry()) + { - set = ActiveSet("TensorImage"); - SetLevelWindowProp(set,"opaclevelwindow", olw); + QmitkRenderWindow* selectedRenderWindow = 0; + bool PlanarFigureInitializedWindow = false; - set = ActiveSet("Image"); - SetLevelWindowProp(set,"opaclevelwindow", olw); + QmitkRenderWindow* RenderWindow1 = + this->GetActiveStdMultiWidget()->GetRenderWindow1(); - m_Controls->m_OpacityMinFaLabel->setText(QString::number(l,'f',2) + " : " + QString::number(u,'f',2)); + if (m_SelectedNode->GetBoolProperty("PlanarFigureInitializedWindow", + PlanarFigureInitializedWindow, RenderWindow1->GetRenderer())) + { + selectedRenderWindow = RenderWindow1; + } - if(m_MultiWidget) - m_MultiWidget->RequestUpdate(); + QmitkRenderWindow* RenderWindow2 = + this->GetActiveStdMultiWidget()->GetRenderWindow2(); -} + if (!selectedRenderWindow && m_SelectedNode->GetBoolProperty( + "PlanarFigureInitializedWindow", PlanarFigureInitializedWindow, + RenderWindow2->GetRenderer())) + { + selectedRenderWindow = RenderWindow2; + } -void QmitkControlVisualizationPropertiesView::ScalingCheckbox() -{ - m_Controls->m_ScalingFrame->setVisible( - m_Controls->m_ScalingCheckbox->isChecked()); - - if(!m_Controls->m_ScalingCheckbox->isChecked()) - { - m_Controls->m_AdditionalScaling->setCurrentIndex(0); - m_Controls->m_ScalingFactor->setValue(1.0); - } -} + QmitkRenderWindow* RenderWindow3 = + this->GetActiveStdMultiWidget()->GetRenderWindow3(); -void QmitkControlVisualizationPropertiesView::Fiber2DfadingEFX() -{ - if (m_SelectedNode && dynamic_cast(m_SelectedNode->GetData()) ) - { - bool currentMode; - m_SelectedNode->GetBoolProperty("Fiber2DfadeEFX", currentMode); - m_SelectedNode->SetProperty("Fiber2DfadeEFX", mitk::BoolProperty::New(!currentMode)); - dynamic_cast(m_SelectedNode->GetData())->RequestUpdate2D(); - mitk::RenderingManager::GetInstance()->ForceImmediateUpdateAll(); - } + if (!selectedRenderWindow && m_SelectedNode->GetBoolProperty( + "PlanarFigureInitializedWindow", PlanarFigureInitializedWindow, + RenderWindow3->GetRenderer())) + { + selectedRenderWindow = RenderWindow3; + } -} + QmitkRenderWindow* RenderWindow4 = + this->GetActiveStdMultiWidget()->GetRenderWindow4(); -void QmitkControlVisualizationPropertiesView::FiberSlicingThickness2D() -{ - if (m_SelectedNode && dynamic_cast(m_SelectedNode->GetData())) - { - float fibThickness = m_Controls->m_FiberThicknessSlider->value() * 0.1; - float currentThickness = 0; - m_SelectedNode->GetFloatProperty("Fiber2DSliceThickness", currentThickness); - if (fabs(fibThickness-currentThickness)<0.001) - return; - m_SelectedNode->SetProperty("Fiber2DSliceThickness", mitk::FloatProperty::New(fibThickness)); - dynamic_cast(m_SelectedNode->GetData())->RequestUpdate2D(); - mitk::RenderingManager::GetInstance()->ForceImmediateUpdateAll(); - } -} + if (!selectedRenderWindow && m_SelectedNode->GetBoolProperty( + "PlanarFigureInitializedWindow", PlanarFigureInitializedWindow, + RenderWindow4->GetRenderer())) + { + selectedRenderWindow = RenderWindow4; + } -void QmitkControlVisualizationPropertiesView::FiberSlicingUpdateLabel(int value) -{ - QString label = "Range %1 mm"; - label = label.arg(value * 0.1); - m_Controls->label_range->setText(label); - this->FiberSlicingThickness2D(); -} + const mitk::PlaneGeometry* _PlaneGeometry = _PlanarFigure->GetPlaneGeometry(); -void QmitkControlVisualizationPropertiesView::SetFiberBundleCustomColor(const itk::EventObject& /*e*/) -{ - float color[3]; - m_SelectedNode->GetColor(color); - m_Controls->m_Color->setAutoFillBackground(true); - QString styleSheet = "background-color:rgb("; - styleSheet.append(QString::number(color[0]*255.0)); - styleSheet.append(","); - styleSheet.append(QString::number(color[1]*255.0)); - styleSheet.append(","); - styleSheet.append(QString::number(color[2]*255.0)); - styleSheet.append(")"); - m_Controls->m_Color->setStyleSheet(styleSheet); - - m_SelectedNode->SetProperty("color",mitk::ColorProperty::New(color[0], color[1], color[2])); - mitk::FiberBundleX::Pointer fib = dynamic_cast(m_SelectedNode->GetData()); - fib->SetColorCoding(mitk::FiberBundleX::COLORCODING_CUSTOM); - mitk::RenderingManager::GetInstance()->ForceImmediateUpdateAll(); -} + mitk::VnlVector normal = _PlaneGeometry->GetNormalVnl(); -void QmitkControlVisualizationPropertiesView::BundleRepresentationColor() -{ - if(m_SelectedNode) - { - QColor color = QColorDialog::getColor(); - if (!color.isValid()) - return; - - m_Controls->m_Color->setAutoFillBackground(true); - QString styleSheet = "background-color:rgb("; - styleSheet.append(QString::number(color.red())); - styleSheet.append(","); - styleSheet.append(QString::number(color.green())); - styleSheet.append(","); - styleSheet.append(QString::number(color.blue())); - styleSheet.append(")"); - m_Controls->m_Color->setStyleSheet(styleSheet); - - m_SelectedNode->SetProperty("color",mitk::ColorProperty::New(color.red()/255.0, color.green()/255.0, color.blue()/255.0)); - mitk::FiberBundleX::Pointer fib = dynamic_cast(m_SelectedNode->GetData()); - fib->SetColorCoding(mitk::FiberBundleX::COLORCODING_CUSTOM); - mitk::RenderingManager::GetInstance()->ForceImmediateUpdateAll(); - } -} + mitk::Geometry2D::ConstPointer worldGeometry1 = + RenderWindow1->GetRenderer()->GetCurrentWorldGeometry2D(); + mitk::PlaneGeometry::ConstPointer _Plane1 = + dynamic_cast( worldGeometry1.GetPointer() ); + mitk::VnlVector normal1 = _Plane1->GetNormalVnl(); -void QmitkControlVisualizationPropertiesView::BundleRepresentationResetColoring() -{ - if(m_SelectedNode) - { - MITK_INFO << "reset colorcoding to oBased"; - m_Controls->m_Color->setAutoFillBackground(true); - QString styleSheet = "background-color:rgb(255,255,255)"; - m_Controls->m_Color->setStyleSheet(styleSheet); - // m_SelectedNode->SetProperty("color",NULL); - m_SelectedNode->SetProperty("color",mitk::ColorProperty::New(1.0, 1.0, 1.0)); - - mitk::FiberBundleX::Pointer fib = dynamic_cast(m_SelectedNode->GetData()); - fib->SetColorCoding(mitk::FiberBundleX::COLORCODING_ORIENTATION_BASED); - fib->DoColorCodingOrientationBased(); - mitk::RenderingManager::GetInstance()->ForceImmediateUpdateAll(); - } -} + mitk::Geometry2D::ConstPointer worldGeometry2 = + RenderWindow2->GetRenderer()->GetCurrentWorldGeometry2D(); + mitk::PlaneGeometry::ConstPointer _Plane2 = + dynamic_cast( worldGeometry2.GetPointer() ); + mitk::VnlVector normal2 = _Plane2->GetNormalVnl(); -void QmitkControlVisualizationPropertiesView::PlanarFigureFocus() -{ - if(m_SelectedNode) - { - mitk::PlanarFigure* _PlanarFigure = 0; - _PlanarFigure = dynamic_cast (m_SelectedNode->GetData()); + mitk::Geometry2D::ConstPointer worldGeometry3 = + RenderWindow3->GetRenderer()->GetCurrentWorldGeometry2D(); + mitk::PlaneGeometry::ConstPointer _Plane3 = + dynamic_cast( worldGeometry3.GetPointer() ); + mitk::VnlVector normal3 = _Plane3->GetNormalVnl(); - if (_PlanarFigure && _PlanarFigure->GetPlaneGeometry()) - { + normal[0] = fabs(normal[0]); normal[1] = fabs(normal[1]); normal[2] = fabs(normal[2]); + normal1[0] = fabs(normal1[0]); normal1[1] = fabs(normal1[1]); normal1[2] = fabs(normal1[2]); + normal2[0] = fabs(normal2[0]); normal2[1] = fabs(normal2[1]); normal2[2] = fabs(normal2[2]); + normal3[0] = fabs(normal3[0]); normal3[1] = fabs(normal3[1]); normal3[2] = fabs(normal3[2]); - QmitkRenderWindow* selectedRenderWindow = 0; - bool PlanarFigureInitializedWindow = false; - - QmitkRenderWindow* RenderWindow1 = - this->GetActiveStdMultiWidget()->GetRenderWindow1(); - - if (m_SelectedNode->GetBoolProperty("PlanarFigureInitializedWindow", - PlanarFigureInitializedWindow, RenderWindow1->GetRenderer())) - { - selectedRenderWindow = RenderWindow1; - } - - QmitkRenderWindow* RenderWindow2 = - this->GetActiveStdMultiWidget()->GetRenderWindow2(); - - if (!selectedRenderWindow && m_SelectedNode->GetBoolProperty( - "PlanarFigureInitializedWindow", PlanarFigureInitializedWindow, - RenderWindow2->GetRenderer())) - { - selectedRenderWindow = RenderWindow2; - } - - QmitkRenderWindow* RenderWindow3 = - this->GetActiveStdMultiWidget()->GetRenderWindow3(); - - if (!selectedRenderWindow && m_SelectedNode->GetBoolProperty( - "PlanarFigureInitializedWindow", PlanarFigureInitializedWindow, - RenderWindow3->GetRenderer())) - { - selectedRenderWindow = RenderWindow3; - } - - QmitkRenderWindow* RenderWindow4 = - this->GetActiveStdMultiWidget()->GetRenderWindow4(); - - if (!selectedRenderWindow && m_SelectedNode->GetBoolProperty( - "PlanarFigureInitializedWindow", PlanarFigureInitializedWindow, - RenderWindow4->GetRenderer())) - { - selectedRenderWindow = RenderWindow4; - } - - const mitk::PlaneGeometry* _PlaneGeometry = _PlanarFigure->GetPlaneGeometry(); - - mitk::VnlVector normal = _PlaneGeometry->GetNormalVnl(); - - mitk::Geometry2D::ConstPointer worldGeometry1 = - RenderWindow1->GetRenderer()->GetCurrentWorldGeometry2D(); - mitk::PlaneGeometry::ConstPointer _Plane1 = - dynamic_cast( worldGeometry1.GetPointer() ); - mitk::VnlVector normal1 = _Plane1->GetNormalVnl(); - - mitk::Geometry2D::ConstPointer worldGeometry2 = - RenderWindow2->GetRenderer()->GetCurrentWorldGeometry2D(); - mitk::PlaneGeometry::ConstPointer _Plane2 = - dynamic_cast( worldGeometry2.GetPointer() ); - mitk::VnlVector normal2 = _Plane2->GetNormalVnl(); - - mitk::Geometry2D::ConstPointer worldGeometry3 = - RenderWindow3->GetRenderer()->GetCurrentWorldGeometry2D(); - mitk::PlaneGeometry::ConstPointer _Plane3 = - dynamic_cast( worldGeometry3.GetPointer() ); - mitk::VnlVector normal3 = _Plane3->GetNormalVnl(); - - normal[0] = fabs(normal[0]); normal[1] = fabs(normal[1]); normal[2] = fabs(normal[2]); - normal1[0] = fabs(normal1[0]); normal1[1] = fabs(normal1[1]); normal1[2] = fabs(normal1[2]); - normal2[0] = fabs(normal2[0]); normal2[1] = fabs(normal2[1]); normal2[2] = fabs(normal2[2]); - normal3[0] = fabs(normal3[0]); normal3[1] = fabs(normal3[1]); normal3[2] = fabs(normal3[2]); - - double ang1 = angle(normal, normal1); - double ang2 = angle(normal, normal2); - double ang3 = angle(normal, normal3); - - if(ang1 < ang2 && ang1 < ang3) - { - selectedRenderWindow = RenderWindow1; - } - else - { - if(ang2 < ang3) - { - selectedRenderWindow = RenderWindow2; - } - else - { - selectedRenderWindow = RenderWindow3; - } - } - - // make node visible - if (selectedRenderWindow) - { - const mitk::Point3D& centerP = _PlaneGeometry->GetOrigin(); - selectedRenderWindow->GetSliceNavigationController()->ReorientSlices( - centerP, _PlaneGeometry->GetNormal()); - } - } + double ang1 = angle(normal, normal1); + double ang2 = angle(normal, normal2); + double ang3 = angle(normal, normal3); - // set interactor for new node (if not already set) - mitk::PlanarFigureInteractor::Pointer figureInteractor - = dynamic_cast(m_SelectedNode->GetDataInteractor().GetPointer()); + if(ang1 < ang2 && ang1 < ang3) + { + selectedRenderWindow = RenderWindow1; + } + else + { + if(ang2 < ang3) + { + selectedRenderWindow = RenderWindow2; + } + else + { + selectedRenderWindow = RenderWindow3; + } + } - if(figureInteractor.IsNull()) - { - figureInteractor = mitk::PlanarFigureInteractor::New(); - us::Module* planarFigureModule = us::ModuleRegistry::GetModule( "MitkPlanarFigure" ); - figureInteractor->LoadStateMachine("PlanarFigureInteraction.xml", planarFigureModule ); - figureInteractor->SetEventConfig( "PlanarFigureConfig.xml", planarFigureModule ); - figureInteractor->SetDataNode( m_SelectedNode ); - } + // make node visible + if (selectedRenderWindow) + { + const mitk::Point3D& centerP = _PlaneGeometry->GetOrigin(); + selectedRenderWindow->GetSliceNavigationController()->ReorientSlices( + centerP, _PlaneGeometry->GetNormal()); + } + } - m_SelectedNode->SetProperty("planarfigure.iseditable",mitk::BoolProperty::New(true)); - } -} + // set interactor for new node (if not already set) + mitk::PlanarFigureInteractor::Pointer figureInteractor + = dynamic_cast(m_SelectedNode->GetDataInteractor().GetPointer()); -void QmitkControlVisualizationPropertiesView::SetInteractor() -{ - typedef std::vector Container; - Container _NodeSet = this->GetDataManagerSelection(); - mitk::DataNode* node = 0; - mitk::FiberBundleX* bundle = 0; - mitk::FiberBundleInteractor::Pointer bundleInteractor = 0; - - // finally add all nodes to the model - for(Container::const_iterator it=_NodeSet.begin(); it!=_NodeSet.end() - ; it++) - { - node = const_cast(*it); - bundle = dynamic_cast(node->GetData()); - - if(bundle) - { - bundleInteractor = dynamic_cast(node->GetInteractor()); - - if(bundleInteractor.IsNotNull()) - mitk::GlobalInteraction::GetInstance()->RemoveInteractor(bundleInteractor); - - if(!m_Controls->m_Crosshair->isChecked()) - { - m_Controls->m_Crosshair->setChecked(false); - this->GetActiveStdMultiWidget()->GetRenderWindow4()->setCursor(Qt::ArrowCursor); - m_CurrentPickingNode = 0; - } - else - { - m_Controls->m_Crosshair->setChecked(true); - bundleInteractor = mitk::FiberBundleInteractor::New("FiberBundleInteractor", node); - mitk::GlobalInteraction::GetInstance()->AddInteractor(bundleInteractor); - this->GetActiveStdMultiWidget()->GetRenderWindow4()->setCursor(Qt::CrossCursor); - m_CurrentPickingNode = node; - } + if(figureInteractor.IsNull()) + { + figureInteractor = mitk::PlanarFigureInteractor::New(); + us::Module* planarFigureModule = us::ModuleRegistry::GetModule( "MitkPlanarFigure" ); + figureInteractor->LoadStateMachine("PlanarFigureInteraction.xml", planarFigureModule ); + figureInteractor->SetEventConfig( "PlanarFigureConfig.xml", planarFigureModule ); + figureInteractor->SetDataNode( m_SelectedNode ); + } + m_SelectedNode->SetProperty("planarfigure.iseditable",mitk::BoolProperty::New(true)); } - } - } -void QmitkControlVisualizationPropertiesView::PFWidth(int w) +void QmitkControlVisualizationPropertiesView::SetInteractor() { + typedef std::vector Container; + Container _NodeSet = this->GetDataManagerSelection(); + mitk::DataNode* node = 0; + mitk::FiberBundleX* bundle = 0; + mitk::FiberBundleInteractor::Pointer bundleInteractor = 0; - double width = w/10.0; - m_SelectedNode->SetProperty("planarfigure.line.width", mitk::FloatProperty::New(width) ); - m_SelectedNode->SetProperty("planarfigure.shadow.widthmodifier", mitk::FloatProperty::New(width) ); - m_SelectedNode->SetProperty("planarfigure.outline.width", mitk::FloatProperty::New(width) ); - m_SelectedNode->SetProperty("planarfigure.helperline.width", mitk::FloatProperty::New(width) ); - - mitk::RenderingManager::GetInstance()->RequestUpdateAll(); - - QString label = "Width %1"; - label = label.arg(width); - m_Controls->label_pfwidth->setText(label); + // finally add all nodes to the model + for(Container::const_iterator it=_NodeSet.begin(); it!=_NodeSet.end() + ; it++) + { + node = const_cast(*it); + bundle = dynamic_cast(node->GetData()); -} + if(bundle) + { + bundleInteractor = dynamic_cast(node->GetInteractor()); -void QmitkControlVisualizationPropertiesView::PFColor() -{ + if(bundleInteractor.IsNotNull()) + mitk::GlobalInteraction::GetInstance()->RemoveInteractor(bundleInteractor); - QColor color = QColorDialog::getColor(); - if (!color.isValid()) - return; - - m_Controls->m_PFColor->setAutoFillBackground(true); - QString styleSheet = "background-color:rgb("; - styleSheet.append(QString::number(color.red())); - styleSheet.append(","); - styleSheet.append(QString::number(color.green())); - styleSheet.append(","); - styleSheet.append(QString::number(color.blue())); - styleSheet.append(")"); - m_Controls->m_PFColor->setStyleSheet(styleSheet); - - m_SelectedNode->SetProperty( "planarfigure.default.line.color", mitk::ColorProperty::New(color.red()/255.0, color.green()/255.0, color.blue()/255.0)); - m_SelectedNode->SetProperty( "planarfigure.default.outline.color", mitk::ColorProperty::New(color.red()/255.0, color.green()/255.0, color.blue()/255.0)); - m_SelectedNode->SetProperty( "planarfigure.default.helperline.color", mitk::ColorProperty::New(color.red()/255.0, color.green()/255.0, color.blue()/255.0)); - m_SelectedNode->SetProperty( "planarfigure.default.markerline.color", mitk::ColorProperty::New(color.red()/255.0, color.green()/255.0, color.blue()/255.0)); - m_SelectedNode->SetProperty( "planarfigure.default.marker.color", mitk::ColorProperty::New(color.red()/255.0, color.green()/255.0, color.blue()/255.0)); - - m_SelectedNode->SetProperty( "planarfigure.hover.line.color", mitk::ColorProperty::New(color.red()/255.0, color.green()/255.0, color.blue()/255.0) ); - m_SelectedNode->SetProperty( "planarfigure.hover.outline.color", mitk::ColorProperty::New(color.red()/255.0, color.green()/255.0, color.blue()/255.0) ); - m_SelectedNode->SetProperty( "planarfigure.hover.helperline.color", mitk::ColorProperty::New(color.red()/255.0, color.green()/255.0, color.blue()/255.0) ); - m_SelectedNode->SetProperty( "color", mitk::ColorProperty::New(color.red()/255.0, color.green()/255.0, color.blue()/255.0)); - - mitk::RenderingManager::GetInstance()->RequestUpdateAll(); -} + if(!m_Controls->m_Crosshair->isChecked()) + { + m_Controls->m_Crosshair->setChecked(false); + this->GetActiveStdMultiWidget()->GetRenderWindow4()->setCursor(Qt::ArrowCursor); + m_CurrentPickingNode = 0; + } + else + { + m_Controls->m_Crosshair->setChecked(true); + bundleInteractor = mitk::FiberBundleInteractor::New("FiberBundleInteractor", node); + mitk::GlobalInteraction::GetInstance()->AddInteractor(bundleInteractor); + this->GetActiveStdMultiWidget()->GetRenderWindow4()->setCursor(Qt::CrossCursor); + m_CurrentPickingNode = node; + } -void QmitkControlVisualizationPropertiesView::GenerateTdi() -{ - if(m_SelectedNode) - { - mitk::FiberBundleX* bundle = dynamic_cast(m_SelectedNode->GetData()); - if(!bundle) - return; - - typedef float OutPixType; - typedef itk::Image OutImageType; - - // run generator - itk::TractDensityImageFilter< OutImageType >::Pointer generator = itk::TractDensityImageFilter< OutImageType >::New(); - generator->SetFiberBundle(bundle); - generator->SetOutputAbsoluteValues(true); - generator->SetUpsamplingFactor(1); - generator->Update(); - - // get result - OutImageType::Pointer outImg = generator->GetOutput(); - - mitk::Image::Pointer img = mitk::Image::New(); - img->InitializeByItk(outImg.GetPointer()); - img->SetVolume(outImg->GetBufferPointer()); - - // to datastorage - mitk::DataNode::Pointer node = mitk::DataNode::New(); - node->SetData(img); - QString name(m_SelectedNode->GetName().c_str()); - name += "_TDI"; - node->SetName(name.toStdString()); - node->SetVisibility(true); - - GetDataStorage()->Add(node); - } + } + } } void QmitkControlVisualizationPropertiesView::LineWidthChanged() { - if(m_SelectedNode && dynamic_cast(m_SelectedNode->GetData())) - { - int newWidth = m_Controls->m_LineWidth->value(); - int currentWidth = 0; - m_SelectedNode->GetIntProperty("LineWidth", currentWidth); - if (currentWidth==newWidth) - return; - m_SelectedNode->SetIntProperty("LineWidth", newWidth); - dynamic_cast(m_SelectedNode->GetData())->RequestUpdate2D(); - dynamic_cast(m_SelectedNode->GetData())->RequestUpdate3D(); - mitk::RenderingManager::GetInstance()->ForceImmediateUpdateAll(); - } + if(m_SelectedNode && dynamic_cast(m_SelectedNode->GetData())) + { + int newWidth = m_Controls->m_LineWidth->value(); + int currentWidth = 0; + m_SelectedNode->GetIntProperty("LineWidth", currentWidth); + if (currentWidth==newWidth) + return; + m_SelectedNode->SetIntProperty("LineWidth", newWidth); + dynamic_cast(m_SelectedNode->GetData())->RequestUpdate2D(); + dynamic_cast(m_SelectedNode->GetData())->RequestUpdate3D(); + mitk::RenderingManager::GetInstance()->RequestUpdateAll(); + } } void QmitkControlVisualizationPropertiesView::Welcome() { - berry::PlatformUI::GetWorkbench()->GetIntroManager()->ShowIntro( - GetSite()->GetWorkbenchWindow(), false); + berry::PlatformUI::GetWorkbench()->GetIntroManager()->ShowIntro( + GetSite()->GetWorkbenchWindow(), false); } diff --git a/Plugins/org.mitk.gui.qt.diffusionimaging/src/internal/QmitkControlVisualizationPropertiesView.h b/Plugins/org.mitk.gui.qt.diffusionimaging/src/internal/QmitkControlVisualizationPropertiesView.h index 37198bfd6d..9c42cd9d08 100644 --- a/Plugins/org.mitk.gui.qt.diffusionimaging/src/internal/QmitkControlVisualizationPropertiesView.h +++ b/Plugins/org.mitk.gui.qt.diffusionimaging/src/internal/QmitkControlVisualizationPropertiesView.h @@ -1,177 +1,153 @@ /*=================================================================== The Medical Imaging Interaction Toolkit (MITK) Copyright (c) German Cancer Research Center, Division of Medical and Biological Informatics. All rights reserved. This software is distributed WITHOUT ANY WARRANTY; without even the implied warranty of MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See LICENSE.txt or http://www.mitk.org for details. ===================================================================*/ #ifndef _QMITKControlVisualizationPropertiesView_H_INCLUDED #define _QMITKControlVisualizationPropertiesView_H_INCLUDED #include #include #include "berryISelectionListener.h" #include "berryIStructuredSelection.h" #include "berryISizeProvider.h" #include "ui_QmitkControlVisualizationPropertiesViewControls.h" #include "mitkEnumerationProperty.h" /*! * \ingroup org_mitk_gui_qt_diffusionquantification_internal * * \brief QmitkControlVisualizationPropertiesView * * Document your class here. * * \sa QmitkFunctionality */ class QmitkControlVisualizationPropertiesView : public QmitkFunctionality//, public berry::ISizeProvider { friend struct CvpSelListener; // this is needed for all Qt objects that should have a MOC object (everything that derives from QObject) Q_OBJECT public: static const std::string VIEW_ID; QmitkControlVisualizationPropertiesView(); QmitkControlVisualizationPropertiesView(const QmitkControlVisualizationPropertiesView& other); virtual ~QmitkControlVisualizationPropertiesView(); virtual void CreateQtPartControl(QWidget *parent); /// \brief Creation of the connections of main and control widget virtual void CreateConnections(); /// \brief Called when the functionality is activated virtual void Activated(); virtual void Deactivated(); virtual void StdMultiWidgetAvailable (QmitkStdMultiWidget &stdMultiWidget); virtual void StdMultiWidgetNotAvailable(); - mitk::DataStorage::SetOfObjects::Pointer ActiveSet(std::string); - - void SetBoolProp (mitk::DataStorage::SetOfObjects::Pointer,std::string,bool); - void SetIntProp (mitk::DataStorage::SetOfObjects::Pointer,std::string,int); - void SetFloatProp(mitk::DataStorage::SetOfObjects::Pointer,std::string,float); - void SetLevelWindowProp(mitk::DataStorage::SetOfObjects::Pointer,std::string,mitk::LevelWindow); - void SetEnumProp (mitk::DataStorage::SetOfObjects::Pointer,std::string,mitk::EnumerationProperty::Pointer); - - virtual int GetSizeFlags(bool width); - virtual int ComputePreferredSize(bool width, int availableParallel, int availablePerpendicular, int preferredResult); - protected slots: - void DisplayIndexChanged(int); - void TextIntON(); - void Reinit(); - - void VisibleOdfsON(int view); void VisibleOdfsON_S(); void VisibleOdfsON_T(); void VisibleOdfsON_C(); void ShowMaxNumberChanged(); void NormalizationDropdownChanged(int); void ScalingFactorChanged(double); void AdditionalScaling(int); - void IndexParam1Changed(double); - void IndexParam2Changed(double); - void OpacityChanged(double,double); void ScalingCheckbox(); void OnThickSlicesModeSelected( QAction* action ); void OnTSNumChanged(int num); - void BundleRepresentationColor(); void BundleRepresentationResetColoring(); void PlanarFigureFocus(); void Fiber2DfadingEFX(); void FiberSlicingThickness2D(); void FiberSlicingUpdateLabel(int); + void LineWidthChanged(); void SetInteractor(); - void PFWidth(int); - void PFColor(); - - void LineWidthChanged(); - - void GenerateTdi(); void Welcome(); protected: virtual void NodeRemoved(const mitk::DataNode* node); /// \brief called by QmitkFunctionality when DataManager's selection has changed virtual void OnSelectionChanged( std::vector nodes ); virtual void NodeAdded(const mitk::DataNode *node); void SetFiberBundleCustomColor(const itk::EventObject& /*e*/); + void SetFiberBundleOpacity(const itk::EventObject& /*e*/); bool IsPlaneRotated(); void SliceRotation(const itk::EventObject&); Ui::QmitkControlVisualizationPropertiesViewControls* m_Controls; QmitkStdMultiWidget* m_MultiWidget; berry::ISelectionListener::Pointer m_SelListener; berry::IStructuredSelection::ConstPointer m_CurrentSelection; - bool m_FoundSingleOdfImage; - bool m_IsInitialized; mitk::DataNode::Pointer m_NodeUsedForOdfVisualization; QIcon* m_IconTexOFF; QIcon* m_IconTexON; QIcon* m_IconGlyOFF_T; QIcon* m_IconGlyON_T; QIcon* m_IconGlyOFF_C; QIcon* m_IconGlyON_C; QIcon* m_IconGlyOFF_S; QIcon* m_IconGlyON_S; bool m_TexIsOn; bool m_GlyIsOn_T; bool m_GlyIsOn_C; bool m_GlyIsOn_S; int currentThickSlicesMode; QLabel* m_TSLabel; QMenu* m_MyMenu; // for planarfigure and bundle handling: - mitk::DataNode* m_SelectedNode; + mitk::DataNode::Pointer m_SelectedNode; mitk::DataNode* m_CurrentPickingNode; unsigned long m_SlicesRotationObserverTag1; unsigned long m_SlicesRotationObserverTag2; unsigned long m_FiberBundleObserverTag; + unsigned long m_FiberBundleObserveOpacityTag; mitk::ColorProperty::Pointer m_Color; + mitk::FloatProperty::Pointer m_Opacity; }; #endif // _QMITKControlVisualizationPropertiesView_H_INCLUDED diff --git a/Plugins/org.mitk.gui.qt.diffusionimaging/src/internal/QmitkControlVisualizationPropertiesViewControls.ui b/Plugins/org.mitk.gui.qt.diffusionimaging/src/internal/QmitkControlVisualizationPropertiesViewControls.ui index 01ef2755f9..b9366d9c7d 100644 --- a/Plugins/org.mitk.gui.qt.diffusionimaging/src/internal/QmitkControlVisualizationPropertiesViewControls.ui +++ b/Plugins/org.mitk.gui.qt.diffusionimaging/src/internal/QmitkControlVisualizationPropertiesViewControls.ui @@ -1,965 +1,702 @@ QmitkControlVisualizationPropertiesViewControls 0 0 567 619 0 100 0 0 QmitkTemplate 0 0 0 0 QFrame::NoFrame QFrame::Raised 0 0 0 0 0 0 QFrame::NoFrame QFrame::Raised 0 0 0 0 - - - - Reinit view - - - - - - - - - - - - false - - - false - - - - - - - Texture interpolation ON - - - - - - - - - - - - true - - - false - - - - - - - Toggle visibility of ODF glyphs (axial) - - - - - - - - - - - - - :/QmitkDiffusionImaging/glyphsoff_T.png - :/QmitkDiffusionImaging/glyphson_T.png:/QmitkDiffusionImaging/glyphsoff_T.png - - - true - - - false - - - - - - - Toggle visibility of ODF glyphs (sagittal) - - - - - - - - - - - - - :/QmitkDiffusionImaging/glyphsoff_S.png - :/QmitkDiffusionImaging/glyphson_S.png:/QmitkDiffusionImaging/glyphsoff_S.png - - - true - - - false - - - - - - - Toggle visibility of ODF glyphs (coronal) - - - - - - - - - - - - - :/QmitkDiffusionImaging/glyphsoff_C.png - :/QmitkDiffusionImaging/glyphson_C.png:/QmitkDiffusionImaging/glyphsoff_C.png - - - true - - - false - - - Multislice Projection MIP QToolButton::MenuButtonPopup Qt::NoArrow - - - - Channel - - - - - - - 300 - - - Qt::Horizontal - - - - - - QFrame::NoFrame QFrame::Plain 0 0 0 0 - - - Qt::Horizontal + + + Toggle visibility of ODF glyphs (axial) - - - 20 - 20 - + + - + + + + + + + + + :/QmitkDiffusionImaging/glyphsoff_T.png + :/QmitkDiffusionImaging/glyphson_T.png:/QmitkDiffusionImaging/glyphsoff_T.png + + + true + + + false + + + + + + + Toggle visibility of ODF glyphs (sagittal) + + + + + + + + + + + + + :/QmitkDiffusionImaging/glyphsoff_S.png + :/QmitkDiffusionImaging/glyphson_S.png:/QmitkDiffusionImaging/glyphsoff_S.png + + + true + + + false + + + + + + + Toggle visibility of ODF glyphs (coronal) + + + + + + + + + + + + + :/QmitkDiffusionImaging/glyphsoff_C.png + :/QmitkDiffusionImaging/glyphson_C.png:/QmitkDiffusionImaging/glyphsoff_C.png + + + true + + + false + + #Glyphs 9999 + + + + Qt::Horizontal + + + + 20 + 20 + + + + - - - QFrame::NoFrame - - - QFrame::Plain - - - - 0 - - - 0 - - - 0 - - - 0 - - - - - Opacity - - - - - - - 100 - - - Qt::Horizontal - - - - - - - - 80 - 0 - - - - 0.0 : 0.0 - - - - - - - - + QFrame::NoFrame QFrame::Raised 0 0 0 0 0 QFrame::NoFrame QFrame::Raised 0 0 0 0 6 0 QFrame::NoFrame QFrame::Plain 0 0 0 0 false None By GFA By ASR * Additional scaling factor + + 3 + + + 999999999.000000000000000 + + + 0.100000000000000 + + + 1.000000000000000 + Scaling QFrame::NoFrame QFrame::Plain 0 0 0 0 0 ODF normalization false Min-Max Max None - - - - QFrame::NoFrame - - - QFrame::Raised - - - - 0 - - - 0 - - - 0 - - - 0 - - - - - Param1 - - - - - - - 9999.989999999999782 - - - - - - - Param2 - - - - - - - 9999.989999999999782 - - - - - - QFrame::NoFrame QFrame::Raised 0 0 0 0 QFrame::NoFrame QFrame::Raised 0 0 0 0 - - - - Uniform Color for Bundle - - - - - - Reset to Default Coloring + + + :/QmitkDiffusionImaging/reset.png:/QmitkDiffusionImaging/reset.png + Position Crosshair by 3D-Click + + + :/QmitkDiffusionImaging/crosshair.png:/QmitkDiffusionImaging/crosshair.png + true false - - - - Generate Tract Density Image - - - - - - - - - 2D Fiberfading on/off Qt::Horizontal 40 20 QFrame::NoFrame QFrame::Raised 0 0 0 0 2D Clipping 100 10 10 10 Qt::Horizontal 90 0 10000 16777215 Range QFrame::NoFrame QFrame::Raised 0 0 0 0 Line Width 1 10 - - - - QFrame::NoFrame - - - QFrame::Raised - - - - 0 - - - 0 - - - 0 - - - 0 - - - - - Focus Planar Figure - - - - - - - - - - - 0 - 0 - - - - Select ROI color. - - - - - - - - - - Adjust 2D line width. - - - 1 - - - 100 - - - 20 - - - Qt::Horizontal - - - - - - - - 80 - 0 - - - - Width - - - Qt::AlignLeading|Qt::AlignLeft|Qt::AlignVCenter - - - - - - 50 false false <!DOCTYPE HTML PUBLIC "-//W3C//DTD HTML 4.0//EN" "http://www.w3.org/TR/REC-html40/strict.dtd"> <html><head><meta name="qrichtext" content="1" /><style type="text/css"> p, li { white-space: pre-wrap; } </style></head><body style=" font-family:'Ubuntu'; font-size:11pt; font-weight:400; font-style:normal;"> -<p style=" margin-top:0px; margin-bottom:0px; margin-left:0px; margin-right:0px; -qt-block-indent:0; text-indent:0px;"><span style=" color:#ff0000;"> ODF Visualisation not possible in rotated planes. </span></p> -<p style=" margin-top:0px; margin-bottom:0px; margin-left:0px; margin-right:0px; -qt-block-indent:0; text-indent:0px;"><span style=" color:#ff0000;"> Use 'Reinit' on the image node to reset. </span></p></body></html> +<p align="center" style=" margin-top:0px; margin-bottom:0px; margin-left:0px; margin-right:0px; -qt-block-indent:0; text-indent:0px;"><span style=" color:#ff0000;">One or more slices are rotated. ODF Visualisation is not possible in rotated planes. Use 'Reinit' on the image node to reset. </span></p></body></html> Qt::AutoText + + true + Qt::Vertical 20 40 - - - ctkRangeSlider - QWidget -
ctkRangeSlider.h
- - QmitkDataStorageComboBox.h diff --git a/Plugins/org.mitk.gui.qt.diffusionimaging/src/internal/QmitkFiberProcessingView.cpp b/Plugins/org.mitk.gui.qt.diffusionimaging/src/internal/QmitkFiberProcessingView.cpp index f959406314..e116a924b7 100644 --- a/Plugins/org.mitk.gui.qt.diffusionimaging/src/internal/QmitkFiberProcessingView.cpp +++ b/Plugins/org.mitk.gui.qt.diffusionimaging/src/internal/QmitkFiberProcessingView.cpp @@ -1,1470 +1,1487 @@ /*=================================================================== The Medical Imaging Interaction Toolkit (MITK) Copyright (c) German Cancer Research Center, Division of Medical and Biological Informatics. All rights reserved. This software is distributed WITHOUT ANY WARRANTY; without even the implied warranty of MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See LICENSE.txt or http://www.mitk.org for details. ===================================================================*/ // Blueberry #include #include // Qmitk #include "QmitkFiberProcessingView.h" #include // Qt #include // MITK #include #include #include #include #include #include #include #include #include #include #include #include "usModuleRegistry.h" #include #include "mitkNodePredicateDataType.h" #include #include #include #include // ITK #include #include #include #include #include #include #include #define _USE_MATH_DEFINES #include const std::string QmitkFiberProcessingView::VIEW_ID = "org.mitk.views.fiberprocessing"; const std::string id_DataManager = "org.mitk.views.datamanager"; using namespace mitk; QmitkFiberProcessingView::QmitkFiberProcessingView() : QmitkFunctionality() , m_Controls( 0 ) , m_MultiWidget( NULL ) , m_CircleCounter(0) , m_PolygonCounter(0) , m_UpsamplingFactor(1) { } // Destructor QmitkFiberProcessingView::~QmitkFiberProcessingView() { } void QmitkFiberProcessingView::CreateQtPartControl( QWidget *parent ) { // build up qt view, unless already done if ( !m_Controls ) { // create GUI widgets from the Qt Designer's .ui file m_Controls = new Ui::QmitkFiberProcessingViewControls; m_Controls->setupUi( parent ); connect( m_Controls->m_CircleButton, SIGNAL( clicked() ), this, SLOT( OnDrawCircle() ) ); connect( m_Controls->m_PolygonButton, SIGNAL( clicked() ), this, SLOT( OnDrawPolygon() ) ); connect(m_Controls->PFCompoANDButton, SIGNAL(clicked()), this, SLOT(GenerateAndComposite()) ); connect(m_Controls->PFCompoORButton, SIGNAL(clicked()), this, SLOT(GenerateOrComposite()) ); connect(m_Controls->PFCompoNOTButton, SIGNAL(clicked()), this, SLOT(GenerateNotComposite()) ); connect(m_Controls->m_GenerateRoiImage, SIGNAL(clicked()), this, SLOT(GenerateRoiImage()) ); connect(m_Controls->m_JoinBundles, SIGNAL(clicked()), this, SLOT(JoinBundles()) ); connect(m_Controls->m_SubstractBundles, SIGNAL(clicked()), this, SLOT(SubstractBundles()) ); connect(m_Controls->m_ExtractFibersButton, SIGNAL(clicked()), this, SLOT(Extract())); connect(m_Controls->m_RemoveButton, SIGNAL(clicked()), this, SLOT(Remove())); connect(m_Controls->m_ModifyButton, SIGNAL(clicked()), this, SLOT(Modify())); connect(m_Controls->m_ExtractionMethodBox, SIGNAL(currentIndexChanged(int)), this, SLOT(UpdateGui())); connect(m_Controls->m_RemovalMethodBox, SIGNAL(currentIndexChanged(int)), this, SLOT(UpdateGui())); connect(m_Controls->m_ModificationMethodBox, SIGNAL(currentIndexChanged(int)), this, SLOT(UpdateGui())); m_Controls->m_ColorMapBox->SetDataStorage(this->GetDataStorage()); mitk::TNodePredicateDataType::Pointer isMitkImage = mitk::TNodePredicateDataType::New(); mitk::NodePredicateDataType::Pointer isDwi = mitk::NodePredicateDataType::New("DiffusionImage"); mitk::NodePredicateDataType::Pointer isDti = mitk::NodePredicateDataType::New("TensorImage"); mitk::NodePredicateDataType::Pointer isQbi = mitk::NodePredicateDataType::New("QBallImage"); mitk::NodePredicateOr::Pointer isDiffusionImage = mitk::NodePredicateOr::New(isDwi, isDti); isDiffusionImage = mitk::NodePredicateOr::New(isDiffusionImage, isQbi); mitk::NodePredicateNot::Pointer noDiffusionImage = mitk::NodePredicateNot::New(isDiffusionImage); mitk::NodePredicateAnd::Pointer finalPredicate = mitk::NodePredicateAnd::New(isMitkImage, noDiffusionImage); m_Controls->m_ColorMapBox->SetPredicate(finalPredicate); } UpdateGui(); } void QmitkFiberProcessingView::Modify() { switch (m_Controls->m_ModificationMethodBox->currentIndex()) { case 0: { ResampleSelectedBundles(); break; } case 1: { CompressSelectedBundles(); break; } case 2: { DoImageColorCoding(); break; } case 3: { MirrorFibers(); break; } + case 4: + { + WeightFibers(); + break; + } } } +void QmitkFiberProcessingView::WeightFibers() +{ + float weight = this->m_Controls->m_BundleWeightBox->value(); + for (int i=0; i(m_SelectedFB.at(i)->GetData()); + fib->SetFiberWeights(weight); + } + +} + void QmitkFiberProcessingView::Remove() { switch (m_Controls->m_RemovalMethodBox->currentIndex()) { case 0: { RemoveDir(); break; } case 1: { PruneBundle(); break; } case 2: { ApplyCurvatureThreshold(); break; } case 3: { RemoveWithMask(false); break; } case 4: { RemoveWithMask(true); break; } } } void QmitkFiberProcessingView::Extract() { switch (m_Controls->m_ExtractionMethodBox->currentIndex()) { case 0: { ExtractWithPlanarFigure(); break; } case 1: { switch (m_Controls->m_ExtractionBoxMask->currentIndex()) { { case 0: ExtractWithMask(true, false); break; } { case 1: ExtractWithMask(true, true); break; } { case 2: ExtractWithMask(false, false); break; } { case 3: ExtractWithMask(false, true); break; } } break; } } } void QmitkFiberProcessingView::PruneBundle() { int minLength = this->m_Controls->m_PruneFibersMinBox->value(); int maxLength = this->m_Controls->m_PruneFibersMaxBox->value(); for (int i=0; i(m_SelectedFB.at(i)->GetData()); if (!fib->RemoveShortFibers(minLength)) QMessageBox::information(NULL, "No output generated:", "The resulting fiber bundle contains no fibers."); else if (!fib->RemoveLongFibers(maxLength)) QMessageBox::information(NULL, "No output generated:", "The resulting fiber bundle contains no fibers."); } RenderingManager::GetInstance()->RequestUpdateAll(); } void QmitkFiberProcessingView::ApplyCurvatureThreshold() { int angle = this->m_Controls->m_CurvSpinBox->value(); int dist = this->m_Controls->m_CurvDistanceSpinBox->value(); std::vector< DataNode::Pointer > nodes = m_SelectedFB; for (int i=0; i(nodes.at(i)->GetData()); itk::FiberCurvatureFilter::Pointer filter = itk::FiberCurvatureFilter::New(); filter->SetInputFiberBundle(fib); filter->SetAngularDeviation(angle); filter->SetDistance(dist); filter->SetRemoveFibers(m_Controls->m_RemoveCurvedFibersBox->isChecked()); filter->Update(); mitk::FiberBundleX::Pointer newFib = filter->GetOutputFiberBundle(); if (newFib->GetNumFibers()>0) { nodes.at(i)->SetVisibility(false); DataNode::Pointer newNode = DataNode::New(); newNode->SetData(newFib); newNode->SetName(nodes.at(i)->GetName()+"_Curvature"); GetDefaultDataStorage()->Add(newNode, nodes.at(i)); } else QMessageBox::information(NULL, "No output generated:", "The resulting fiber bundle contains no fibers."); // if (!fib->ApplyCurvatureThreshold(mm, this->m_Controls->m_RemoveCurvedFibersBox->isChecked())) // QMessageBox::information(NULL, "No output generated:", "The resulting fiber bundle contains no fibers."); } RenderingManager::GetInstance()->RequestUpdateAll(); } void QmitkFiberProcessingView::RemoveDir() { for (unsigned int i=0; i(m_SelectedFB.at(i)->GetData()); vnl_vector_fixed dir; dir[0] = m_Controls->m_ExtractDirX->value(); dir[1] = m_Controls->m_ExtractDirY->value(); dir[2] = m_Controls->m_ExtractDirZ->value(); fib->RemoveDir(dir,cos((float)m_Controls->m_ExtractAngle->value()*M_PI/180)); } RenderingManager::GetInstance()->RequestUpdateAll(); } void QmitkFiberProcessingView::RemoveWithMask(bool removeInside) { if (m_MaskImageNode.IsNull()) return; mitk::Image::Pointer mitkMask = dynamic_cast(m_MaskImageNode->GetData()); for (unsigned int i=0; i(m_SelectedFB.at(i)->GetData()); QString name(m_SelectedFB.at(i)->GetName().c_str()); itkUCharImageType::Pointer mask = itkUCharImageType::New(); mitk::CastToItkImage(mitkMask, mask); mitk::FiberBundleX::Pointer newFib = fib->RemoveFibersOutside(mask, removeInside); if (newFib->GetNumFibers()<=0) { QMessageBox::information(NULL, "No output generated:", "The resulting fiber bundle contains no fibers."); continue; } DataNode::Pointer newNode = DataNode::New(); newNode->SetData(newFib); if (removeInside) name += "_Inside"; else name += "_Outside"; newNode->SetName(name.toStdString()); GetDefaultDataStorage()->Add(newNode); m_SelectedFB.at(i)->SetVisibility(false); } } void QmitkFiberProcessingView::ExtractWithMask(bool onlyEnds, bool invert) { if (m_MaskImageNode.IsNull()) return; mitk::Image::Pointer mitkMask = dynamic_cast(m_MaskImageNode->GetData()); for (unsigned int i=0; i(m_SelectedFB.at(i)->GetData()); QString name(m_SelectedFB.at(i)->GetName().c_str()); itkUCharImageType::Pointer mask = itkUCharImageType::New(); mitk::CastToItkImage(mitkMask, mask); mitk::FiberBundleX::Pointer newFib = fib->ExtractFiberSubset(mask, onlyEnds, invert); if (newFib->GetNumFibers()<=0) { QMessageBox::information(NULL, "No output generated:", "The resulting fiber bundle contains no fibers."); continue; } DataNode::Pointer newNode = DataNode::New(); newNode->SetData(newFib); if (invert) { name += "_not"; if (onlyEnds) name += "-ending-in-mask"; else name += "-passing-mask"; } else { if (onlyEnds) name += "_ending-in-mask"; else name += "_passing-mask"; } newNode->SetName(name.toStdString()); GetDefaultDataStorage()->Add(newNode); m_SelectedFB.at(i)->SetVisibility(false); } } void QmitkFiberProcessingView::GenerateRoiImage() { if (m_SelectedPF.empty()) return; mitk::BaseGeometry::Pointer geometry; if (!m_SelectedFB.empty()) { mitk::FiberBundleX::Pointer fib = dynamic_cast(m_SelectedFB.front()->GetData()); geometry = fib->GetGeometry(); } else if (m_SelectedImage) geometry = m_SelectedImage->GetGeometry(); else return; itk::Vector spacing = geometry->GetSpacing(); spacing /= m_UpsamplingFactor; mitk::Point3D newOrigin = geometry->GetOrigin(); mitk::Geometry3D::BoundsArrayType bounds = geometry->GetBounds(); newOrigin[0] += bounds.GetElement(0); newOrigin[1] += bounds.GetElement(2); newOrigin[2] += bounds.GetElement(4); itk::Matrix direction; itk::ImageRegion<3> imageRegion; for (int i=0; i<3; i++) for (int j=0; j<3; j++) direction[j][i] = geometry->GetMatrixColumn(i)[j]/spacing[j]; imageRegion.SetSize(0, geometry->GetExtent(0)*m_UpsamplingFactor); imageRegion.SetSize(1, geometry->GetExtent(1)*m_UpsamplingFactor); imageRegion.SetSize(2, geometry->GetExtent(2)*m_UpsamplingFactor); m_PlanarFigureImage = itkUCharImageType::New(); m_PlanarFigureImage->SetSpacing( spacing ); // Set the image spacing m_PlanarFigureImage->SetOrigin( newOrigin ); // Set the image origin m_PlanarFigureImage->SetDirection( direction ); // Set the image direction m_PlanarFigureImage->SetRegions( imageRegion ); m_PlanarFigureImage->Allocate(); m_PlanarFigureImage->FillBuffer( 0 ); Image::Pointer tmpImage = Image::New(); tmpImage->InitializeByItk(m_PlanarFigureImage.GetPointer()); tmpImage->SetVolume(m_PlanarFigureImage->GetBufferPointer()); std::string name = m_SelectedPF.at(0)->GetName(); WritePfToImage(m_SelectedPF.at(0), tmpImage); for (unsigned int i=1; iGetName(); WritePfToImage(m_SelectedPF.at(i), tmpImage); } DataNode::Pointer node = DataNode::New(); tmpImage = Image::New(); tmpImage->InitializeByItk(m_PlanarFigureImage.GetPointer()); tmpImage->SetVolume(m_PlanarFigureImage->GetBufferPointer()); node->SetData(tmpImage); node->SetName(name); this->GetDefaultDataStorage()->Add(node); } void QmitkFiberProcessingView::WritePfToImage(mitk::DataNode::Pointer node, mitk::Image* image) { if (dynamic_cast(node->GetData())) { m_PlanarFigure = dynamic_cast(node->GetData()); AccessFixedDimensionByItk_2( image, InternalReorientImagePlane, 3, m_PlanarFigure->GetGeometry(), -1); AccessFixedDimensionByItk_2( m_InternalImage, InternalCalculateMaskFromPlanarFigure, 3, 2, node->GetName() ); } else if (dynamic_cast(node->GetData())) { mitk::PlanarFigureComposite* pfc = dynamic_cast(node->GetData()); for (int j=0; jgetNumberOfChildren(); j++) { WritePfToImage(pfc->getDataNodeAt(j), image); } } } template < typename TPixel, unsigned int VImageDimension > void QmitkFiberProcessingView::InternalReorientImagePlane( const itk::Image< TPixel, VImageDimension > *image, mitk::BaseGeometry* planegeo3D, int additionalIndex ) { typedef itk::Image< TPixel, VImageDimension > ImageType; typedef itk::Image< float, VImageDimension > FloatImageType; typedef itk::ResampleImageFilter ResamplerType; typename ResamplerType::Pointer resampler = ResamplerType::New(); mitk::PlaneGeometry* planegeo = dynamic_cast(planegeo3D); float upsamp = m_UpsamplingFactor; float gausssigma = 0.5; // Spacing typename ResamplerType::SpacingType spacing = planegeo->GetSpacing(); spacing[0] = image->GetSpacing()[0] / upsamp; spacing[1] = image->GetSpacing()[1] / upsamp; spacing[2] = image->GetSpacing()[2]; resampler->SetOutputSpacing( spacing ); // Size typename ResamplerType::SizeType size; size[0] = planegeo->GetExtentInMM(0) / spacing[0]; size[1] = planegeo->GetExtentInMM(1) / spacing[1]; size[2] = 1; resampler->SetSize( size ); // Origin typename mitk::Point3D orig = planegeo->GetOrigin(); typename mitk::Point3D corrorig; planegeo3D->WorldToIndex(orig,corrorig); corrorig[0] += 0.5/upsamp; corrorig[1] += 0.5/upsamp; corrorig[2] += 0; planegeo3D->IndexToWorld(corrorig,corrorig); resampler->SetOutputOrigin(corrorig ); // Direction typename ResamplerType::DirectionType direction; typename mitk::AffineTransform3D::MatrixType matrix = planegeo->GetIndexToWorldTransform()->GetMatrix(); for(int c=0; cSetOutputDirection( direction ); // Gaussian interpolation if(gausssigma != 0) { double sigma[3]; for( unsigned int d = 0; d < 3; d++ ) sigma[d] = gausssigma * image->GetSpacing()[d]; double alpha = 2.0; typedef itk::GaussianInterpolateImageFunction GaussianInterpolatorType; typename GaussianInterpolatorType::Pointer interpolator = GaussianInterpolatorType::New(); interpolator->SetInputImage( image ); interpolator->SetParameters( sigma, alpha ); resampler->SetInterpolator( interpolator ); } else { typedef typename itk::LinearInterpolateImageFunction InterpolatorType; typename InterpolatorType::Pointer interpolator = InterpolatorType::New(); interpolator->SetInputImage( image ); resampler->SetInterpolator( interpolator ); } resampler->SetInput( image ); resampler->SetDefaultPixelValue(0); resampler->Update(); if(additionalIndex < 0) { this->m_InternalImage = mitk::Image::New(); this->m_InternalImage->InitializeByItk( resampler->GetOutput() ); this->m_InternalImage->SetVolume( resampler->GetOutput()->GetBufferPointer() ); } } template < typename TPixel, unsigned int VImageDimension > void QmitkFiberProcessingView::InternalCalculateMaskFromPlanarFigure( itk::Image< TPixel, VImageDimension > *image, unsigned int axis, std::string ) { typedef itk::Image< TPixel, VImageDimension > ImageType; typedef itk::CastImageFilter< ImageType, itkUCharImageType > CastFilterType; // Generate mask image as new image with same header as input image and // initialize with "1". itkUCharImageType::Pointer newMaskImage = itkUCharImageType::New(); newMaskImage->SetSpacing( image->GetSpacing() ); // Set the image spacing newMaskImage->SetOrigin( image->GetOrigin() ); // Set the image origin newMaskImage->SetDirection( image->GetDirection() ); // Set the image direction newMaskImage->SetRegions( image->GetLargestPossibleRegion() ); newMaskImage->Allocate(); newMaskImage->FillBuffer( 1 ); // Generate VTK polygon from (closed) PlanarFigure polyline // (The polyline points are shifted by -0.5 in z-direction to make sure // that the extrusion filter, which afterwards elevates all points by +0.5 // in z-direction, creates a 3D object which is cut by the the plane z=0) const PlaneGeometry *planarFigurePlaneGeometry = m_PlanarFigure->GetPlaneGeometry(); const PlanarFigure::PolyLineType planarFigurePolyline = m_PlanarFigure->GetPolyLine( 0 ); const BaseGeometry *imageGeometry3D = m_InternalImage->GetGeometry( 0 ); vtkPolyData *polyline = vtkPolyData::New(); polyline->Allocate( 1, 1 ); // Determine x- and y-dimensions depending on principal axis int i0, i1; switch ( axis ) { case 0: i0 = 1; i1 = 2; break; case 1: i0 = 0; i1 = 2; break; case 2: default: i0 = 0; i1 = 1; break; } // Create VTK polydata object of polyline contour vtkPoints *points = vtkPoints::New(); PlanarFigure::PolyLineType::const_iterator it; unsigned int numberOfPoints = 0; for ( it = planarFigurePolyline.begin(); it != planarFigurePolyline.end(); ++it ) { Point3D point3D; // Convert 2D point back to the local index coordinates of the selected image Point2D point2D = *it; planarFigurePlaneGeometry->WorldToIndex(point2D, point2D); point2D[0] -= 0.5/m_UpsamplingFactor; point2D[1] -= 0.5/m_UpsamplingFactor; planarFigurePlaneGeometry->IndexToWorld(point2D, point2D); planarFigurePlaneGeometry->Map( point2D, point3D ); // Polygons (partially) outside of the image bounds can not be processed further due to a bug in vtkPolyDataToImageStencil if ( !imageGeometry3D->IsInside( point3D ) ) { float bounds[2] = {0,0}; bounds[0] = this->m_InternalImage->GetLargestPossibleRegion().GetSize().GetElement(i0); bounds[1] = this->m_InternalImage->GetLargestPossibleRegion().GetSize().GetElement(i1); imageGeometry3D->WorldToIndex( point3D, point3D ); if (point3D[i0]<0) point3D[i0] = 0.0; else if (point3D[i0]>bounds[0]) point3D[i0] = bounds[0]-0.001; if (point3D[i1]<0) point3D[i1] = 0.0; else if (point3D[i1]>bounds[1]) point3D[i1] = bounds[1]-0.001; points->InsertNextPoint( point3D[i0], point3D[i1], -0.5 ); numberOfPoints++; } else { imageGeometry3D->WorldToIndex( point3D, point3D ); // Add point to polyline array points->InsertNextPoint( point3D[i0], point3D[i1], -0.5 ); numberOfPoints++; } } polyline->SetPoints( points ); points->Delete(); vtkIdType *ptIds = new vtkIdType[numberOfPoints]; for ( vtkIdType i = 0; i < numberOfPoints; ++i ) ptIds[i] = i; polyline->InsertNextCell( VTK_POLY_LINE, numberOfPoints, ptIds ); // Extrude the generated contour polygon vtkLinearExtrusionFilter *extrudeFilter = vtkLinearExtrusionFilter::New(); extrudeFilter->SetInputData( polyline ); extrudeFilter->SetScaleFactor( 1 ); extrudeFilter->SetExtrusionTypeToNormalExtrusion(); extrudeFilter->SetVector( 0.0, 0.0, 1.0 ); // Make a stencil from the extruded polygon vtkPolyDataToImageStencil *polyDataToImageStencil = vtkPolyDataToImageStencil::New(); polyDataToImageStencil->SetInputConnection( extrudeFilter->GetOutputPort() ); // Export from ITK to VTK (to use a VTK filter) typedef itk::VTKImageImport< itkUCharImageType > ImageImportType; typedef itk::VTKImageExport< itkUCharImageType > ImageExportType; typename ImageExportType::Pointer itkExporter = ImageExportType::New(); itkExporter->SetInput( newMaskImage ); vtkImageImport *vtkImporter = vtkImageImport::New(); this->ConnectPipelines( itkExporter, vtkImporter ); vtkImporter->Update(); // Apply the generated image stencil to the input image vtkImageStencil *imageStencilFilter = vtkImageStencil::New(); imageStencilFilter->SetInputConnection( vtkImporter->GetOutputPort() ); imageStencilFilter->SetStencilConnection(polyDataToImageStencil->GetOutputPort() ); imageStencilFilter->ReverseStencilOff(); imageStencilFilter->SetBackgroundValue( 0 ); imageStencilFilter->Update(); // Export from VTK back to ITK vtkImageExport *vtkExporter = vtkImageExport::New(); vtkExporter->SetInputConnection( imageStencilFilter->GetOutputPort() ); vtkExporter->Update(); typename ImageImportType::Pointer itkImporter = ImageImportType::New(); this->ConnectPipelines( vtkExporter, itkImporter ); itkImporter->Update(); // calculate cropping bounding box m_InternalImageMask3D = itkImporter->GetOutput(); m_InternalImageMask3D->SetDirection(image->GetDirection()); itk::ImageRegionConstIterator itmask(m_InternalImageMask3D, m_InternalImageMask3D->GetLargestPossibleRegion()); itk::ImageRegionIterator itimage(image, image->GetLargestPossibleRegion()); itmask.GoToBegin(); itimage.GoToBegin(); typename ImageType::SizeType lowersize = {{9999999999,9999999999,9999999999}}; typename ImageType::SizeType uppersize = {{0,0,0}}; while( !itmask.IsAtEnd() ) { if(itmask.Get() == 0) itimage.Set(0); else { typename ImageType::IndexType index = itimage.GetIndex(); typename ImageType::SizeType signedindex; signedindex[0] = index[0]; signedindex[1] = index[1]; signedindex[2] = index[2]; lowersize[0] = signedindex[0] < lowersize[0] ? signedindex[0] : lowersize[0]; lowersize[1] = signedindex[1] < lowersize[1] ? signedindex[1] : lowersize[1]; lowersize[2] = signedindex[2] < lowersize[2] ? signedindex[2] : lowersize[2]; uppersize[0] = signedindex[0] > uppersize[0] ? signedindex[0] : uppersize[0]; uppersize[1] = signedindex[1] > uppersize[1] ? signedindex[1] : uppersize[1]; uppersize[2] = signedindex[2] > uppersize[2] ? signedindex[2] : uppersize[2]; } ++itmask; ++itimage; } typename ImageType::IndexType index; index[0] = lowersize[0]; index[1] = lowersize[1]; index[2] = lowersize[2]; typename ImageType::SizeType size; size[0] = uppersize[0] - lowersize[0] + 1; size[1] = uppersize[1] - lowersize[1] + 1; size[2] = uppersize[2] - lowersize[2] + 1; itk::ImageRegion<3> cropRegion = itk::ImageRegion<3>(index, size); // crop internal mask typedef itk::RegionOfInterestImageFilter< itkUCharImageType, itkUCharImageType > ROIMaskFilterType; typename ROIMaskFilterType::Pointer roi2 = ROIMaskFilterType::New(); roi2->SetRegionOfInterest(cropRegion); roi2->SetInput(m_InternalImageMask3D); roi2->Update(); m_InternalImageMask3D = roi2->GetOutput(); Image::Pointer tmpImage = Image::New(); tmpImage->InitializeByItk(m_InternalImageMask3D.GetPointer()); tmpImage->SetVolume(m_InternalImageMask3D->GetBufferPointer()); Image::Pointer tmpImage2 = Image::New(); tmpImage2->InitializeByItk(m_PlanarFigureImage.GetPointer()); const BaseGeometry *pfImageGeometry3D = tmpImage2->GetGeometry( 0 ); const BaseGeometry *intImageGeometry3D = tmpImage->GetGeometry( 0 ); typedef itk::ImageRegionIteratorWithIndex IteratorType; IteratorType imageIterator (m_InternalImageMask3D, m_InternalImageMask3D->GetRequestedRegion()); imageIterator.GoToBegin(); while ( !imageIterator.IsAtEnd() ) { unsigned char val = imageIterator.Value(); if (val>0) { itk::Index<3> index = imageIterator.GetIndex(); Point3D point; point[0] = index[0]; point[1] = index[1]; point[2] = index[2]; intImageGeometry3D->IndexToWorld(point, point); pfImageGeometry3D->WorldToIndex(point, point); point[i0] += 0.5; point[i1] += 0.5; index[0] = point[0]; index[1] = point[1]; index[2] = point[2]; if (pfImageGeometry3D->IsIndexInside(index)) m_PlanarFigureImage->SetPixel(index, 1); } ++imageIterator; } // Clean up VTK objects polyline->Delete(); extrudeFilter->Delete(); polyDataToImageStencil->Delete(); vtkImporter->Delete(); imageStencilFilter->Delete(); //vtkExporter->Delete(); // TODO: crashes when outcommented; memory leak?? delete[] ptIds; } void QmitkFiberProcessingView::StdMultiWidgetAvailable (QmitkStdMultiWidget &stdMultiWidget) { m_MultiWidget = &stdMultiWidget; } void QmitkFiberProcessingView::StdMultiWidgetNotAvailable() { m_MultiWidget = NULL; } void QmitkFiberProcessingView::UpdateGui() { m_Controls->m_FibLabel->setText("mandatory"); m_Controls->m_PfLabel->setText("needed for extraction"); m_Controls->m_InputData->setTitle("Please Select Input Data"); m_Controls->m_RemoveButton->setEnabled(false); m_Controls->m_PlanarFigureButtonsFrame->setEnabled(false); m_Controls->PFCompoANDButton->setEnabled(false); m_Controls->PFCompoORButton->setEnabled(false); m_Controls->PFCompoNOTButton->setEnabled(false); m_Controls->m_GenerateRoiImage->setEnabled(false); m_Controls->m_ExtractFibersButton->setEnabled(false); m_Controls->m_ModifyButton->setEnabled(false); m_Controls->m_JoinBundles->setEnabled(false); m_Controls->m_SubstractBundles->setEnabled(false); // disable alle frames + m_Controls->m_BundleWeightFrame->setVisible(false); m_Controls->m_ExtractionBoxMask->setVisible(false); m_Controls->m_ExtactionFramePF->setVisible(false); m_Controls->m_RemoveDirectionFrame->setVisible(false); m_Controls->m_RemoveLengthFrame->setVisible(false); m_Controls->m_RemoveCurvatureFrame->setVisible(false); m_Controls->m_SmoothFibersFrame->setVisible(false); m_Controls->m_CompressFibersFrame->setVisible(false); m_Controls->m_ColorFibersFrame->setVisible(false); m_Controls->m_MirrorFibersFrame->setVisible(false); bool pfSelected = !m_SelectedPF.empty(); bool fibSelected = !m_SelectedFB.empty(); bool multipleFibsSelected = (m_SelectedFB.size()>1); bool maskSelected = m_MaskImageNode.IsNotNull(); bool imageSelected = m_SelectedImage.IsNotNull(); // toggle visibility of elements according to selected method switch ( m_Controls->m_ExtractionMethodBox->currentIndex() ) { case 0: m_Controls->m_ExtactionFramePF->setVisible(true); break; case 1: m_Controls->m_ExtractionBoxMask->setVisible(true); break; } switch ( m_Controls->m_RemovalMethodBox->currentIndex() ) { case 0: m_Controls->m_RemoveDirectionFrame->setVisible(true); if ( fibSelected ) m_Controls->m_RemoveButton->setEnabled(true); break; case 1: m_Controls->m_RemoveLengthFrame->setVisible(true); if ( fibSelected ) m_Controls->m_RemoveButton->setEnabled(true); break; case 2: m_Controls->m_RemoveCurvatureFrame->setVisible(true); if ( fibSelected ) m_Controls->m_RemoveButton->setEnabled(true); break; case 3: break; case 4: break; } switch ( m_Controls->m_ModificationMethodBox->currentIndex() ) { case 0: m_Controls->m_SmoothFibersFrame->setVisible(true); break; case 1: m_Controls->m_CompressFibersFrame->setVisible(true); break; case 2: m_Controls->m_ColorFibersFrame->setVisible(true); break; case 3: m_Controls->m_MirrorFibersFrame->setVisible(true); break; + case 4: + m_Controls->m_BundleWeightFrame->setVisible(true); } // are fiber bundles selected? if ( fibSelected ) { m_Controls->m_ModifyButton->setEnabled(true); m_Controls->m_PlanarFigureButtonsFrame->setEnabled(true); m_Controls->m_FibLabel->setText(QString(m_SelectedFB.at(0)->GetName().c_str())); // one bundle and one planar figure needed to extract fibers if (pfSelected) { m_Controls->m_InputData->setTitle("Input Data"); m_Controls->m_PfLabel->setText(QString(m_SelectedPF.at(0)->GetName().c_str())); m_Controls->m_ExtractFibersButton->setEnabled(true); } // more than two bundles needed to join/subtract if (multipleFibsSelected) { m_Controls->m_FibLabel->setText("multiple bundles selected"); m_Controls->m_JoinBundles->setEnabled(true); m_Controls->m_SubstractBundles->setEnabled(true); } if (maskSelected) { m_Controls->m_RemoveButton->setEnabled(true); m_Controls->m_ExtractFibersButton->setEnabled(true); } } // are planar figures selected? if (pfSelected) { if ( fibSelected || m_SelectedImage.IsNotNull()) m_Controls->m_GenerateRoiImage->setEnabled(true); if (m_SelectedPF.size() > 1) { m_Controls->PFCompoANDButton->setEnabled(true); m_Controls->PFCompoORButton->setEnabled(true); } else m_Controls->PFCompoNOTButton->setEnabled(true); } // is image selected if (imageSelected || maskSelected) { m_Controls->m_PlanarFigureButtonsFrame->setEnabled(true); } } void QmitkFiberProcessingView::NodeRemoved(const mitk::DataNode* node) { std::vector nodes; OnSelectionChanged(nodes); } void QmitkFiberProcessingView::NodeAdded(const mitk::DataNode* node) { std::vector nodes; OnSelectionChanged(nodes); } void QmitkFiberProcessingView::OnSelectionChanged( std::vector nodes ) { //reset existing Vectors containing FiberBundles and PlanarFigures from a previous selection m_SelectedFB.clear(); m_SelectedPF.clear(); m_SelectedSurfaces.clear(); m_SelectedImage = NULL; m_MaskImageNode = NULL; for( std::vector::iterator it = nodes.begin(); it != nodes.end(); ++it ) { mitk::DataNode::Pointer node = *it; if ( dynamic_cast(node->GetData()) ) m_SelectedFB.push_back(node); else if (dynamic_cast(node->GetData()) || dynamic_cast(node->GetData()) || dynamic_cast(node->GetData())) m_SelectedPF.push_back(node); else if (dynamic_cast(node->GetData())) { m_SelectedImage = dynamic_cast(node->GetData()); bool isBinary = false; node->GetPropertyValue("binary", isBinary); if (isBinary) m_MaskImageNode = node; } else if (dynamic_cast(node->GetData())) m_SelectedSurfaces.push_back(dynamic_cast(node->GetData())); } if (m_SelectedFB.empty()) { int maxLayer = 0; itk::VectorContainer::ConstPointer nodes = this->GetDefaultDataStorage()->GetAll(); for (unsigned int i=0; iSize(); i++) if (dynamic_cast(nodes->at(i)->GetData())) { mitk::DataStorage::SetOfObjects::ConstPointer sources = GetDataStorage()->GetSources(nodes->at(i)); if (sources->Size()>0) continue; int layer = 0; nodes->at(i)->GetPropertyValue("layer", layer); if (layer>=maxLayer) { maxLayer = layer; m_SelectedFB.clear(); m_SelectedFB.push_back(nodes->at(i)); } } } if (m_SelectedPF.empty()) { int maxLayer = 0; itk::VectorContainer::ConstPointer nodes = this->GetDefaultDataStorage()->GetAll(); for (unsigned int i=0; iSize(); i++) if (dynamic_cast(nodes->at(i)->GetData()) || dynamic_cast(nodes->at(i)->GetData()) || dynamic_cast(nodes->at(i)->GetData())) { mitk::DataStorage::SetOfObjects::ConstPointer sources = GetDataStorage()->GetSources(nodes->at(i)); if (sources->Size()>0) continue; int layer = 0; nodes->at(i)->GetPropertyValue("layer", layer); if (layer>=maxLayer) { maxLayer = layer; m_SelectedPF.clear(); m_SelectedPF.push_back(nodes->at(i)); } } } UpdateGui(); } void QmitkFiberProcessingView::OnDrawPolygon() { mitk::PlanarPolygon::Pointer figure = mitk::PlanarPolygon::New(); figure->ClosedOn(); this->AddFigureToDataStorage(figure, QString("Polygon%1").arg(++m_PolygonCounter)); } void QmitkFiberProcessingView::OnDrawCircle() { mitk::PlanarCircle::Pointer figure = mitk::PlanarCircle::New(); this->AddFigureToDataStorage(figure, QString("Circle%1").arg(++m_CircleCounter)); } void QmitkFiberProcessingView::Activated() { } void QmitkFiberProcessingView::AddFigureToDataStorage(mitk::PlanarFigure* figure, const QString& name, const char *, mitk::BaseProperty* ) { // initialize figure's geometry with empty geometry mitk::PlaneGeometry::Pointer emptygeometry = mitk::PlaneGeometry::New(); figure->SetPlaneGeometry( emptygeometry ); //set desired data to DataNode where Planarfigure is stored mitk::DataNode::Pointer newNode = mitk::DataNode::New(); newNode->SetName(name.toStdString()); newNode->SetData(figure); newNode->SetBoolProperty("planarfigure.3drendering", true); mitk::PlanarFigureInteractor::Pointer figureInteractor = dynamic_cast(newNode->GetDataInteractor().GetPointer()); if(figureInteractor.IsNull()) { figureInteractor = mitk::PlanarFigureInteractor::New(); us::Module* planarFigureModule = us::ModuleRegistry::GetModule( "MitkPlanarFigure" ); figureInteractor->LoadStateMachine("PlanarFigureInteraction.xml", planarFigureModule ); figureInteractor->SetEventConfig( "PlanarFigureConfig.xml", planarFigureModule ); figureInteractor->SetDataNode(newNode); } // figure drawn on the topmost layer / image GetDataStorage()->Add(newNode ); for(unsigned int i = 0; i < m_SelectedPF.size(); i++) m_SelectedPF[i]->SetSelected(false); newNode->SetSelected(true); m_SelectedPF.clear(); m_SelectedPF.push_back(newNode); UpdateGui(); } void QmitkFiberProcessingView::ExtractWithPlanarFigure() { if ( m_SelectedFB.empty() || m_SelectedPF.empty() ){ QMessageBox::information( NULL, "Warning", "No fibe bundle selected!"); return; } std::vector fiberBundles = m_SelectedFB; mitk::DataNode::Pointer planarFigure = m_SelectedPF.at(0); for (unsigned int i=0; i(fiberBundles.at(i)->GetData()); mitk::BaseData::Pointer roi = planarFigure->GetData(); mitk::FiberBundleX::Pointer extFB = fib->ExtractFiberSubset(roi); if (extFB->GetNumFibers()<=0) { QMessageBox::information(NULL, "No output generated:", "The resulting fiber bundle contains no fibers."); continue; } mitk::DataNode::Pointer node; node = mitk::DataNode::New(); node->SetData(extFB); QString name(fiberBundles.at(i)->GetName().c_str()); name += "_"; name += planarFigure->GetName().c_str(); node->SetName(name.toStdString()); fiberBundles.at(i)->SetVisibility(false); GetDataStorage()->Add(node); } } void QmitkFiberProcessingView::GenerateAndComposite() { mitk::PlanarFigureComposite::Pointer PFCAnd = mitk::PlanarFigureComposite::New(); PFCAnd->setOperationType(mitk::PFCOMPOSITION_AND_OPERATION); for( std::vector::iterator it = m_SelectedPF.begin(); it != m_SelectedPF.end(); ++it ) { mitk::DataNode::Pointer nodePF = *it; PFCAnd->addPlanarFigure( nodePF->GetData() ); PFCAnd->addDataNode( nodePF ); PFCAnd->setDisplayName("AND"); } AddCompositeToDatastorage(PFCAnd); } void QmitkFiberProcessingView::GenerateOrComposite() { mitk::PlanarFigureComposite::Pointer PFCOr = mitk::PlanarFigureComposite::New(); PFCOr->setOperationType(mitk::PFCOMPOSITION_OR_OPERATION); for( std::vector::iterator it = m_SelectedPF.begin(); it != m_SelectedPF.end(); ++it ) { mitk::DataNode::Pointer nodePF = *it; PFCOr->addPlanarFigure( nodePF->GetData() ); PFCOr->addDataNode( nodePF ); PFCOr->setDisplayName("OR"); } AddCompositeToDatastorage(PFCOr); } void QmitkFiberProcessingView::GenerateNotComposite() { mitk::PlanarFigureComposite::Pointer PFCNot = mitk::PlanarFigureComposite::New(); PFCNot->setOperationType(mitk::PFCOMPOSITION_NOT_OPERATION); for( std::vector::iterator it = m_SelectedPF.begin(); it != m_SelectedPF.end(); ++it ) { mitk::DataNode::Pointer nodePF = *it; PFCNot->addPlanarFigure( nodePF->GetData() ); PFCNot->addDataNode( nodePF ); PFCNot->setDisplayName("NOT"); } AddCompositeToDatastorage(PFCNot); } /* CLEANUP NEEDED */ void QmitkFiberProcessingView::AddCompositeToDatastorage(mitk::PlanarFigureComposite::Pointer pfc, mitk::DataNode::Pointer parentNode ) { mitk::DataNode::Pointer newPFCNode; newPFCNode = mitk::DataNode::New(); newPFCNode->SetName( pfc->getDisplayName() ); newPFCNode->SetData(pfc); switch (pfc->getOperationType()) { case 0: { if (parentNode.IsNotNull()) GetDataStorage()->Add(newPFCNode, parentNode); else GetDataStorage()->Add(newPFCNode); //iterate through its childs for(int i=0; igetNumberOfChildren(); ++i) { mitk::BaseData::Pointer tmpPFchild = pfc->getChildAt(i); mitk::DataNode::Pointer savedPFchildNode = pfc->getDataNodeAt(i); mitk::PlanarFigureComposite::Pointer pfcompcast= dynamic_cast(tmpPFchild.GetPointer()); if ( pfcompcast.IsNotNull() ) { // child is of type planar Figure composite // make new node of the child, cuz later the child has to be removed of its old position in datamanager // feed new dataNode with information of the savedDataNode, which is gonna be removed soon mitk::DataNode::Pointer newChildPFCNode; newChildPFCNode = mitk::DataNode::New(); newChildPFCNode->SetData(tmpPFchild); newChildPFCNode->SetName( savedPFchildNode->GetName() ); pfcompcast->setDisplayName( savedPFchildNode->GetName() ); //name might be changed in DataManager by user //update inside vector the dataNodePointer pfc->replaceDataNodeAt(i, newChildPFCNode); AddCompositeToDatastorage(pfcompcast, newPFCNode); //the current PFCNode becomes the childs parent // remove savedNode here, cuz otherwise its children will change their position in the dataNodeManager // without having its parent anymore GetDataStorage()->Remove(savedPFchildNode); } else { // child is not of type PlanarFigureComposite, so its one of the planarFigures // create new dataNode containing the data of the old dataNode, but position in dataManager will be // modified cuz we re setting a (new) parent. mitk::DataNode::Pointer newPFchildNode = mitk::DataNode::New(); newPFchildNode->SetName(savedPFchildNode->GetName() ); newPFchildNode->SetData(tmpPFchild); newPFchildNode->SetVisibility(true); newPFchildNode->SetBoolProperty("planarfigure.3drendering", true); // replace the dataNode in PFComp DataNodeVector pfc->replaceDataNodeAt(i, newPFchildNode); // remove old child position in dataStorage GetDataStorage()->Remove(savedPFchildNode); //add new child to datamanager with its new position as child of newPFCNode parent GetDataStorage()->Add(newPFchildNode, newPFCNode); } } break; } case 1: { if (!parentNode.IsNull()) GetDataStorage()->Add(newPFCNode, parentNode); else GetDataStorage()->Add(newPFCNode); for(int i=0; igetNumberOfChildren(); ++i) { mitk::BaseData::Pointer tmpPFchild = pfc->getChildAt(i); mitk::DataNode::Pointer savedPFchildNode = pfc->getDataNodeAt(i); mitk::PlanarFigureComposite::Pointer pfcompcast= dynamic_cast(tmpPFchild.GetPointer()); if ( !pfcompcast.IsNull() ) { // child is of type planar Figure composite // make new node of the child, cuz later the child has to be removed of its old position in datamanager // feed new dataNode with information of the savedDataNode, which is gonna be removed soon mitk::DataNode::Pointer newChildPFCNode; newChildPFCNode = mitk::DataNode::New(); newChildPFCNode->SetData(tmpPFchild); newChildPFCNode->SetName( savedPFchildNode->GetName() ); pfcompcast->setDisplayName( savedPFchildNode->GetName() ); //name might be changed in DataManager by user //update inside vector the dataNodePointer pfc->replaceDataNodeAt(i, newChildPFCNode); AddCompositeToDatastorage(pfcompcast, newPFCNode); //the current PFCNode becomes the childs parent // remove old child position in dataStorage GetDataStorage()->Remove(savedPFchildNode); } else { // child is not of type PlanarFigureComposite, so its one of the planarFigures // create new dataNode containing the data of the old dataNode, but position in dataManager will be // modified cuz we re setting a (new) parent. mitk::DataNode::Pointer newPFchildNode = mitk::DataNode::New(); newPFchildNode->SetName(savedPFchildNode->GetName() ); newPFchildNode->SetData(tmpPFchild); newPFchildNode->SetVisibility(true); newPFchildNode->SetBoolProperty("planarfigure.3drendering", true); // replace the dataNode in PFComp DataNodeVector pfc->replaceDataNodeAt(i, newPFchildNode); // remove old child position in dataStorage GetDataStorage()->Remove(savedPFchildNode); //add new child to datamanager with its new position as child of newPFCNode parent GetDataStorage()->Add(newPFchildNode, newPFCNode); } } break; } case 2: { if (!parentNode.IsNull()) GetDataStorage()->Add(newPFCNode, parentNode); else GetDataStorage()->Add(newPFCNode); //iterate through its childs for(int i=0; igetNumberOfChildren(); ++i) { mitk::BaseData::Pointer tmpPFchild = pfc->getChildAt(i); mitk::DataNode::Pointer savedPFchildNode = pfc->getDataNodeAt(i); mitk::PlanarFigureComposite::Pointer pfcompcast= dynamic_cast(tmpPFchild.GetPointer()); if ( !pfcompcast.IsNull() ) { // child is of type planar Figure composite // makeRemoveBundle new node of the child, cuz later the child has to be removed of its old position in datamanager // feed new dataNode with information of the savedDataNode, which is gonna be removed soon mitk::DataNode::Pointer newChildPFCNode; newChildPFCNode = mitk::DataNode::New(); newChildPFCNode->SetData(tmpPFchild); newChildPFCNode->SetName( savedPFchildNode->GetName() ); pfcompcast->setDisplayName( savedPFchildNode->GetName() ); //name might be changed in DataManager by user //update inside vector the dataNodePointer pfc->replaceDataNodeAt(i, newChildPFCNode); AddCompositeToDatastorage(pfcompcast, newPFCNode); //the current PFCNode becomes the childs parent // remove old child position in dataStorage GetDataStorage()->Remove(savedPFchildNode); } else { // child is not of type PlanarFigureComposite, so its one of the planarFigures // create new dataNode containing the data of the old dataNode, but position in dataManager will be // modified cuz we re setting a (new) parent. mitk::DataNode::Pointer newPFchildNode = mitk::DataNode::New(); newPFchildNode->SetName(savedPFchildNode->GetName() ); newPFchildNode->SetData(tmpPFchild); newPFchildNode->SetVisibility(true); newPFchildNode->SetBoolProperty("planarfigure.3drendering", true); // replace the dataNode in PFComp DataNodeVector pfc->replaceDataNodeAt(i, newPFchildNode); // remove old child position in dataStorage GetDataStorage()->Remove(savedPFchildNode); //add new child to datamanager with its new position as child of newPFCNode parent GetDataStorage()->Add(newPFchildNode, newPFCNode); } } break; } default: MITK_DEBUG << "we have an UNDEFINED composition... ERROR" ; break; } for(unsigned int i = 0; i < m_SelectedPF.size(); i++) m_SelectedPF[i]->SetSelected(false); newPFCNode->SetSelected(true); m_SelectedPF.clear(); m_SelectedPF.push_back(newPFCNode); UpdateGui(); } void QmitkFiberProcessingView::JoinBundles() { if ( m_SelectedFB.size()<2 ){ QMessageBox::information( NULL, "Warning", "Select at least two fiber bundles!"); MITK_WARN("QmitkFiberProcessingView") << "Select at least two fiber bundles!"; return; } mitk::FiberBundleX::Pointer newBundle = dynamic_cast(m_SelectedFB.at(0)->GetData()); m_SelectedFB.at(0)->SetVisibility(false); QString name(""); name += QString(m_SelectedFB.at(0)->GetName().c_str()); for (unsigned int i=1; iAddBundle(dynamic_cast(m_SelectedFB.at(i)->GetData())); name += "+"+QString(m_SelectedFB.at(i)->GetName().c_str()); m_SelectedFB.at(i)->SetVisibility(false); } mitk::DataNode::Pointer fbNode = mitk::DataNode::New(); fbNode->SetData(newBundle); fbNode->SetName(name.toStdString()); fbNode->SetVisibility(true); GetDataStorage()->Add(fbNode); } void QmitkFiberProcessingView::SubstractBundles() { if ( m_SelectedFB.size()<2 ){ QMessageBox::information( NULL, "Warning", "Select at least two fiber bundles!"); MITK_WARN("QmitkFiberProcessingView") << "Select at least two fiber bundles!"; return; } mitk::FiberBundleX::Pointer newBundle = dynamic_cast(m_SelectedFB.at(0)->GetData()); m_SelectedFB.at(0)->SetVisibility(false); QString name(""); name += QString(m_SelectedFB.at(0)->GetName().c_str()); for (unsigned int i=1; iSubtractBundle(dynamic_cast(m_SelectedFB.at(i)->GetData())); if (newBundle.IsNull()) break; name += "-"+QString(m_SelectedFB.at(i)->GetName().c_str()); m_SelectedFB.at(i)->SetVisibility(false); } if (newBundle.IsNull()) { QMessageBox::information(NULL, "No output generated:", "The resulting fiber bundle contains no fibers. Did you select the fiber bundles in the correct order? X-Y is not equal to Y-X!"); return; } mitk::DataNode::Pointer fbNode = mitk::DataNode::New(); fbNode->SetData(newBundle); fbNode->SetName(name.toStdString()); fbNode->SetVisibility(true); GetDataStorage()->Add(fbNode); } void QmitkFiberProcessingView::ResampleSelectedBundles() { double factor = this->m_Controls->m_SmoothFibersBox->value(); for (unsigned int i=0; i(m_SelectedFB.at(i)->GetData()); fib->ResampleSpline(factor); } RenderingManager::GetInstance()->RequestUpdateAll(); } void QmitkFiberProcessingView::CompressSelectedBundles() { double factor = this->m_Controls->m_ErrorThresholdBox->value(); for (unsigned int i=0; i(m_SelectedFB.at(i)->GetData()); fib->Compress(factor); } RenderingManager::GetInstance()->RequestUpdateAll(); } void QmitkFiberProcessingView::DoImageColorCoding() { if (m_Controls->m_ColorMapBox->GetSelectedNode().IsNull()) { QMessageBox::information(NULL, "Bundle coloring aborted:", "No image providing the scalar values for coloring the selected bundle available."); return; } for(unsigned int i=0; i(m_SelectedFB.at(i)->GetData()); - fib->SetFAMap(dynamic_cast(m_Controls->m_ColorMapBox->GetSelectedNode()->GetData())); - fib->SetColorCoding(mitk::FiberBundleX::COLORCODING_FA_BASED); - fib->DoColorCodingFaBased(); + fib->ColorFibersByScalarMap(dynamic_cast(m_Controls->m_ColorMapBox->GetSelectedNode()->GetData()), m_Controls->m_FiberOpacityBox->isChecked()); } if(m_MultiWidget) m_MultiWidget->RequestUpdate(); } void QmitkFiberProcessingView::MirrorFibers() { unsigned int axis = this->m_Controls->m_MirrorFibersBox->currentIndex(); for (int i=0; i(m_SelectedFB.at(i)->GetData()); fib->MirrorFibers(axis); } if (m_SelectedSurfaces.size()>0) { for (int i=0; i poly = surf->GetVtkPolyData(); vtkSmartPointer vtkNewPoints = vtkSmartPointer::New(); for (int i=0; iGetNumberOfPoints(); i++) { double* point = poly->GetPoint(i); point[axis] *= -1; vtkNewPoints->InsertNextPoint(point); } poly->SetPoints(vtkNewPoints); surf->CalculateBoundingBox(); } } RenderingManager::GetInstance()->RequestUpdateAll(); } diff --git a/Plugins/org.mitk.gui.qt.diffusionimaging/src/internal/QmitkFiberProcessingView.h b/Plugins/org.mitk.gui.qt.diffusionimaging/src/internal/QmitkFiberProcessingView.h index 175c8d8889..24d0569311 100644 --- a/Plugins/org.mitk.gui.qt.diffusionimaging/src/internal/QmitkFiberProcessingView.h +++ b/Plugins/org.mitk.gui.qt.diffusionimaging/src/internal/QmitkFiberProcessingView.h @@ -1,188 +1,189 @@ /*=================================================================== The Medical Imaging Interaction Toolkit (MITK) Copyright (c) German Cancer Research Center, Division of Medical and Biological Informatics. All rights reserved. This software is distributed WITHOUT ANY WARRANTY; without even the implied warranty of MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See LICENSE.txt or http://www.mitk.org for details. ===================================================================*/ #ifndef QmitkFiberProcessingView_h #define QmitkFiberProcessingView_h #include #include "ui_QmitkFiberProcessingViewControls.h" #include #include #include #include #include #include #include #include #include #include #include #include #include #include #include #include #include #include /*! \brief View to process fiber bundles. Supplies methods to extract fibers from the bundle, join and subtract bundles and much more. \sa QmitkFunctionality \ingroup Functionalities */ class QmitkFiberProcessingView : public QmitkFunctionality { // this is needed for all Qt objects that should have a Qt meta-object // (everything that derives from QObject and wants to have signal/slots) Q_OBJECT public: typedef itk::Image< unsigned char, 3 > itkUCharImageType; static const std::string VIEW_ID; QmitkFiberProcessingView(); virtual ~QmitkFiberProcessingView(); virtual void CreateQtPartControl(QWidget *parent); virtual void StdMultiWidgetAvailable (QmitkStdMultiWidget &stdMultiWidget); virtual void StdMultiWidgetNotAvailable(); virtual void Activated(); protected slots: void OnDrawCircle(); ///< add circle interactors etc. void OnDrawPolygon(); ///< add circle interactors etc. void GenerateAndComposite(); void GenerateOrComposite(); void GenerateNotComposite(); void JoinBundles(); ///< merge selected fiber bundles void SubstractBundles(); ///< subtract bundle A from bundle B. Not commutative! Defined by order of selection. void GenerateRoiImage(); ///< generate binary image of selected planar figures. void Remove(); void Extract(); void Modify(); void UpdateGui(); ///< update button activity etc. dpending on current datamanager selection virtual void AddFigureToDataStorage(mitk::PlanarFigure* figure, const QString& name, const char *propertyKey = NULL, mitk::BaseProperty *property = NULL ); protected: void MirrorFibers(); ///< mirror bundle on the specified plane void ResampleSelectedBundles(); ///< smooth fiber bundle using the specified number of sampling points per cm. void DoImageColorCoding(); ///< color fibers by selected scalar image void CompressSelectedBundles(); ///< remove points below certain error threshold + void WeightFibers(); void RemoveWithMask(bool removeInside); void RemoveDir(); void ApplyCurvatureThreshold(); ///< remove/split fibers with a too high curvature threshold void PruneBundle(); ///< remove too short/too long fibers void ExtractWithMask(bool onlyEnds, bool invert); void ExtractWithPlanarFigure(); /// \brief called by QmitkFunctionality when DataManager's selection has changed virtual void OnSelectionChanged( std::vector nodes ); Ui::QmitkFiberProcessingViewControls* m_Controls; QmitkStdMultiWidget* m_MultiWidget; /** Connection from VTK to ITK */ template void ConnectPipelines(VTK_Exporter* exporter, ITK_Importer importer) { importer->SetUpdateInformationCallback(exporter->GetUpdateInformationCallback()); importer->SetPipelineModifiedCallback(exporter->GetPipelineModifiedCallback()); importer->SetWholeExtentCallback(exporter->GetWholeExtentCallback()); importer->SetSpacingCallback(exporter->GetSpacingCallback()); importer->SetOriginCallback(exporter->GetOriginCallback()); importer->SetScalarTypeCallback(exporter->GetScalarTypeCallback()); importer->SetNumberOfComponentsCallback(exporter->GetNumberOfComponentsCallback()); importer->SetPropagateUpdateExtentCallback(exporter->GetPropagateUpdateExtentCallback()); importer->SetUpdateDataCallback(exporter->GetUpdateDataCallback()); importer->SetDataExtentCallback(exporter->GetDataExtentCallback()); importer->SetBufferPointerCallback(exporter->GetBufferPointerCallback()); importer->SetCallbackUserData(exporter->GetCallbackUserData()); } template void ConnectPipelines(ITK_Exporter exporter, VTK_Importer* importer) { importer->SetUpdateInformationCallback(exporter->GetUpdateInformationCallback()); importer->SetPipelineModifiedCallback(exporter->GetPipelineModifiedCallback()); importer->SetWholeExtentCallback(exporter->GetWholeExtentCallback()); importer->SetSpacingCallback(exporter->GetSpacingCallback()); importer->SetOriginCallback(exporter->GetOriginCallback()); importer->SetScalarTypeCallback(exporter->GetScalarTypeCallback()); importer->SetNumberOfComponentsCallback(exporter->GetNumberOfComponentsCallback()); importer->SetPropagateUpdateExtentCallback(exporter->GetPropagateUpdateExtentCallback()); importer->SetUpdateDataCallback(exporter->GetUpdateDataCallback()); importer->SetDataExtentCallback(exporter->GetDataExtentCallback()); importer->SetBufferPointerCallback(exporter->GetBufferPointerCallback()); importer->SetCallbackUserData(exporter->GetCallbackUserData()); } template < typename TPixel, unsigned int VImageDimension > void InternalCalculateMaskFromPlanarFigure( itk::Image< TPixel, VImageDimension > *image, unsigned int axis, std::string nodeName ); template < typename TPixel, unsigned int VImageDimension > void InternalReorientImagePlane( const itk::Image< TPixel, VImageDimension > *image, mitk::BaseGeometry* planegeo3D, int additionalIndex ); int m_CircleCounter; ///< used for data node naming int m_PolygonCounter; ///< used for data node naming std::vector m_SelectedFB; ///< selected fiber bundle nodes std::vector m_SelectedPF; ///< selected planar figure nodes std::vector m_SelectedSurfaces; mitk::Image::Pointer m_SelectedImage; mitk::Image::Pointer m_InternalImage; mitk::PlanarFigure::Pointer m_PlanarFigure; itkUCharImageType::Pointer m_InternalImageMask3D; itkUCharImageType::Pointer m_PlanarFigureImage; float m_UpsamplingFactor; ///< upsampling factor for all image generations mitk::DataNode::Pointer m_MaskImageNode; void AddCompositeToDatastorage(mitk::PlanarFigureComposite::Pointer pfc, mitk::DataNode::Pointer parentNode=NULL); void debugPFComposition(mitk::PlanarFigureComposite::Pointer , int ); void WritePfToImage(mitk::DataNode::Pointer node, mitk::Image* image); mitk::DataNode::Pointer GenerateTractDensityImage(mitk::FiberBundleX::Pointer fib, bool binary, bool absolute); mitk::DataNode::Pointer GenerateColorHeatmap(mitk::FiberBundleX::Pointer fib); mitk::DataNode::Pointer GenerateFiberEndingsImage(mitk::FiberBundleX::Pointer fib); mitk::DataNode::Pointer GenerateFiberEndingsPointSet(mitk::FiberBundleX::Pointer fib); void NodeAdded( const mitk::DataNode* node ); void NodeRemoved(const mitk::DataNode* node); }; #endif // _QMITKFIBERTRACKINGVIEW_H_INCLUDED diff --git a/Plugins/org.mitk.gui.qt.diffusionimaging/src/internal/QmitkFiberProcessingViewControls.ui b/Plugins/org.mitk.gui.qt.diffusionimaging/src/internal/QmitkFiberProcessingViewControls.ui index 29ec29686a..51bfb4158d 100644 --- a/Plugins/org.mitk.gui.qt.diffusionimaging/src/internal/QmitkFiberProcessingViewControls.ui +++ b/Plugins/org.mitk.gui.qt.diffusionimaging/src/internal/QmitkFiberProcessingViewControls.ui @@ -1,1284 +1,1320 @@ QmitkFiberProcessingViewControls 0 0 386 540 Form - + 0 0 0 355 302 Fiber Extraction Extract a fiber subset from the selected fiber bundle using manually placed planar figures as waypoints or binary regions of interest. false 0 0 200 16777215 11 Extract fibers passing through selected ROI or composite ROI. Select ROI and fiber bundle to execute. Extract Qt::Vertical 20 40 0 0 Ending in mask Not ending in mask Passing mask Not passing mask QFrame::NoFrame QFrame::Raised 9 9 9 9 0 false 0 0 16777215 16777215 11 Generate a binary image containing all selected ROIs. Select at least one ROI (planar figure) and a reference fiber bundle or image. Generate ROI Image 0 0 200 0 16777215 60 QFrame::NoFrame QFrame::Raised 0 0 0 0 false 60 16777215 Create OR composition with selected ROIs. OR Qt::Horizontal 40 20 false 60 16777215 Create NOT composition from selected ROI. NOT false 60 16777215 Create AND composition with selected ROIs. AND 0 0 200 0 16777215 60 QFrame::NoFrame QFrame::Raised 0 0 0 0 30 30 Draw circular ROI. Select reference fiber bundle to execute. :/QmitkDiffusionImaging/circle.png:/QmitkDiffusionImaging/circle.png 32 32 false true - - - - - 30 - 30 - - - - Draw rectangular ROI. Select reference fiber bundle to execute. - - - - - - - :/QmitkDiffusionImaging/rectangle.png:/QmitkDiffusionImaging/rectangle.png + + + + Qt::Horizontal - + - 32 - 32 + 40 + 20 - - true - - - true - - + - + 30 30 Draw polygonal ROI. Select reference fiber bundle to execute. :/QmitkDiffusionImaging/polygon.png:/QmitkDiffusionImaging/polygon.png 32 32 true true - - - - Qt::Horizontal - - - - 40 - 20 - - - - 0 0 Extract using planar figures Extract using binary ROI image 0 - -70 - 355 + 0 + 270 380 Fiber Removal Remove fibers that satisfy certain criteria from the selected bundle. 0 0 Remove fibers in direction Remove fibers by length Remove fibers by curvature Remove fiber parts outside mask Remove fiber parts inside mask QFrame::NoFrame QFrame::Raised 0 0 0 0 Qt::Horizontal 40 20 Minimum fiber length in mm 0 999999999 20 Max. Length: Min. Length: Maximum fiber length in mm 0 999999999 300 QFrame::NoFrame QFrame::Raised 0 0 0 0 0 X: Y: Z: Angle: Angular deviation threshold in degree 1 90.000000000000000 1.000000000000000 5.000000000000000 QFrame::NoFrame QFrame::Raised 0 0 0 0 If unchecked, the fiber exceeding the threshold will be split in two instead of removed. Remove Fiber false QFrame::NoFrame QFrame::Raised 0 0 0 0 0 Max. Angular Deviation: Qt::Horizontal 40 20 Maximum angular deviation in degree 180.000000000000000 0.100000000000000 15.000000000000000 Distance: Distance in mm 1 999.000000000000000 1.000000000000000 10.000000000000000 false 0 0 200 16777215 11 - Remove all fiber parts outside of the mask. + Remove Qt::Vertical 20 40 0 0 - 280 - 294 + 355 + 349 Bundle Modification Modify the selected bundle with operations such as fiber resampling, FA coloring, etc. QFrame::NoFrame QFrame::Raised 0 0 0 0 0 Error threshold in mm: 999999999.000000000000000 0.100000000000000 0.100000000000000 - - + + QFrame::NoFrame QFrame::Raised - + 0 0 0 0 0 - - - 0.010000000000000 - - - 999999999.000000000000000 - - - 1.000000000000000 - + + + + Axial + + + + + Sagittal + + + + + Coronal + + - + - Point distance in mm: + Select direction: QFrame::NoFrame QFrame::Raised 0 0 0 0 0 - - - Scalar map: + + + + + + + If checked, the image values are not only used to color the fibers but are also used as opaxity values. + + + Values as opacity + + + true + + + - - - - false - - - - 0 - 0 - - - - - 200 - 16777215 - - - - - 11 - - - - Remove all fiber parts outside of the mask. - - - Execute - - - 0 0 Smooth fibers Compress fibers Color fibers by scalar map (e.g. FA) Mirror fibers + + + Weight Bundle + + - + + + + QFrame::NoFrame + + + QFrame::Raised + + + + 0 + + + 0 + + + 0 + + + 0 + + + 0 + + + + + 0.010000000000000 + + + 999999999.000000000000000 + + + 1.000000000000000 + + + + + + + Point distance in mm: + + + + + + + Qt::Vertical 20 40 - - + + + + false + + + + 0 + 0 + + + + + 200 + 16777215 + + + + + 11 + + + + + + + Execute + + + + + QFrame::NoFrame QFrame::Raised - + 0 0 0 0 0 - - - - - Axial - - - - - Sagittal - - - - - Coronal - - - - - + - Select direction: + Weight: + + + + + + + 7 + + + 1.000000000000000 + + + 0.100000000000000 + + + 1.000000000000000 0 0 360 61 Binary Bundle Operations Join or subtract bundles. false 0 0 200 16777215 11 Returns all fibers contained in bundle X that are not contained in bundle Y (not commutative!). Select at least two fiber bundles to execute. Substract false 0 0 200 16777215 11 Merge selected fiber bundles. Select at least two fiber bundles to execute. Join Qt::Vertical 20 40 Please Select Input Data <html><head/><body><p><span style=" color:#ff0000;">mandatory</span></p></body></html> true <html><head/><body><p><span style=" color:#969696;">needed for extraction</span></p></body></html> true Input DTI Fiber Bundle: Binary seed ROI. If not specified, the whole image area is seeded. ROI: Qt::Vertical 20 40 QmitkDataStorageComboBox QComboBox
QmitkDataStorageComboBox.h
 diff --git a/Plugins/org.mitk.gui.qt.diffusionimaging/src/internal/QmitkFiberfoxView.cpp b/Plugins/org.mitk.gui.qt.diffusionimaging/src/internal/QmitkFiberfoxView.cpp index b6a345e6d9..fd750f32f1 100644 --- a/Plugins/org.mitk.gui.qt.diffusionimaging/src/internal/QmitkFiberfoxView.cpp +++ b/Plugins/org.mitk.gui.qt.diffusionimaging/src/internal/QmitkFiberfoxView.cpp @@ -1,2694 +1,2694 @@ /*=================================================================== The Medical Imaging Interaction Toolkit (MITK) Copyright (c) German Cancer Research Center, Division of Medical and Biological Informatics. All rights reserved. This software is distributed WITHOUT ANY WARRANTY; without even the implied warranty of MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See LICENSE.txt or http://www.mitk.org for details. ===================================================================*/ //misc #define _USE_MATH_DEFINES #include // Blueberry #include #include // Qmitk #include "QmitkFiberfoxView.h" // MITK #include #include #include #include #include #include #include #include #include #include #include #include #include #include #include #include #include #include #include #include #include #include #include #include #include #include #include #include "usModuleRegistry.h" #include #include #include #include #include #include #include #include #include #include "mitkNodePredicateDataType.h" #include #include #include #include #define _USE_MATH_DEFINES #include QmitkFiberfoxWorker::QmitkFiberfoxWorker(QmitkFiberfoxView* view) : m_View(view) { } void QmitkFiberfoxWorker::run() { try{ switch (m_FilterType) { case 0: m_View->m_TractsToDwiFilter->Update(); break; case 1: m_View->m_ArtifactsToDwiFilter->Update(); break; } } catch( ... ) { } m_View->m_Thread.quit(); } const std::string QmitkFiberfoxView::VIEW_ID = "org.mitk.views.fiberfoxview"; QmitkFiberfoxView::QmitkFiberfoxView() : QmitkAbstractView() , m_Controls( 0 ) , m_SelectedImage( NULL ) , m_Worker(this) , m_ThreadIsRunning(false) { m_Worker.moveToThread(&m_Thread); connect(&m_Thread, SIGNAL(started()), this, SLOT(BeforeThread())); connect(&m_Thread, SIGNAL(started()), &m_Worker, SLOT(run())); connect(&m_Thread, SIGNAL(finished()), this, SLOT(AfterThread())); connect(&m_Thread, SIGNAL(terminated()), this, SLOT(AfterThread())); m_SimulationTimer = new QTimer(this); } void QmitkFiberfoxView::KillThread() { MITK_INFO << "Aborting DWI simulation."; switch (m_Worker.m_FilterType) { case 0: m_TractsToDwiFilter->SetAbortGenerateData(true); break; case 1: m_ArtifactsToDwiFilter->SetAbortGenerateData(true); break; } m_Controls->m_AbortSimulationButton->setEnabled(false); m_Controls->m_AbortSimulationButton->setText("Aborting simulation ..."); } void QmitkFiberfoxView::BeforeThread() { m_SimulationTime = QTime::currentTime(); m_SimulationTimer->start(100); m_Controls->m_AbortSimulationButton->setVisible(true); m_Controls->m_GenerateImageButton->setVisible(false); m_Controls->m_SimulationStatusText->setVisible(true); m_ThreadIsRunning = true; } void QmitkFiberfoxView::AfterThread() { UpdateSimulationStatus(); m_SimulationTimer->stop(); m_Controls->m_AbortSimulationButton->setVisible(false); m_Controls->m_AbortSimulationButton->setEnabled(true); m_Controls->m_AbortSimulationButton->setText("Abort simulation"); m_Controls->m_GenerateImageButton->setVisible(true); m_ThreadIsRunning = false; QString statusText; FiberfoxParameters parameters; mitk::Image::Pointer mitkImage = mitk::Image::New(); switch (m_Worker.m_FilterType) { case 0: { statusText = QString(m_TractsToDwiFilter->GetStatusText().c_str()); if (m_TractsToDwiFilter->GetAbortGenerateData()) { MITK_INFO << "Simulation aborted."; return; } parameters = m_TractsToDwiFilter->GetParameters(); mitkImage = mitk::GrabItkImageMemory( m_TractsToDwiFilter->GetOutput() ); mitkImage->SetProperty( mitk::DiffusionPropertyHelper::GRADIENTCONTAINERPROPERTYNAME.c_str(), mitk::GradientDirectionsProperty::New( parameters.m_SignalGen.GetGradientDirections() )); mitkImage->SetProperty( mitk::DiffusionPropertyHelper::REFERENCEBVALUEPROPERTYNAME.c_str(), mitk::FloatProperty::New( parameters.m_SignalGen.m_Bvalue )); mitk::DiffusionPropertyHelper propertyHelper( mitkImage ); propertyHelper.InitializeImage(); parameters.m_Misc.m_ResultNode->SetData( mitkImage ); parameters.m_Misc.m_ResultNode->SetName(parameters.m_Misc.m_ParentNode->GetName() +"_D"+QString::number(parameters.m_SignalGen.m_ImageRegion.GetSize(0)).toStdString() +"-"+QString::number(parameters.m_SignalGen.m_ImageRegion.GetSize(1)).toStdString() +"-"+QString::number(parameters.m_SignalGen.m_ImageRegion.GetSize(2)).toStdString() +"_S"+QString::number(parameters.m_SignalGen.m_ImageSpacing[0]).toStdString() +"-"+QString::number(parameters.m_SignalGen.m_ImageSpacing[1]).toStdString() +"-"+QString::number(parameters.m_SignalGen.m_ImageSpacing[2]).toStdString() +"_b"+QString::number(parameters.m_SignalGen.m_Bvalue).toStdString() +"_"+parameters.m_Misc.m_SignalModelString +parameters.m_Misc.m_ArtifactModelString); GetDataStorage()->Add(parameters.m_Misc.m_ResultNode, parameters.m_Misc.m_ParentNode); parameters.m_Misc.m_ResultNode->SetProperty( "levelwindow", mitk::LevelWindowProperty::New(m_TractsToDwiFilter->GetLevelWindow()) ); if (m_Controls->m_VolumeFractionsBox->isChecked()) { std::vector< itk::TractsToDWIImageFilter< short >::ItkDoubleImgType::Pointer > volumeFractions = m_TractsToDwiFilter->GetVolumeFractions(); for (unsigned int k=0; kInitializeByItk(volumeFractions.at(k).GetPointer()); image->SetVolume(volumeFractions.at(k)->GetBufferPointer()); mitk::DataNode::Pointer node = mitk::DataNode::New(); node->SetData( image ); node->SetName(parameters.m_Misc.m_ParentNode->GetName()+"_CompartmentVolume-"+QString::number(k).toStdString()); GetDataStorage()->Add(node, parameters.m_Misc.m_ParentNode); } } m_TractsToDwiFilter = NULL; break; } case 1: { statusText = QString(m_ArtifactsToDwiFilter->GetStatusText().c_str()); if (m_ArtifactsToDwiFilter->GetAbortGenerateData()) { MITK_INFO << "Simulation aborted."; return; } parameters = m_ArtifactsToDwiFilter->GetParameters().CopyParameters(); mitk::Image::Pointer diffImg = dynamic_cast(parameters.m_Misc.m_ParentNode->GetData()); mitkImage = mitk::GrabItkImageMemory( m_ArtifactsToDwiFilter->GetOutput() ); mitkImage->SetProperty( mitk::DiffusionPropertyHelper::GRADIENTCONTAINERPROPERTYNAME.c_str(), mitk::GradientDirectionsProperty::New( static_cast( diffImg->GetProperty(mitk::DiffusionPropertyHelper::GRADIENTCONTAINERPROPERTYNAME.c_str()).GetPointer() )->GetGradientDirectionsContainer() ) ); mitkImage->SetProperty( mitk::DiffusionPropertyHelper::REFERENCEBVALUEPROPERTYNAME.c_str(), mitk::FloatProperty::New( static_cast( diffImg->GetProperty(mitk::DiffusionPropertyHelper::REFERENCEBVALUEPROPERTYNAME.c_str()).GetPointer() )->GetValue() ) ); mitk::DiffusionPropertyHelper propertyHelper( mitkImage ); propertyHelper.InitializeImage(); parameters.m_Misc.m_ResultNode->SetData( mitkImage ); parameters.m_Misc.m_ResultNode->SetName(parameters.m_Misc.m_ParentNode->GetName()+parameters.m_Misc.m_ArtifactModelString); GetDataStorage()->Add(parameters.m_Misc.m_ResultNode, parameters.m_Misc.m_ParentNode); m_ArtifactsToDwiFilter = NULL; break; } } mitk::BaseData::Pointer basedata = parameters.m_Misc.m_ResultNode->GetData(); if (basedata.IsNotNull()) { mitk::RenderingManager::GetInstance()->InitializeViews( basedata->GetTimeGeometry(), mitk::RenderingManager::REQUEST_UPDATE_ALL, true ); mitk::RenderingManager::GetInstance()->RequestUpdateAll(); } if (!parameters.m_Misc.m_OutputPath.empty()) { try{ QString outputFileName(parameters.m_Misc.m_OutputPath.c_str()); outputFileName += parameters.m_Misc.m_ResultNode->GetName().c_str(); outputFileName.replace(QString("."), QString("_")); outputFileName += ".dwi"; QString status("Saving output image to "); status += outputFileName; m_Controls->m_SimulationStatusText->append(status); mitk::IOUtil::SaveBaseData(mitkImage, outputFileName.toStdString()); m_Controls->m_SimulationStatusText->append("File saved successfully."); } catch (itk::ExceptionObject &e) { QString status("Exception during DWI writing: "); status += e.GetDescription(); m_Controls->m_SimulationStatusText->append(status); } catch (...) { m_Controls->m_SimulationStatusText->append("Unknown exception during DWI writing!"); } } parameters.m_SignalGen.m_FrequencyMap = NULL; } void QmitkFiberfoxView::UpdateSimulationStatus() { QString statusText; switch (m_Worker.m_FilterType) { case 0: statusText = QString(m_TractsToDwiFilter->GetStatusText().c_str()); break; case 1: statusText = QString(m_ArtifactsToDwiFilter->GetStatusText().c_str()); break; } if (QString::compare(m_SimulationStatusText,statusText)!=0) { m_Controls->m_SimulationStatusText->clear(); statusText = "
"+statusText+"
"; m_Controls->m_SimulationStatusText->setText(statusText); QScrollBar *vScrollBar = m_Controls->m_SimulationStatusText->verticalScrollBar(); vScrollBar->triggerAction(QScrollBar::SliderToMaximum); } } // Destructor QmitkFiberfoxView::~QmitkFiberfoxView() { delete m_SimulationTimer; } void QmitkFiberfoxView::CreateQtPartControl( QWidget *parent ) { // build up qt view, unless already done if ( !m_Controls ) { // create GUI widgets from the Qt Designer's .ui file m_Controls = new Ui::QmitkFiberfoxViewControls; m_Controls->setupUi( parent ); // commented out m_Controls->m_DiffusionDirectionBox->setVisible(false); m_Controls->label_3->setVisible(false); m_Controls->m_SeparationAngleBox->setVisible(false); m_Controls->label_4->setVisible(false); // m_Controls->m_StickWidget1->setVisible(true); m_Controls->m_StickWidget2->setVisible(false); m_Controls->m_ZeppelinWidget1->setVisible(false); m_Controls->m_ZeppelinWidget2->setVisible(false); m_Controls->m_TensorWidget1->setVisible(false); m_Controls->m_TensorWidget2->setVisible(false); m_Controls->m_BallWidget1->setVisible(true); m_Controls->m_BallWidget2->setVisible(false); m_Controls->m_AstrosticksWidget1->setVisible(false); m_Controls->m_AstrosticksWidget2->setVisible(false); m_Controls->m_DotWidget1->setVisible(false); m_Controls->m_DotWidget2->setVisible(false); m_Controls->m_PrototypeWidget1->setVisible(false); m_Controls->m_PrototypeWidget2->setVisible(false); m_Controls->m_PrototypeWidget3->setVisible(false); m_Controls->m_PrototypeWidget4->setVisible(false); m_Controls->m_PrototypeWidget3->SetMinFa(0.0); m_Controls->m_PrototypeWidget3->SetMaxFa(0.15); m_Controls->m_PrototypeWidget4->SetMinFa(0.0); m_Controls->m_PrototypeWidget4->SetMaxFa(0.15); m_Controls->m_PrototypeWidget3->SetMinAdc(0.0); m_Controls->m_PrototypeWidget3->SetMaxAdc(0.001); m_Controls->m_PrototypeWidget4->SetMinAdc(0.003); m_Controls->m_PrototypeWidget4->SetMaxAdc(0.004); m_Controls->m_Comp4FractionFrame->setVisible(false); m_Controls->m_DiffusionPropsMessage->setVisible(false); m_Controls->m_GeometryMessage->setVisible(false); m_Controls->m_AdvancedSignalOptionsFrame->setVisible(false); m_Controls->m_AdvancedFiberOptionsFrame->setVisible(false); m_Controls->m_VarianceBox->setVisible(false); m_Controls->m_NoiseFrame->setVisible(false); m_Controls->m_GhostFrame->setVisible(false); m_Controls->m_DistortionsFrame->setVisible(false); m_Controls->m_EddyFrame->setVisible(false); m_Controls->m_SpikeFrame->setVisible(false); m_Controls->m_AliasingFrame->setVisible(false); m_Controls->m_MotionArtifactFrame->setVisible(false); m_ParameterFile = QDir::currentPath()+"/param.ffp"; m_Controls->m_AbortSimulationButton->setVisible(false); m_Controls->m_SimulationStatusText->setVisible(false); m_Controls->m_FrequencyMapBox->SetDataStorage(this->GetDataStorage()); m_Controls->m_Comp4VolumeFraction->SetDataStorage(this->GetDataStorage()); m_Controls->m_MaskComboBox->SetDataStorage(this->GetDataStorage()); m_Controls->m_TemplateComboBox->SetDataStorage(this->GetDataStorage()); m_Controls->m_FiberBundleComboBox->SetDataStorage(this->GetDataStorage()); mitk::TNodePredicateDataType::Pointer isFiberBundle = mitk::TNodePredicateDataType::New(); mitk::TNodePredicateDataType::Pointer isMitkImage = mitk::TNodePredicateDataType::New(); mitk::NodePredicateIsDWI::Pointer isDwi = mitk::NodePredicateIsDWI::New( ); mitk::NodePredicateDataType::Pointer isDti = mitk::NodePredicateDataType::New("TensorImage"); mitk::NodePredicateDataType::Pointer isQbi = mitk::NodePredicateDataType::New("QBallImage"); mitk::NodePredicateOr::Pointer isDiffusionImage = mitk::NodePredicateOr::New(isDwi, isDti); isDiffusionImage = mitk::NodePredicateOr::New(isDiffusionImage, isQbi); mitk::NodePredicateNot::Pointer noDiffusionImage = mitk::NodePredicateNot::New(isDiffusionImage); mitk::NodePredicateAnd::Pointer isNonDiffMitkImage = mitk::NodePredicateAnd::New(isMitkImage, noDiffusionImage); mitk::NodePredicateProperty::Pointer isBinaryPredicate = mitk::NodePredicateProperty::New("binary", mitk::BoolProperty::New(true)); mitk::NodePredicateAnd::Pointer isBinaryMitkImage = mitk::NodePredicateAnd::New( isNonDiffMitkImage, isBinaryPredicate ); m_Controls->m_FrequencyMapBox->SetPredicate(isNonDiffMitkImage); m_Controls->m_Comp4VolumeFraction->SetPredicate(isNonDiffMitkImage); m_Controls->m_MaskComboBox->SetPredicate(isBinaryMitkImage); m_Controls->m_MaskComboBox->SetZeroEntryText("--"); m_Controls->m_TemplateComboBox->SetPredicate(isMitkImage); m_Controls->m_TemplateComboBox->SetZeroEntryText("--"); m_Controls->m_FiberBundleComboBox->SetPredicate(isFiberBundle); m_Controls->m_FiberBundleComboBox->SetZeroEntryText("--"); // mitk::NodePredicateDimension::Pointer dimensionPredicate = mitk::NodePredicateDimension::New(3); connect( m_SimulationTimer, SIGNAL(timeout()), this, SLOT(UpdateSimulationStatus()) ); connect((QObject*) m_Controls->m_AbortSimulationButton, SIGNAL(clicked()), (QObject*) this, SLOT(KillThread())); connect((QObject*) m_Controls->m_GenerateImageButton, SIGNAL(clicked()), (QObject*) this, SLOT(GenerateImage())); connect((QObject*) m_Controls->m_GenerateFibersButton, SIGNAL(clicked()), (QObject*) this, SLOT(GenerateFibers())); connect((QObject*) m_Controls->m_CircleButton, SIGNAL(clicked()), (QObject*) this, SLOT(OnDrawROI())); connect((QObject*) m_Controls->m_FlipButton, SIGNAL(clicked()), (QObject*) this, SLOT(OnFlipButton())); connect((QObject*) m_Controls->m_JoinBundlesButton, SIGNAL(clicked()), (QObject*) this, SLOT(JoinBundles())); connect((QObject*) m_Controls->m_VarianceBox, SIGNAL(valueChanged(double)), (QObject*) this, SLOT(OnVarianceChanged(double))); connect((QObject*) m_Controls->m_DistributionBox, SIGNAL(currentIndexChanged(int)), (QObject*) this, SLOT(OnDistributionChanged(int))); connect((QObject*) m_Controls->m_FiberDensityBox, SIGNAL(valueChanged(int)), (QObject*) this, SLOT(OnFiberDensityChanged(int))); connect((QObject*) m_Controls->m_FiberSamplingBox, SIGNAL(valueChanged(double)), (QObject*) this, SLOT(OnFiberSamplingChanged(double))); connect((QObject*) m_Controls->m_TensionBox, SIGNAL(valueChanged(double)), (QObject*) this, SLOT(OnTensionChanged(double))); connect((QObject*) m_Controls->m_ContinuityBox, SIGNAL(valueChanged(double)), (QObject*) this, SLOT(OnContinuityChanged(double))); connect((QObject*) m_Controls->m_BiasBox, SIGNAL(valueChanged(double)), (QObject*) this, SLOT(OnBiasChanged(double))); connect((QObject*) m_Controls->m_AddNoise, SIGNAL(stateChanged(int)), (QObject*) this, SLOT(OnAddNoise(int))); connect((QObject*) m_Controls->m_AddGhosts, SIGNAL(stateChanged(int)), (QObject*) this, SLOT(OnAddGhosts(int))); connect((QObject*) m_Controls->m_AddDistortions, SIGNAL(stateChanged(int)), (QObject*) this, SLOT(OnAddDistortions(int))); connect((QObject*) m_Controls->m_AddEddy, SIGNAL(stateChanged(int)), (QObject*) this, SLOT(OnAddEddy(int))); connect((QObject*) m_Controls->m_AddSpikes, SIGNAL(stateChanged(int)), (QObject*) this, SLOT(OnAddSpikes(int))); connect((QObject*) m_Controls->m_AddAliasing, SIGNAL(stateChanged(int)), (QObject*) this, SLOT(OnAddAliasing(int))); connect((QObject*) m_Controls->m_AddMotion, SIGNAL(stateChanged(int)), (QObject*) this, SLOT(OnAddMotion(int))); connect((QObject*) m_Controls->m_ConstantRadiusBox, SIGNAL(stateChanged(int)), (QObject*) this, SLOT(OnConstantRadius(int))); connect((QObject*) m_Controls->m_CopyBundlesButton, SIGNAL(clicked()), (QObject*) this, SLOT(CopyBundles())); connect((QObject*) m_Controls->m_TransformBundlesButton, SIGNAL(clicked()), (QObject*) this, SLOT(ApplyTransform())); connect((QObject*) m_Controls->m_AlignOnGrid, SIGNAL(clicked()), (QObject*) this, SLOT(AlignOnGrid())); connect((QObject*) m_Controls->m_Compartment1Box, SIGNAL(currentIndexChanged(int)), (QObject*) this, SLOT(Comp1ModelFrameVisibility(int))); connect((QObject*) m_Controls->m_Compartment2Box, SIGNAL(currentIndexChanged(int)), (QObject*) this, SLOT(Comp2ModelFrameVisibility(int))); connect((QObject*) m_Controls->m_Compartment3Box, SIGNAL(currentIndexChanged(int)), (QObject*) this, SLOT(Comp3ModelFrameVisibility(int))); connect((QObject*) m_Controls->m_Compartment4Box, SIGNAL(currentIndexChanged(int)), (QObject*) this, SLOT(Comp4ModelFrameVisibility(int))); connect((QObject*) m_Controls->m_AdvancedOptionsBox, SIGNAL( stateChanged(int)), (QObject*) this, SLOT(ShowAdvancedOptions(int))); connect((QObject*) m_Controls->m_AdvancedOptionsBox_2, SIGNAL( stateChanged(int)), (QObject*) this, SLOT(ShowAdvancedOptions(int))); connect((QObject*) m_Controls->m_SaveParametersButton, SIGNAL(clicked()), (QObject*) this, SLOT(SaveParameters())); connect((QObject*) m_Controls->m_LoadParametersButton, SIGNAL(clicked()), (QObject*) this, SLOT(LoadParameters())); connect((QObject*) m_Controls->m_OutputPathButton, SIGNAL(clicked()), (QObject*) this, SLOT(SetOutputPath())); connect((QObject*) m_Controls->m_MaskComboBox, SIGNAL(currentIndexChanged(int)), (QObject*) this, SLOT(OnMaskSelected(int))); connect((QObject*) m_Controls->m_TemplateComboBox, SIGNAL(currentIndexChanged(int)), (QObject*) this, SLOT(OnTemplateSelected(int))); connect((QObject*) m_Controls->m_FiberBundleComboBox, SIGNAL(currentIndexChanged(int)), (QObject*) this, SLOT(OnFibSelected(int))); } } void QmitkFiberfoxView::OnMaskSelected(int value) { UpdateGui(); } void QmitkFiberfoxView::OnTemplateSelected(int value) { UpdateGui(); } void QmitkFiberfoxView::OnFibSelected(int value) { UpdateGui(); } template< class ScalarType > FiberfoxParameters< ScalarType > QmitkFiberfoxView::UpdateImageParameters() { FiberfoxParameters< ScalarType > parameters; parameters.m_Misc.m_OutputPath = ""; parameters.m_Misc.m_CheckAdvancedFiberOptionsBox = m_Controls->m_AdvancedOptionsBox->isChecked(); parameters.m_Misc.m_CheckAdvancedSignalOptionsBox = m_Controls->m_AdvancedOptionsBox_2->isChecked(); parameters.m_Misc.m_CheckOutputVolumeFractionsBox = m_Controls->m_VolumeFractionsBox->isChecked(); string outputPath = m_Controls->m_SavePathEdit->text().toStdString(); if (outputPath.compare("-")!=0) { parameters.m_Misc.m_OutputPath = outputPath; parameters.m_Misc.m_OutputPath += "/"; } if (m_Controls->m_MaskComboBox->GetSelectedNode().IsNotNull()) { mitk::Image::Pointer mitkMaskImage = dynamic_cast(m_Controls->m_MaskComboBox->GetSelectedNode()->GetData()); mitk::CastToItkImage(mitkMaskImage, parameters.m_SignalGen.m_MaskImage); itk::ImageDuplicator::Pointer duplicator = itk::ImageDuplicator::New(); duplicator->SetInputImage(parameters.m_SignalGen.m_MaskImage); duplicator->Update(); parameters.m_SignalGen.m_MaskImage = duplicator->GetOutput(); } if (m_Controls->m_TemplateComboBox->GetSelectedNode().IsNotNull() && mitk::DiffusionPropertyHelper::IsDiffusionWeightedImage( dynamic_cast(m_Controls->m_TemplateComboBox->GetSelectedNode()->GetData()))) // use parameters of selected DWI { mitk::Image::Pointer dwi = dynamic_cast(m_Controls->m_TemplateComboBox->GetSelectedNode()->GetData()); ItkDwiType::Pointer itkVectorImagePointer = ItkDwiType::New(); mitk::CastToItkImage(dwi, itkVectorImagePointer); parameters.m_SignalGen.m_ImageRegion = itkVectorImagePointer->GetLargestPossibleRegion(); parameters.m_SignalGen.m_ImageSpacing = itkVectorImagePointer->GetSpacing(); parameters.m_SignalGen.m_ImageOrigin = itkVectorImagePointer->GetOrigin(); parameters.m_SignalGen.m_ImageDirection = itkVectorImagePointer->GetDirection(); parameters.m_SignalGen.m_Bvalue = static_cast(dwi->GetProperty(mitk::DiffusionPropertyHelper::REFERENCEBVALUEPROPERTYNAME.c_str()).GetPointer() )->GetValue(); parameters.m_SignalGen.SetGradienDirections(static_cast( dwi->GetProperty(mitk::DiffusionPropertyHelper::GRADIENTCONTAINERPROPERTYNAME.c_str()).GetPointer() )->GetGradientDirectionsContainer()); } else if (m_Controls->m_TemplateComboBox->GetSelectedNode().IsNotNull()) // use geometry of selected image { mitk::Image::Pointer img = dynamic_cast(m_Controls->m_TemplateComboBox->GetSelectedNode()->GetData()); itk::Image< float, 3 >::Pointer itkImg = itk::Image< float, 3 >::New(); CastToItkImage< itk::Image< float, 3 > >(img, itkImg); parameters.m_SignalGen.m_ImageRegion = itkImg->GetLargestPossibleRegion(); parameters.m_SignalGen.m_ImageSpacing = itkImg->GetSpacing(); parameters.m_SignalGen.m_ImageOrigin = itkImg->GetOrigin(); parameters.m_SignalGen.m_ImageDirection = itkImg->GetDirection(); parameters.m_SignalGen.SetNumWeightedVolumes(m_Controls->m_NumGradientsBox->value()); parameters.m_SignalGen.m_Bvalue = m_Controls->m_BvalueBox->value(); } else // use GUI parameters { parameters.m_SignalGen.m_ImageRegion.SetSize(0, m_Controls->m_SizeX->value()); parameters.m_SignalGen.m_ImageRegion.SetSize(1, m_Controls->m_SizeY->value()); parameters.m_SignalGen.m_ImageRegion.SetSize(2, m_Controls->m_SizeZ->value()); parameters.m_SignalGen.m_ImageSpacing[0] = m_Controls->m_SpacingX->value(); parameters.m_SignalGen.m_ImageSpacing[1] = m_Controls->m_SpacingY->value(); parameters.m_SignalGen.m_ImageSpacing[2] = m_Controls->m_SpacingZ->value(); parameters.m_SignalGen.m_ImageOrigin[0] = parameters.m_SignalGen.m_ImageSpacing[0]/2; parameters.m_SignalGen.m_ImageOrigin[1] = parameters.m_SignalGen.m_ImageSpacing[1]/2; parameters.m_SignalGen.m_ImageOrigin[2] = parameters.m_SignalGen.m_ImageSpacing[2]/2; parameters.m_SignalGen.m_ImageDirection.SetIdentity(); parameters.m_SignalGen.SetNumWeightedVolumes(m_Controls->m_NumGradientsBox->value()); parameters.m_SignalGen.m_Bvalue = m_Controls->m_BvalueBox->value(); parameters.m_SignalGen.GenerateGradientHalfShell(); } // signal relaxation parameters.m_SignalGen.m_DoSimulateRelaxation = m_Controls->m_RelaxationBox->isChecked(); parameters.m_SignalGen.m_SimulateKspaceAcquisition = parameters.m_SignalGen.m_DoSimulateRelaxation; if (parameters.m_SignalGen.m_DoSimulateRelaxation && m_Controls->m_FiberBundleComboBox->GetSelectedNode().IsNotNull() ) parameters.m_Misc.m_ArtifactModelString += "_RELAX"; // N/2 ghosts parameters.m_Misc.m_CheckAddGhostsBox = m_Controls->m_AddGhosts->isChecked(); if (m_Controls->m_AddGhosts->isChecked()) { parameters.m_SignalGen.m_SimulateKspaceAcquisition = true; parameters.m_Misc.m_ArtifactModelString += "_GHOST"; parameters.m_SignalGen.m_KspaceLineOffset = m_Controls->m_kOffsetBox->value(); parameters.m_Misc.m_ResultNode->AddProperty("Fiberfox.Ghost", DoubleProperty::New(parameters.m_SignalGen.m_KspaceLineOffset)); } else parameters.m_SignalGen.m_KspaceLineOffset = 0; // Aliasing parameters.m_Misc.m_CheckAddAliasingBox = m_Controls->m_AddAliasing->isChecked(); if (m_Controls->m_AddAliasing->isChecked()) { parameters.m_SignalGen.m_SimulateKspaceAcquisition = true; parameters.m_Misc.m_ArtifactModelString += "_ALIASING"; parameters.m_SignalGen.m_CroppingFactor = (100-m_Controls->m_WrapBox->value())/100; parameters.m_Misc.m_ResultNode->AddProperty("Fiberfox.Aliasing", DoubleProperty::New(m_Controls->m_WrapBox->value())); } // Spikes parameters.m_Misc.m_CheckAddSpikesBox = m_Controls->m_AddSpikes->isChecked(); if (m_Controls->m_AddSpikes->isChecked()) { parameters.m_SignalGen.m_SimulateKspaceAcquisition = true; parameters.m_SignalGen.m_Spikes = m_Controls->m_SpikeNumBox->value(); parameters.m_SignalGen.m_SpikeAmplitude = m_Controls->m_SpikeScaleBox->value(); parameters.m_Misc.m_ArtifactModelString += "_SPIKES"; parameters.m_Misc.m_ResultNode->AddProperty("Fiberfox.Spikes.Number", IntProperty::New(parameters.m_SignalGen.m_Spikes)); parameters.m_Misc.m_ResultNode->AddProperty("Fiberfox.Spikes.Amplitude", DoubleProperty::New(parameters.m_SignalGen.m_SpikeAmplitude)); } // gibbs ringing parameters.m_SignalGen.m_DoAddGibbsRinging = m_Controls->m_AddGibbsRinging->isChecked(); if (m_Controls->m_AddGibbsRinging->isChecked()) { parameters.m_SignalGen.m_SimulateKspaceAcquisition = true; parameters.m_Misc.m_ResultNode->AddProperty("Fiberfox.Ringing", BoolProperty::New(true)); parameters.m_Misc.m_ArtifactModelString += "_RINGING"; } // add distortions parameters.m_Misc.m_CheckAddDistortionsBox = m_Controls->m_AddDistortions->isChecked(); if (m_Controls->m_AddDistortions->isChecked() && m_Controls->m_FrequencyMapBox->GetSelectedNode().IsNotNull()) { mitk::DataNode::Pointer fMapNode = m_Controls->m_FrequencyMapBox->GetSelectedNode(); mitk::Image* img = dynamic_cast(fMapNode->GetData()); ItkDoubleImgType::Pointer itkImg = ItkDoubleImgType::New(); CastToItkImage< ItkDoubleImgType >(img, itkImg); if (m_Controls->m_TemplateComboBox->GetSelectedNode().IsNull()) // use geometry of frequency map { parameters.m_SignalGen.m_ImageRegion = itkImg->GetLargestPossibleRegion(); parameters.m_SignalGen.m_ImageSpacing = itkImg->GetSpacing(); parameters.m_SignalGen.m_ImageOrigin = itkImg->GetOrigin(); parameters.m_SignalGen.m_ImageDirection = itkImg->GetDirection(); } if (parameters.m_SignalGen.m_ImageRegion.GetSize(0)==itkImg->GetLargestPossibleRegion().GetSize(0) && parameters.m_SignalGen.m_ImageRegion.GetSize(1)==itkImg->GetLargestPossibleRegion().GetSize(1) && parameters.m_SignalGen.m_ImageRegion.GetSize(2)==itkImg->GetLargestPossibleRegion().GetSize(2)) { parameters.m_SignalGen.m_SimulateKspaceAcquisition = true; itk::ImageDuplicator::Pointer duplicator = itk::ImageDuplicator::New(); duplicator->SetInputImage(itkImg); duplicator->Update(); parameters.m_SignalGen.m_FrequencyMap = duplicator->GetOutput(); parameters.m_Misc.m_ArtifactModelString += "_DISTORTED"; parameters.m_Misc.m_ResultNode->AddProperty("Fiberfox.Distortions", BoolProperty::New(true)); } } parameters.m_SignalGen.m_EddyStrength = 0; parameters.m_Misc.m_CheckAddEddyCurrentsBox = m_Controls->m_AddEddy->isChecked(); if (m_Controls->m_AddEddy->isChecked()) { parameters.m_SignalGen.m_EddyStrength = m_Controls->m_EddyGradientStrength->value(); parameters.m_Misc.m_ArtifactModelString += "_EDDY"; parameters.m_Misc.m_ResultNode->AddProperty("Fiberfox.Eddy-strength", DoubleProperty::New(parameters.m_SignalGen.m_EddyStrength)); } // Motion parameters.m_SignalGen.m_DoAddMotion = m_Controls->m_AddMotion->isChecked(); parameters.m_SignalGen.m_DoRandomizeMotion = m_Controls->m_RandomMotion->isChecked(); parameters.m_SignalGen.m_Translation[0] = m_Controls->m_MaxTranslationBoxX->value(); parameters.m_SignalGen.m_Translation[1] = m_Controls->m_MaxTranslationBoxY->value(); parameters.m_SignalGen.m_Translation[2] = m_Controls->m_MaxTranslationBoxZ->value(); parameters.m_SignalGen.m_Rotation[0] = m_Controls->m_MaxRotationBoxX->value(); parameters.m_SignalGen.m_Rotation[1] = m_Controls->m_MaxRotationBoxY->value(); parameters.m_SignalGen.m_Rotation[2] = m_Controls->m_MaxRotationBoxZ->value(); if ( m_Controls->m_AddMotion->isChecked() && m_Controls->m_FiberBundleComboBox->GetSelectedNode().IsNotNull() ) { parameters.m_Misc.m_ArtifactModelString += "_MOTION"; parameters.m_Misc.m_ResultNode->AddProperty("Fiberfox.Motion.Random", BoolProperty::New(parameters.m_SignalGen.m_DoRandomizeMotion)); parameters.m_Misc.m_ResultNode->AddProperty("Fiberfox.Motion.Translation-x", DoubleProperty::New(parameters.m_SignalGen.m_Translation[0])); parameters.m_Misc.m_ResultNode->AddProperty("Fiberfox.Motion.Translation-y", DoubleProperty::New(parameters.m_SignalGen.m_Translation[1])); parameters.m_Misc.m_ResultNode->AddProperty("Fiberfox.Motion.Translation-z", DoubleProperty::New(parameters.m_SignalGen.m_Translation[2])); parameters.m_Misc.m_ResultNode->AddProperty("Fiberfox.Motion.Rotation-x", DoubleProperty::New(parameters.m_SignalGen.m_Rotation[0])); parameters.m_Misc.m_ResultNode->AddProperty("Fiberfox.Motion.Rotation-y", DoubleProperty::New(parameters.m_SignalGen.m_Rotation[1])); parameters.m_Misc.m_ResultNode->AddProperty("Fiberfox.Motion.Rotation-z", DoubleProperty::New(parameters.m_SignalGen.m_Rotation[2])); } // other imaging parameters parameters.m_SignalGen.m_tLine = m_Controls->m_LineReadoutTimeBox->value(); parameters.m_SignalGen.m_tInhom = m_Controls->m_T2starBox->value(); parameters.m_SignalGen.m_tEcho = m_Controls->m_TEbox->value(); parameters.m_SignalGen.m_DoDisablePartialVolume = m_Controls->m_EnforcePureFiberVoxelsBox->isChecked(); parameters.m_SignalGen.m_AxonRadius = m_Controls->m_FiberRadius->value(); parameters.m_SignalGen.m_SignalScale = m_Controls->m_SignalScaleBox->value(); // adjust echo time if needed if ( parameters.m_SignalGen.m_tEcho < parameters.m_SignalGen.m_ImageRegion.GetSize(1)*parameters.m_SignalGen.m_tLine ) { this->m_Controls->m_TEbox->setValue( parameters.m_SignalGen.m_ImageRegion.GetSize(1)*parameters.m_SignalGen.m_tLine ); parameters.m_SignalGen.m_tEcho = m_Controls->m_TEbox->value(); QMessageBox::information( NULL, "Warning", "Echo time is too short! Time not sufficient to read slice. Automaticall adjusted to "+QString::number(parameters.m_SignalGen.m_tEcho)+" ms"); } // Noise parameters.m_Misc.m_CheckAddNoiseBox = m_Controls->m_AddNoise->isChecked(); if (m_Controls->m_AddNoise->isChecked()) { double noiseVariance = m_Controls->m_NoiseLevel->value(); { switch (m_Controls->m_NoiseDistributionBox->currentIndex()) { case 0: { parameters.m_NoiseModel = new mitk::RicianNoiseModel(); parameters.m_Misc.m_ArtifactModelString += "_RICIAN-"; parameters.m_Misc.m_ResultNode->AddProperty("Fiberfox.Noise-Distribution", StringProperty::New("Rician")); break; } case 1: { parameters.m_NoiseModel = new mitk::ChiSquareNoiseModel(); parameters.m_Misc.m_ArtifactModelString += "_CHISQUARED-"; parameters.m_Misc.m_ResultNode->AddProperty("Fiberfox.Noise-Distribution", StringProperty::New("Chi-squared")); break; } default: { parameters.m_NoiseModel = new mitk::RicianNoiseModel(); parameters.m_Misc.m_ArtifactModelString += "_RICIAN-"; parameters.m_Misc.m_ResultNode->AddProperty("Fiberfox.Noise-Distribution", StringProperty::New("Rician")); } } } parameters.m_NoiseModel->SetNoiseVariance(noiseVariance); parameters.m_Misc.m_ArtifactModelString += QString::number(noiseVariance).toStdString(); parameters.m_Misc.m_ResultNode->AddProperty("Fiberfox.Noise-Variance", DoubleProperty::New(noiseVariance)); } // adjusting line readout time to the adapted image size needed for the DFT unsigned int y = parameters.m_SignalGen.m_ImageRegion.GetSize(1); y += y%2; if ( y>parameters.m_SignalGen.m_ImageRegion.GetSize(1) ) parameters.m_SignalGen.m_tLine *= (double)parameters.m_SignalGen.m_ImageRegion.GetSize(1)/y; // signal models { // compartment 1 switch (m_Controls->m_Compartment1Box->currentIndex()) { case 0: { mitk::StickModel* model = new mitk::StickModel(); model->SetGradientList(parameters.m_SignalGen.GetGradientDirections()); model->SetBvalue(parameters.m_SignalGen.m_Bvalue); model->SetDiffusivity(m_Controls->m_StickWidget1->GetD()); model->SetT2(m_Controls->m_StickWidget1->GetT2()); model->m_CompartmentId = 1; parameters.m_FiberModelList.push_back(model); parameters.m_Misc.m_SignalModelString += "Stick"; parameters.m_Misc.m_ResultNode->AddProperty("Fiberfox.Compartment1.Description", StringProperty::New("Intra-axonal compartment") ); parameters.m_Misc.m_ResultNode->AddProperty("Fiberfox.Compartment1.Model", StringProperty::New("Stick") ); parameters.m_Misc.m_ResultNode->AddProperty("Fiberfox.Compartment1.D", DoubleProperty::New(m_Controls->m_StickWidget1->GetD()) ); parameters.m_Misc.m_ResultNode->AddProperty("Fiberfox.Compartment1.T2", DoubleProperty::New(model->GetT2()) ); break; } case 1: { mitk::TensorModel* model = new mitk::TensorModel(); model->SetGradientList(parameters.m_SignalGen.GetGradientDirections()); model->SetBvalue(parameters.m_SignalGen.m_Bvalue); model->SetDiffusivity1(m_Controls->m_ZeppelinWidget1->GetD1()); model->SetDiffusivity2(m_Controls->m_ZeppelinWidget1->GetD2()); model->SetDiffusivity3(m_Controls->m_ZeppelinWidget1->GetD2()); model->SetT2(m_Controls->m_ZeppelinWidget1->GetT2()); model->m_CompartmentId = 1; parameters.m_FiberModelList.push_back(model); parameters.m_Misc.m_SignalModelString += "Zeppelin"; parameters.m_Misc.m_ResultNode->AddProperty("Fiberfox.Compartment1.Description", StringProperty::New("Intra-axonal compartment") ); parameters.m_Misc.m_ResultNode->AddProperty("Fiberfox.Compartment1.Model", StringProperty::New("Zeppelin") ); parameters.m_Misc.m_ResultNode->AddProperty("Fiberfox.Compartment1.D1", DoubleProperty::New(m_Controls->m_ZeppelinWidget1->GetD1()) ); parameters.m_Misc.m_ResultNode->AddProperty("Fiberfox.Compartment1.D2", DoubleProperty::New(m_Controls->m_ZeppelinWidget1->GetD2()) ); parameters.m_Misc.m_ResultNode->AddProperty("Fiberfox.Compartment1.T2", DoubleProperty::New(model->GetT2()) ); break; } case 2: { mitk::TensorModel* model = new mitk::TensorModel(); model->SetGradientList(parameters.m_SignalGen.GetGradientDirections()); model->SetBvalue(parameters.m_SignalGen.m_Bvalue); model->SetDiffusivity1(m_Controls->m_TensorWidget1->GetD1()); model->SetDiffusivity2(m_Controls->m_TensorWidget1->GetD2()); model->SetDiffusivity3(m_Controls->m_TensorWidget1->GetD3()); model->SetT2(m_Controls->m_TensorWidget1->GetT2()); model->m_CompartmentId = 1; parameters.m_FiberModelList.push_back(model); parameters.m_Misc.m_SignalModelString += "Tensor"; parameters.m_Misc.m_ResultNode->AddProperty("Fiberfox.Compartment1.Description", StringProperty::New("Intra-axonal compartment") ); parameters.m_Misc.m_ResultNode->AddProperty("Fiberfox.Compartment1.Model", StringProperty::New("Tensor") ); parameters.m_Misc.m_ResultNode->AddProperty("Fiberfox.Compartment1.D1", DoubleProperty::New(m_Controls->m_TensorWidget1->GetD1()) ); parameters.m_Misc.m_ResultNode->AddProperty("Fiberfox.Compartment1.D2", DoubleProperty::New(m_Controls->m_TensorWidget1->GetD2()) ); parameters.m_Misc.m_ResultNode->AddProperty("Fiberfox.Compartment1.D3", DoubleProperty::New(m_Controls->m_TensorWidget1->GetD3()) ); parameters.m_Misc.m_ResultNode->AddProperty("Fiberfox.Compartment1.T2", DoubleProperty::New(model->GetT2()) ); break; } case 3: { mitk::RawShModel* model = new mitk::RawShModel(); parameters.m_SignalGen.m_DoSimulateRelaxation = false; model->SetGradientList(parameters.m_SignalGen.GetGradientDirections()); model->SetMaxNumKernels(m_Controls->m_PrototypeWidget1->GetNumberOfSamples()); model->SetFaRange(m_Controls->m_PrototypeWidget1->GetMinFa(), m_Controls->m_PrototypeWidget1->GetMaxFa()); model->SetAdcRange(m_Controls->m_PrototypeWidget1->GetMinAdc(), m_Controls->m_PrototypeWidget1->GetMaxAdc()); model->m_CompartmentId = 1; parameters.m_FiberModelList.push_back(model); parameters.m_Misc.m_SignalModelString += "Prototype"; parameters.m_Misc.m_ResultNode->AddProperty("Fiberfox.Compartment1.Description", StringProperty::New("Intra-axonal compartment") ); parameters.m_Misc.m_ResultNode->AddProperty("Fiberfox.Compartment1.Model", StringProperty::New("Prototype") ); break; } } // compartment 2 switch (m_Controls->m_Compartment2Box->currentIndex()) { case 0: break; case 1: { mitk::StickModel* model = new mitk::StickModel(); model->SetGradientList(parameters.m_SignalGen.GetGradientDirections()); model->SetBvalue(parameters.m_SignalGen.m_Bvalue); model->SetDiffusivity(m_Controls->m_StickWidget2->GetD()); model->SetT2(m_Controls->m_StickWidget2->GetT2()); model->m_CompartmentId = 2; parameters.m_FiberModelList.push_back(model); parameters.m_Misc.m_SignalModelString += "Stick"; parameters.m_Misc.m_ResultNode->AddProperty("Fiberfox.Compartment2.Description", StringProperty::New("Inter-axonal compartment") ); parameters.m_Misc.m_ResultNode->AddProperty("Fiberfox.Compartment2.Model", StringProperty::New("Stick") ); parameters.m_Misc.m_ResultNode->AddProperty("Fiberfox.Compartment2.D", DoubleProperty::New(m_Controls->m_StickWidget2->GetD()) ); parameters.m_Misc.m_ResultNode->AddProperty("Fiberfox.Compartment2.T2", DoubleProperty::New(model->GetT2()) ); break; } case 2: { mitk::TensorModel* model = new mitk::TensorModel(); model->SetGradientList(parameters.m_SignalGen.GetGradientDirections()); model->SetBvalue(parameters.m_SignalGen.m_Bvalue); model->SetDiffusivity1(m_Controls->m_ZeppelinWidget2->GetD1()); model->SetDiffusivity2(m_Controls->m_ZeppelinWidget2->GetD2()); model->SetDiffusivity3(m_Controls->m_ZeppelinWidget2->GetD2()); model->SetT2(m_Controls->m_ZeppelinWidget2->GetT2()); model->m_CompartmentId = 2; parameters.m_FiberModelList.push_back(model); parameters.m_Misc.m_SignalModelString += "Zeppelin"; parameters.m_Misc.m_ResultNode->AddProperty("Fiberfox.Compartment2.Description", StringProperty::New("Inter-axonal compartment") ); parameters.m_Misc.m_ResultNode->AddProperty("Fiberfox.Compartment2.Model", StringProperty::New("Zeppelin") ); parameters.m_Misc.m_ResultNode->AddProperty("Fiberfox.Compartment2.D1", DoubleProperty::New(m_Controls->m_ZeppelinWidget2->GetD1()) ); parameters.m_Misc.m_ResultNode->AddProperty("Fiberfox.Compartment2.D2", DoubleProperty::New(m_Controls->m_ZeppelinWidget2->GetD2()) ); parameters.m_Misc.m_ResultNode->AddProperty("Fiberfox.Compartment2.T2", DoubleProperty::New(model->GetT2()) ); break; } case 3: { mitk::TensorModel* model = new mitk::TensorModel(); model->SetGradientList(parameters.m_SignalGen.GetGradientDirections()); model->SetBvalue(parameters.m_SignalGen.m_Bvalue); model->SetDiffusivity1(m_Controls->m_TensorWidget2->GetD1()); model->SetDiffusivity2(m_Controls->m_TensorWidget2->GetD2()); model->SetDiffusivity3(m_Controls->m_TensorWidget2->GetD3()); model->SetT2(m_Controls->m_TensorWidget2->GetT2()); model->m_CompartmentId = 2; parameters.m_FiberModelList.push_back(model); parameters.m_Misc.m_SignalModelString += "Tensor"; parameters.m_Misc.m_ResultNode->AddProperty("Fiberfox.Compartment2.Description", StringProperty::New("Inter-axonal compartment") ); parameters.m_Misc.m_ResultNode->AddProperty("Fiberfox.Compartment2.Model", StringProperty::New("Tensor") ); parameters.m_Misc.m_ResultNode->AddProperty("Fiberfox.Compartment2.D1", DoubleProperty::New(m_Controls->m_TensorWidget2->GetD1()) ); parameters.m_Misc.m_ResultNode->AddProperty("Fiberfox.Compartment2.D2", DoubleProperty::New(m_Controls->m_TensorWidget2->GetD2()) ); parameters.m_Misc.m_ResultNode->AddProperty("Fiberfox.Compartment2.D3", DoubleProperty::New(m_Controls->m_TensorWidget2->GetD3()) ); parameters.m_Misc.m_ResultNode->AddProperty("Fiberfox.Compartment2.T2", DoubleProperty::New(model->GetT2()) ); break; } } // compartment 3 switch (m_Controls->m_Compartment3Box->currentIndex()) { case 0: { mitk::BallModel* model = new mitk::BallModel(); model->SetGradientList(parameters.m_SignalGen.GetGradientDirections()); model->SetBvalue(parameters.m_SignalGen.m_Bvalue); model->SetDiffusivity(m_Controls->m_BallWidget1->GetD()); model->SetT2(m_Controls->m_BallWidget1->GetT2()); model->m_CompartmentId = 3; parameters.m_NonFiberModelList.push_back(model); parameters.m_Misc.m_SignalModelString += "Ball"; parameters.m_Misc.m_ResultNode->AddProperty("Fiberfox.Compartment3.Description", StringProperty::New("Extra-axonal compartment 1") ); parameters.m_Misc.m_ResultNode->AddProperty("Fiberfox.Compartment3.Model", StringProperty::New("Ball") ); parameters.m_Misc.m_ResultNode->AddProperty("Fiberfox.Compartment3.D", DoubleProperty::New(m_Controls->m_BallWidget1->GetD()) ); parameters.m_Misc.m_ResultNode->AddProperty("Fiberfox.Compartment3.T2", DoubleProperty::New(model->GetT2()) ); break; } case 1: { mitk::AstroStickModel* model = new mitk::AstroStickModel(); model->SetGradientList(parameters.m_SignalGen.GetGradientDirections()); model->SetBvalue(parameters.m_SignalGen.m_Bvalue); model->SetDiffusivity(m_Controls->m_AstrosticksWidget1->GetD()); model->SetT2(m_Controls->m_AstrosticksWidget1->GetT2()); model->SetRandomizeSticks(m_Controls->m_AstrosticksWidget1->GetRandomizeSticks()); model->m_CompartmentId = 3; parameters.m_NonFiberModelList.push_back(model); parameters.m_Misc.m_SignalModelString += "Astrosticks"; parameters.m_Misc.m_ResultNode->AddProperty("Fiberfox.Compartment3.Description", StringProperty::New("Extra-axonal compartment 1") ); parameters.m_Misc.m_ResultNode->AddProperty("Fiberfox.Compartment3.Model", StringProperty::New("Astrosticks") ); parameters.m_Misc.m_ResultNode->AddProperty("Fiberfox.Compartment3.D", DoubleProperty::New(m_Controls->m_AstrosticksWidget1->GetD()) ); parameters.m_Misc.m_ResultNode->AddProperty("Fiberfox.Compartment3.T2", DoubleProperty::New(model->GetT2()) ); parameters.m_Misc.m_ResultNode->AddProperty("Fiberfox.Compartment3.RandomSticks", BoolProperty::New(m_Controls->m_AstrosticksWidget1->GetRandomizeSticks()) ); break; } case 2: { mitk::DotModel* model = new mitk::DotModel(); model->SetGradientList(parameters.m_SignalGen.GetGradientDirections()); model->SetT2(m_Controls->m_DotWidget1->GetT2()); model->m_CompartmentId = 3; parameters.m_NonFiberModelList.push_back(model); parameters.m_Misc.m_SignalModelString += "Dot"; parameters.m_Misc.m_ResultNode->AddProperty("Fiberfox.Compartment3.Description", StringProperty::New("Extra-axonal compartment 1") ); parameters.m_Misc.m_ResultNode->AddProperty("Fiberfox.Compartment3.Model", StringProperty::New("Dot") ); parameters.m_Misc.m_ResultNode->AddProperty("Fiberfox.Compartment3.T2", DoubleProperty::New(model->GetT2()) ); break; } case 3: { mitk::RawShModel* model = new mitk::RawShModel(); parameters.m_SignalGen.m_DoSimulateRelaxation = false; model->SetGradientList(parameters.m_SignalGen.GetGradientDirections()); model->SetMaxNumKernels(m_Controls->m_PrototypeWidget3->GetNumberOfSamples()); model->SetFaRange(m_Controls->m_PrototypeWidget3->GetMinFa(), m_Controls->m_PrototypeWidget3->GetMaxFa()); model->SetAdcRange(m_Controls->m_PrototypeWidget3->GetMinAdc(), m_Controls->m_PrototypeWidget3->GetMaxAdc()); model->m_CompartmentId = 3; parameters.m_NonFiberModelList.push_back(model); parameters.m_Misc.m_SignalModelString += "Prototype"; parameters.m_Misc.m_ResultNode->AddProperty("Fiberfox.Compartment3.Description", StringProperty::New("Extra-axonal compartment 1") ); parameters.m_Misc.m_ResultNode->AddProperty("Fiberfox.Compartment3.Model", StringProperty::New("Prototype") ); break; } } // compartment 4 ItkDoubleImgType::Pointer comp4VolumeImage = NULL; ItkDoubleImgType::Pointer comp3VolumeImage = NULL; if (m_Controls->m_Compartment4Box->currentIndex()>0) { mitk::DataNode::Pointer volumeNode = m_Controls->m_Comp4VolumeFraction->GetSelectedNode(); if (volumeNode.IsNull()) { QMessageBox::information( NULL, "Information", "No volume fraction image selected! Second extra-axonal compartment has been disabled for this simultation."); MITK_WARN << "No volume fraction image selected! Second extra-axonal compartment has been disabled."; } else { MITK_INFO << "Rescaling volume fraction image..."; comp4VolumeImage = ItkDoubleImgType::New(); mitk::Image* img = dynamic_cast(volumeNode->GetData()); CastToItkImage< ItkDoubleImgType >(img, comp4VolumeImage); double max = itk::NumericTraits::min(); double min = itk::NumericTraits::max(); itk::ImageRegionIterator< ItkDoubleImgType > it(comp4VolumeImage, comp4VolumeImage->GetLargestPossibleRegion()); while(!it.IsAtEnd()) { if (parameters.m_SignalGen.m_MaskImage.IsNotNull() && parameters.m_SignalGen.m_MaskImage->GetPixel(it.GetIndex())<=0) { it.Set(0.0); ++it; continue; } -// if (it.Get()>900) -// it.Set(900); + if (it.Get()>900) + it.Set(900); if (it.Get()>max) max = it.Get(); if (it.Get()::Pointer scaler = itk::ShiftScaleImageFilter< ItkDoubleImgType, ItkDoubleImgType >::New(); scaler->SetInput(comp4VolumeImage); scaler->SetShift(-min); scaler->SetScale(1.0/(max-min)); scaler->Update(); comp4VolumeImage = scaler->GetOutput(); // itk::ImageFileWriter< ItkDoubleImgType >::Pointer wr = itk::ImageFileWriter< ItkDoubleImgType >::New(); // wr->SetInput(comp4VolumeImage); // wr->SetFileName("/local/comp4.nrrd"); // wr->Update(); // if (max>1 || min<0) // are volume fractions between 0 and 1? // { // itk::RescaleIntensityImageFilter::Pointer rescaler = itk::RescaleIntensityImageFilter::New(); // rescaler->SetInput(0, comp4VolumeImage); // rescaler->SetOutputMaximum(1); // rescaler->SetOutputMinimum(0); // rescaler->Update(); // comp4VolumeImage = rescaler->GetOutput(); // } itk::InvertIntensityImageFilter< ItkDoubleImgType, ItkDoubleImgType >::Pointer inverter = itk::InvertIntensityImageFilter< ItkDoubleImgType, ItkDoubleImgType >::New(); inverter->SetMaximum(1.0); inverter->SetInput(comp4VolumeImage); inverter->Update(); comp3VolumeImage = inverter->GetOutput(); } } if (comp4VolumeImage.IsNotNull()) { switch (m_Controls->m_Compartment4Box->currentIndex()) { case 0: break; case 1: { mitk::BallModel* model = new mitk::BallModel(); model->SetGradientList(parameters.m_SignalGen.GetGradientDirections()); model->SetBvalue(parameters.m_SignalGen.m_Bvalue); model->SetDiffusivity(m_Controls->m_BallWidget2->GetD()); model->SetT2(m_Controls->m_BallWidget2->GetT2()); model->SetVolumeFractionImage(comp4VolumeImage); model->m_CompartmentId = 4; parameters.m_NonFiberModelList.back()->SetVolumeFractionImage(comp3VolumeImage); parameters.m_NonFiberModelList.push_back(model); parameters.m_Misc.m_SignalModelString += "Ball"; parameters.m_Misc.m_ResultNode->AddProperty("Fiberfox.Compartment4.Description", StringProperty::New("Extra-axonal compartment 2") ); parameters.m_Misc.m_ResultNode->AddProperty("Fiberfox.Compartment4.Model", StringProperty::New("Ball") ); parameters.m_Misc.m_ResultNode->AddProperty("Fiberfox.Compartment4.D", DoubleProperty::New(m_Controls->m_BallWidget2->GetD()) ); parameters.m_Misc.m_ResultNode->AddProperty("Fiberfox.Compartment4.T2", DoubleProperty::New(model->GetT2()) ); break; } case 2: { mitk::AstroStickModel* model = new mitk::AstroStickModel(); model->SetGradientList(parameters.m_SignalGen.GetGradientDirections()); model->SetBvalue(parameters.m_SignalGen.m_Bvalue); model->SetDiffusivity(m_Controls->m_AstrosticksWidget2->GetD()); model->SetT2(m_Controls->m_AstrosticksWidget2->GetT2()); model->SetRandomizeSticks(m_Controls->m_AstrosticksWidget2->GetRandomizeSticks()); parameters.m_NonFiberModelList.back()->SetVolumeFractionImage(comp3VolumeImage); model->SetVolumeFractionImage(comp4VolumeImage); model->m_CompartmentId = 4; parameters.m_NonFiberModelList.push_back(model); parameters.m_Misc.m_SignalModelString += "Astrosticks"; parameters.m_Misc.m_ResultNode->AddProperty("Fiberfox.Compartment4.Description", StringProperty::New("Extra-axonal compartment 2") ); parameters.m_Misc.m_ResultNode->AddProperty("Fiberfox.Compartment4.Model", StringProperty::New("Astrosticks") ); parameters.m_Misc.m_ResultNode->AddProperty("Fiberfox.Compartment4.D", DoubleProperty::New(m_Controls->m_AstrosticksWidget2->GetD()) ); parameters.m_Misc.m_ResultNode->AddProperty("Fiberfox.Compartment4.T2", DoubleProperty::New(model->GetT2()) ); parameters.m_Misc.m_ResultNode->AddProperty("Fiberfox.Compartment4.RandomSticks", BoolProperty::New(m_Controls->m_AstrosticksWidget2->GetRandomizeSticks()) ); break; } case 3: { mitk::DotModel* model = new mitk::DotModel(); model->SetGradientList(parameters.m_SignalGen.GetGradientDirections()); model->SetT2(m_Controls->m_DotWidget2->GetT2()); model->SetVolumeFractionImage(comp4VolumeImage); model->m_CompartmentId = 4; parameters.m_NonFiberModelList.back()->SetVolumeFractionImage(comp3VolumeImage); parameters.m_NonFiberModelList.push_back(model); parameters.m_Misc.m_SignalModelString += "Dot"; parameters.m_Misc.m_ResultNode->AddProperty("Fiberfox.Compartment4.Description", StringProperty::New("Extra-axonal compartment 2") ); parameters.m_Misc.m_ResultNode->AddProperty("Fiberfox.Compartment4.Model", StringProperty::New("Dot") ); parameters.m_Misc.m_ResultNode->AddProperty("Fiberfox.Compartment4.T2", DoubleProperty::New(model->GetT2()) ); break; } case 4: { mitk::RawShModel* model = new mitk::RawShModel(); parameters.m_SignalGen.m_DoSimulateRelaxation = false; model->SetGradientList(parameters.m_SignalGen.GetGradientDirections()); model->SetMaxNumKernels(m_Controls->m_PrototypeWidget4->GetNumberOfSamples()); model->SetFaRange(m_Controls->m_PrototypeWidget4->GetMinFa(), m_Controls->m_PrototypeWidget4->GetMaxFa()); model->SetAdcRange(m_Controls->m_PrototypeWidget4->GetMinAdc(), m_Controls->m_PrototypeWidget4->GetMaxAdc()); model->SetVolumeFractionImage(comp4VolumeImage); model->m_CompartmentId = 4; parameters.m_NonFiberModelList.back()->SetVolumeFractionImage(comp3VolumeImage); parameters.m_NonFiberModelList.push_back(model); parameters.m_Misc.m_SignalModelString += "Prototype"; parameters.m_Misc.m_ResultNode->AddProperty("Fiberfox.Compartment4.Description", StringProperty::New("Extra-axonal compartment 2") ); parameters.m_Misc.m_ResultNode->AddProperty("Fiberfox.Compartment4.Model", StringProperty::New("Prototype") ); break; } } } } parameters.m_SignalGen.m_FiberSeparationThreshold = m_Controls->m_SeparationAngleBox->value(); switch (m_Controls->m_DiffusionDirectionBox->currentIndex()) { case 0: parameters.m_SignalGen.m_DiffusionDirectionMode = SignalGenerationParameters::FIBER_TANGENT_DIRECTIONS; break; case 1: parameters.m_SignalGen.m_DiffusionDirectionMode = SignalGenerationParameters::MAIN_FIBER_DIRECTIONS; break; case 2: parameters.m_SignalGen.m_DiffusionDirectionMode = SignalGenerationParameters::RANDOM_DIRECTIONS; parameters.m_SignalGen.m_DoAddMotion = false; parameters.m_SignalGen.m_DoAddGibbsRinging = false; parameters.m_SignalGen.m_KspaceLineOffset = 0.0; parameters.m_SignalGen.m_FrequencyMap = NULL; parameters.m_SignalGen.m_CroppingFactor = 1.0; parameters.m_SignalGen.m_EddyStrength = 0; break; default: parameters.m_SignalGen.m_DiffusionDirectionMode = SignalGenerationParameters::FIBER_TANGENT_DIRECTIONS; } parameters.m_Misc.m_ResultNode->AddProperty("Fiberfox.SignalScale", IntProperty::New(parameters.m_SignalGen.m_SignalScale)); parameters.m_Misc.m_ResultNode->AddProperty("Fiberfox.FiberRadius", IntProperty::New(parameters.m_SignalGen.m_AxonRadius)); parameters.m_Misc.m_ResultNode->AddProperty("Fiberfox.Tinhom", DoubleProperty::New(parameters.m_SignalGen.m_tInhom)); parameters.m_Misc.m_ResultNode->AddProperty("Fiberfox.Tline", DoubleProperty::New(parameters.m_SignalGen.m_tLine)); parameters.m_Misc.m_ResultNode->AddProperty("Fiberfox.TE", DoubleProperty::New(parameters.m_SignalGen.m_tEcho)); parameters.m_Misc.m_ResultNode->AddProperty("Fiberfox.b-value", DoubleProperty::New(parameters.m_SignalGen.m_Bvalue)); parameters.m_Misc.m_ResultNode->AddProperty("Fiberfox.NoPartialVolume", BoolProperty::New(parameters.m_SignalGen.m_DoDisablePartialVolume)); parameters.m_Misc.m_ResultNode->AddProperty("Fiberfox.Relaxation", BoolProperty::New(parameters.m_SignalGen.m_DoSimulateRelaxation)); parameters.m_Misc.m_ResultNode->AddProperty("binary", BoolProperty::New(false)); parameters.m_Misc.m_CheckRealTimeFibersBox = m_Controls->m_RealTimeFibers->isChecked(); parameters.m_Misc.m_CheckAdvancedFiberOptionsBox = m_Controls->m_AdvancedOptionsBox->isChecked(); parameters.m_Misc.m_CheckIncludeFiducialsBox = m_Controls->m_IncludeFiducials->isChecked(); parameters.m_Misc.m_CheckConstantRadiusBox = m_Controls->m_ConstantRadiusBox->isChecked(); switch(m_Controls->m_DistributionBox->currentIndex()) { case 0: parameters.m_FiberGen.m_Distribution = FiberGenerationParameters::DISTRIBUTE_UNIFORM; break; case 1: parameters.m_FiberGen.m_Distribution = FiberGenerationParameters::DISTRIBUTE_GAUSSIAN; break; default: parameters.m_FiberGen.m_Distribution = FiberGenerationParameters::DISTRIBUTE_UNIFORM; } parameters.m_FiberGen.m_Variance = m_Controls->m_VarianceBox->value(); parameters.m_FiberGen.m_Density = m_Controls->m_FiberDensityBox->value(); parameters.m_FiberGen.m_Sampling = m_Controls->m_FiberSamplingBox->value(); parameters.m_FiberGen.m_Tension = m_Controls->m_TensionBox->value(); parameters.m_FiberGen.m_Continuity = m_Controls->m_ContinuityBox->value(); parameters.m_FiberGen.m_Bias = m_Controls->m_BiasBox->value(); parameters.m_FiberGen.m_Rotation[0] = m_Controls->m_XrotBox->value(); parameters.m_FiberGen.m_Rotation[1] = m_Controls->m_YrotBox->value(); parameters.m_FiberGen.m_Rotation[2] = m_Controls->m_ZrotBox->value(); parameters.m_FiberGen.m_Translation[0] = m_Controls->m_XtransBox->value(); parameters.m_FiberGen.m_Translation[1] = m_Controls->m_YtransBox->value(); parameters.m_FiberGen.m_Translation[2] = m_Controls->m_ZtransBox->value(); parameters.m_FiberGen.m_Scale[0] = m_Controls->m_XscaleBox->value(); parameters.m_FiberGen.m_Scale[1] = m_Controls->m_YscaleBox->value(); parameters.m_FiberGen.m_Scale[2] = m_Controls->m_ZscaleBox->value(); return parameters; } void QmitkFiberfoxView::SaveParameters() { FiberfoxParameters<> ffParamaters = UpdateImageParameters(); QString filename = QFileDialog::getSaveFileName( 0, tr("Save Parameters"), m_ParameterFile, tr("Fiberfox Parameters (*.ffp)") ); bool ok = true; bool first = true; bool dosampling = false; mitk::Image::Pointer diffImg = NULL; itk::Image< itk::DiffusionTensor3D< double >, 3 >::Pointer tensorImage = NULL; const int shOrder = 2; typedef itk::AnalyticalDiffusionQballReconstructionImageFilter QballFilterType; QballFilterType::CoefficientImageType::Pointer itkFeatureImage = NULL; ItkDoubleImgType::Pointer adcImage = NULL; for (unsigned int i=0; i* model = NULL; if (i* >(ffParamaters.m_FiberModelList.at(i)); else model = dynamic_cast< mitk::RawShModel<>* >(ffParamaters.m_NonFiberModelList.at(i-ffParamaters.m_FiberModelList.size())); if (model!=0 && model->GetNumberOfKernels()<=0) { if (first==true) { if (QMessageBox::question(NULL, "Prototype signal sampling", "Do you want to sample prototype signals from the selected diffusion-weighted imag and save them?",QMessageBox::Yes,QMessageBox::No)==QMessageBox::Yes) dosampling = true; first = false; if (dosampling && (m_Controls->m_TemplateComboBox->GetSelectedNode().IsNull() || !mitk::DiffusionPropertyHelper::IsDiffusionWeightedImage( dynamic_cast(m_Controls->m_TemplateComboBox->GetSelectedNode()->GetData())))) { QMessageBox::information(NULL, "Parameter file not saved", "No diffusion-weighted image selected to sample signal from."); return; } else if (dosampling) { diffImg = dynamic_cast(m_Controls->m_TemplateComboBox->GetSelectedNode()->GetData()); typedef itk::DiffusionTensor3DReconstructionImageFilter< short, short, double > TensorReconstructionImageFilterType; TensorReconstructionImageFilterType::Pointer filter = TensorReconstructionImageFilterType::New(); ItkDwiType::Pointer itkVectorImagePointer = ItkDwiType::New(); mitk::CastToItkImage(diffImg, itkVectorImagePointer); filter->SetGradientImage( static_cast( diffImg->GetProperty(mitk::DiffusionPropertyHelper::GRADIENTCONTAINERPROPERTYNAME.c_str()).GetPointer() )->GetGradientDirectionsContainer(), itkVectorImagePointer ); filter->SetBValue( static_cast(diffImg->GetProperty(mitk::DiffusionPropertyHelper::REFERENCEBVALUEPROPERTYNAME.c_str()).GetPointer() )->GetValue() ); filter->Update(); tensorImage = filter->GetOutput(); const int NumCoeffs = (shOrder*shOrder + shOrder + 2)/2 + shOrder; QballFilterType::Pointer qballfilter = QballFilterType::New(); qballfilter->SetGradientImage( static_cast( diffImg->GetProperty(mitk::DiffusionPropertyHelper::GRADIENTCONTAINERPROPERTYNAME.c_str()).GetPointer() )->GetGradientDirectionsContainer(), itkVectorImagePointer ); qballfilter->SetBValue( static_cast(diffImg->GetProperty(mitk::DiffusionPropertyHelper::REFERENCEBVALUEPROPERTYNAME.c_str()).GetPointer() )->GetValue() ); qballfilter->SetLambda(0.006); qballfilter->SetNormalizationMethod(QballFilterType::QBAR_RAW_SIGNAL); qballfilter->Update(); itkFeatureImage = qballfilter->GetCoefficientImage(); itk::AdcImageFilter< short, double >::Pointer adcFilter = itk::AdcImageFilter< short, double >::New(); adcFilter->SetInput( itkVectorImagePointer ); adcFilter->SetGradientDirections( static_cast( diffImg->GetProperty(mitk::DiffusionPropertyHelper::GRADIENTCONTAINERPROPERTYNAME.c_str()).GetPointer() )->GetGradientDirectionsContainer() ); adcFilter->SetB_value( static_cast(diffImg->GetProperty(mitk::DiffusionPropertyHelper::REFERENCEBVALUEPROPERTYNAME.c_str()).GetPointer() )->GetValue() ); adcFilter->Update(); adcImage = adcFilter->GetOutput(); } } if (dosampling && diffImg.IsNotNull()) { ok = model->SampleKernels(diffImg, ffParamaters.m_SignalGen.m_MaskImage, tensorImage, itkFeatureImage, adcImage); if (!ok) { QMessageBox::information( NULL, "Parameter file not saved", "No valid prototype signals could be sampled."); return; } } } } ffParamaters.SaveParameters(filename.toStdString()); m_ParameterFile = filename; } void QmitkFiberfoxView::LoadParameters() { QString filename = QFileDialog::getOpenFileName(0, tr("Load Parameters"), QString(itksys::SystemTools::GetFilenamePath(m_ParameterFile.toStdString()).c_str()), tr("Fiberfox Parameters (*.ffp)") ); if(filename.isEmpty() || filename.isNull()) return; m_ParameterFile = filename; FiberfoxParameters<> parameters; parameters.LoadParameters(filename.toStdString()); m_Controls->m_RealTimeFibers->setChecked(parameters.m_Misc.m_CheckRealTimeFibersBox); m_Controls->m_AdvancedOptionsBox->setChecked(parameters.m_Misc.m_CheckAdvancedFiberOptionsBox); m_Controls->m_IncludeFiducials->setChecked(parameters.m_Misc.m_CheckIncludeFiducialsBox); m_Controls->m_ConstantRadiusBox->setChecked(parameters.m_Misc.m_CheckConstantRadiusBox); m_Controls->m_DistributionBox->setCurrentIndex(parameters.m_FiberGen.m_Distribution); m_Controls->m_VarianceBox->setValue(parameters.m_FiberGen.m_Variance); m_Controls->m_FiberDensityBox->setValue(parameters.m_FiberGen.m_Density); m_Controls->m_FiberSamplingBox->setValue(parameters.m_FiberGen.m_Sampling); m_Controls->m_TensionBox->setValue(parameters.m_FiberGen.m_Tension); m_Controls->m_ContinuityBox->setValue(parameters.m_FiberGen.m_Continuity); m_Controls->m_BiasBox->setValue(parameters.m_FiberGen.m_Bias); m_Controls->m_XrotBox->setValue(parameters.m_FiberGen.m_Rotation[0]); m_Controls->m_YrotBox->setValue(parameters.m_FiberGen.m_Rotation[1]); m_Controls->m_ZrotBox->setValue(parameters.m_FiberGen.m_Rotation[2]); m_Controls->m_XtransBox->setValue(parameters.m_FiberGen.m_Translation[0]); m_Controls->m_YtransBox->setValue(parameters.m_FiberGen.m_Translation[1]); m_Controls->m_ZtransBox->setValue(parameters.m_FiberGen.m_Translation[2]); m_Controls->m_XscaleBox->setValue(parameters.m_FiberGen.m_Scale[0]); m_Controls->m_YscaleBox->setValue(parameters.m_FiberGen.m_Scale[1]); m_Controls->m_ZscaleBox->setValue(parameters.m_FiberGen.m_Scale[2]); // image generation parameters m_Controls->m_SizeX->setValue(parameters.m_SignalGen.m_ImageRegion.GetSize(0)); m_Controls->m_SizeY->setValue(parameters.m_SignalGen.m_ImageRegion.GetSize(1)); m_Controls->m_SizeZ->setValue(parameters.m_SignalGen.m_ImageRegion.GetSize(2)); m_Controls->m_SpacingX->setValue(parameters.m_SignalGen.m_ImageSpacing[0]); m_Controls->m_SpacingY->setValue(parameters.m_SignalGen.m_ImageSpacing[1]); m_Controls->m_SpacingZ->setValue(parameters.m_SignalGen.m_ImageSpacing[2]); m_Controls->m_NumGradientsBox->setValue(parameters.m_SignalGen.GetNumWeightedVolumes()); m_Controls->m_BvalueBox->setValue(parameters.m_SignalGen.m_Bvalue); m_Controls->m_SignalScaleBox->setValue(parameters.m_SignalGen.m_SignalScale); m_Controls->m_TEbox->setValue(parameters.m_SignalGen.m_tEcho); m_Controls->m_LineReadoutTimeBox->setValue(parameters.m_SignalGen.m_tLine); m_Controls->m_T2starBox->setValue(parameters.m_SignalGen.m_tInhom); m_Controls->m_FiberRadius->setValue(parameters.m_SignalGen.m_AxonRadius); m_Controls->m_RelaxationBox->setChecked(parameters.m_SignalGen.m_DoSimulateRelaxation); m_Controls->m_EnforcePureFiberVoxelsBox->setChecked(parameters.m_SignalGen.m_DoDisablePartialVolume); if (parameters.m_NoiseModel!=NULL) { m_Controls->m_AddNoise->setChecked(parameters.m_Misc.m_CheckAddNoiseBox); if (dynamic_cast*>(parameters.m_NoiseModel)) m_Controls->m_NoiseDistributionBox->setCurrentIndex(0); else if (dynamic_cast*>(parameters.m_NoiseModel)) m_Controls->m_NoiseDistributionBox->setCurrentIndex(1); m_Controls->m_NoiseLevel->setValue(parameters.m_NoiseModel->GetNoiseVariance()); } else m_Controls->m_AddNoise->setChecked(false); m_Controls->m_VolumeFractionsBox->setChecked(parameters.m_Misc.m_CheckOutputVolumeFractionsBox); m_Controls->m_AdvancedOptionsBox_2->setChecked(parameters.m_Misc.m_CheckAdvancedSignalOptionsBox); m_Controls->m_AddGhosts->setChecked(parameters.m_Misc.m_CheckAddGhostsBox); m_Controls->m_AddAliasing->setChecked(parameters.m_Misc.m_CheckAddAliasingBox); m_Controls->m_AddDistortions->setChecked(parameters.m_Misc.m_CheckAddDistortionsBox); m_Controls->m_AddSpikes->setChecked(parameters.m_Misc.m_CheckAddSpikesBox); m_Controls->m_AddEddy->setChecked(parameters.m_Misc.m_CheckAddEddyCurrentsBox); m_Controls->m_kOffsetBox->setValue(parameters.m_SignalGen.m_KspaceLineOffset); m_Controls->m_WrapBox->setValue(100*(1-parameters.m_SignalGen.m_CroppingFactor)); m_Controls->m_SpikeNumBox->setValue(parameters.m_SignalGen.m_Spikes); m_Controls->m_SpikeScaleBox->setValue(parameters.m_SignalGen.m_SpikeAmplitude); m_Controls->m_EddyGradientStrength->setValue(parameters.m_SignalGen.m_EddyStrength); m_Controls->m_AddGibbsRinging->setChecked(parameters.m_SignalGen.m_DoAddGibbsRinging); m_Controls->m_AddMotion->setChecked(parameters.m_SignalGen.m_DoAddMotion); m_Controls->m_RandomMotion->setChecked(parameters.m_SignalGen.m_DoRandomizeMotion); m_Controls->m_MaxTranslationBoxX->setValue(parameters.m_SignalGen.m_Translation[0]); m_Controls->m_MaxTranslationBoxY->setValue(parameters.m_SignalGen.m_Translation[1]); m_Controls->m_MaxTranslationBoxZ->setValue(parameters.m_SignalGen.m_Translation[2]); m_Controls->m_MaxRotationBoxX->setValue(parameters.m_SignalGen.m_Rotation[0]); m_Controls->m_MaxRotationBoxY->setValue(parameters.m_SignalGen.m_Rotation[1]); m_Controls->m_MaxRotationBoxZ->setValue(parameters.m_SignalGen.m_Rotation[2]); m_Controls->m_DiffusionDirectionBox->setCurrentIndex(parameters.m_SignalGen.m_DiffusionDirectionMode); m_Controls->m_SeparationAngleBox->setValue(parameters.m_SignalGen.m_FiberSeparationThreshold); m_Controls->m_Compartment1Box->setCurrentIndex(0); m_Controls->m_Compartment2Box->setCurrentIndex(0); m_Controls->m_Compartment3Box->setCurrentIndex(0); m_Controls->m_Compartment4Box->setCurrentIndex(0); for (unsigned int i=0; i* signalModel = NULL; if (im_CompartmentId) { case 1: { if (dynamic_cast*>(signalModel)) { mitk::StickModel<>* model = dynamic_cast*>(signalModel); m_Controls->m_StickWidget1->SetT2(model->GetT2()); m_Controls->m_StickWidget1->SetD(model->GetDiffusivity()); m_Controls->m_Compartment1Box->setCurrentIndex(0); break; } else if (dynamic_cast*>(signalModel)) { mitk::TensorModel<>* model = dynamic_cast*>(signalModel); m_Controls->m_TensorWidget1->SetT2(model->GetT2()); m_Controls->m_TensorWidget1->SetD1(model->GetDiffusivity1()); m_Controls->m_TensorWidget1->SetD2(model->GetDiffusivity2()); m_Controls->m_TensorWidget1->SetD3(model->GetDiffusivity3()); m_Controls->m_Compartment1Box->setCurrentIndex(2); break; } else if (dynamic_cast*>(signalModel)) { mitk::RawShModel<>* model = dynamic_cast*>(signalModel); m_Controls->m_PrototypeWidget1->SetNumberOfSamples(model->GetMaxNumKernels()); m_Controls->m_PrototypeWidget1->SetMinFa(model->GetFaRange().first); m_Controls->m_PrototypeWidget1->SetMaxFa(model->GetFaRange().second); m_Controls->m_PrototypeWidget1->SetMinAdc(model->GetAdcRange().first); m_Controls->m_PrototypeWidget1->SetMaxAdc(model->GetAdcRange().second); m_Controls->m_Compartment1Box->setCurrentIndex(3); break; } break; } case 2: { if (dynamic_cast*>(signalModel)) { mitk::StickModel<>* model = dynamic_cast*>(signalModel); m_Controls->m_StickWidget2->SetT2(model->GetT2()); m_Controls->m_StickWidget2->SetD(model->GetDiffusivity()); m_Controls->m_Compartment2Box->setCurrentIndex(1); break; } else if (dynamic_cast*>(signalModel)) { mitk::TensorModel<>* model = dynamic_cast*>(signalModel); m_Controls->m_TensorWidget2->SetT2(model->GetT2()); m_Controls->m_TensorWidget2->SetD1(model->GetDiffusivity1()); m_Controls->m_TensorWidget2->SetD2(model->GetDiffusivity2()); m_Controls->m_TensorWidget2->SetD3(model->GetDiffusivity3()); m_Controls->m_Compartment2Box->setCurrentIndex(3); break; } break; } case 3: { if (dynamic_cast*>(signalModel)) { mitk::BallModel<>* model = dynamic_cast*>(signalModel); m_Controls->m_BallWidget1->SetT2(model->GetT2()); m_Controls->m_BallWidget1->SetD(model->GetDiffusivity()); m_Controls->m_Compartment3Box->setCurrentIndex(0); break; } else if (dynamic_cast*>(signalModel)) { mitk::AstroStickModel<>* model = dynamic_cast*>(signalModel); m_Controls->m_AstrosticksWidget1->SetT2(model->GetT2()); m_Controls->m_AstrosticksWidget1->SetD(model->GetDiffusivity()); m_Controls->m_AstrosticksWidget1->SetRandomizeSticks(model->GetRandomizeSticks()); m_Controls->m_Compartment3Box->setCurrentIndex(1); break; } else if (dynamic_cast*>(signalModel)) { mitk::DotModel<>* model = dynamic_cast*>(signalModel); m_Controls->m_DotWidget1->SetT2(model->GetT2()); m_Controls->m_Compartment3Box->setCurrentIndex(2); break; } else if (dynamic_cast*>(signalModel)) { mitk::RawShModel<>* model = dynamic_cast*>(signalModel); m_Controls->m_PrototypeWidget3->SetNumberOfSamples(model->GetMaxNumKernels()); m_Controls->m_PrototypeWidget3->SetMinFa(model->GetFaRange().first); m_Controls->m_PrototypeWidget3->SetMaxFa(model->GetFaRange().second); m_Controls->m_PrototypeWidget3->SetMinAdc(model->GetAdcRange().first); m_Controls->m_PrototypeWidget3->SetMaxAdc(model->GetAdcRange().second); m_Controls->m_Compartment3Box->setCurrentIndex(3); break; } break; } case 4: { if (dynamic_cast*>(signalModel)) { mitk::BallModel<>* model = dynamic_cast*>(signalModel); m_Controls->m_BallWidget2->SetT2(model->GetT2()); m_Controls->m_BallWidget2->SetD(model->GetDiffusivity()); m_Controls->m_Compartment4Box->setCurrentIndex(1); break; } else if (dynamic_cast*>(signalModel)) { mitk::AstroStickModel<>* model = dynamic_cast*>(signalModel); m_Controls->m_AstrosticksWidget2->SetT2(model->GetT2()); m_Controls->m_AstrosticksWidget2->SetD(model->GetDiffusivity()); m_Controls->m_AstrosticksWidget2->SetRandomizeSticks(model->GetRandomizeSticks()); m_Controls->m_Compartment4Box->setCurrentIndex(2); break; } else if (dynamic_cast*>(signalModel)) { mitk::DotModel<>* model = dynamic_cast*>(signalModel); m_Controls->m_DotWidget2->SetT2(model->GetT2()); m_Controls->m_Compartment4Box->setCurrentIndex(3); break; } else if (dynamic_cast*>(signalModel)) { mitk::RawShModel<>* model = dynamic_cast*>(signalModel); m_Controls->m_PrototypeWidget4->SetNumberOfSamples(model->GetMaxNumKernels()); m_Controls->m_PrototypeWidget4->SetMinFa(model->GetFaRange().first); m_Controls->m_PrototypeWidget4->SetMaxFa(model->GetFaRange().second); m_Controls->m_PrototypeWidget4->SetMinAdc(model->GetAdcRange().first); m_Controls->m_PrototypeWidget4->SetMaxAdc(model->GetAdcRange().second); m_Controls->m_Compartment4Box->setCurrentIndex(4); break; } break; } } } } void QmitkFiberfoxView::ShowAdvancedOptions(int state) { if (state) { m_Controls->m_AdvancedFiberOptionsFrame->setVisible(true); m_Controls->m_AdvancedSignalOptionsFrame->setVisible(true); m_Controls->m_AdvancedOptionsBox->setChecked(true); m_Controls->m_AdvancedOptionsBox_2->setChecked(true); } else { m_Controls->m_AdvancedFiberOptionsFrame->setVisible(false); m_Controls->m_AdvancedSignalOptionsFrame->setVisible(false); m_Controls->m_AdvancedOptionsBox->setChecked(false); m_Controls->m_AdvancedOptionsBox_2->setChecked(false); } } void QmitkFiberfoxView::Comp1ModelFrameVisibility(int index) { m_Controls->m_StickWidget1->setVisible(false); m_Controls->m_ZeppelinWidget1->setVisible(false); m_Controls->m_TensorWidget1->setVisible(false); m_Controls->m_PrototypeWidget1->setVisible(false); switch (index) { case 0: m_Controls->m_StickWidget1->setVisible(true); break; case 1: m_Controls->m_ZeppelinWidget1->setVisible(true); break; case 2: m_Controls->m_TensorWidget1->setVisible(true); break; case 3: m_Controls->m_PrototypeWidget1->setVisible(true); break; } } void QmitkFiberfoxView::Comp2ModelFrameVisibility(int index) { m_Controls->m_StickWidget2->setVisible(false); m_Controls->m_ZeppelinWidget2->setVisible(false); m_Controls->m_TensorWidget2->setVisible(false); switch (index) { case 0: break; case 1: m_Controls->m_StickWidget2->setVisible(true); break; case 2: m_Controls->m_ZeppelinWidget2->setVisible(true); break; case 3: m_Controls->m_TensorWidget2->setVisible(true); break; } } void QmitkFiberfoxView::Comp3ModelFrameVisibility(int index) { m_Controls->m_BallWidget1->setVisible(false); m_Controls->m_AstrosticksWidget1->setVisible(false); m_Controls->m_DotWidget1->setVisible(false); m_Controls->m_PrototypeWidget3->setVisible(false); switch (index) { case 0: m_Controls->m_BallWidget1->setVisible(true); break; case 1: m_Controls->m_AstrosticksWidget1->setVisible(true); break; case 2: m_Controls->m_DotWidget1->setVisible(true); break; case 3: m_Controls->m_PrototypeWidget3->setVisible(true); break; } } void QmitkFiberfoxView::Comp4ModelFrameVisibility(int index) { m_Controls->m_BallWidget2->setVisible(false); m_Controls->m_AstrosticksWidget2->setVisible(false); m_Controls->m_DotWidget2->setVisible(false); m_Controls->m_PrototypeWidget4->setVisible(false); m_Controls->m_Comp4FractionFrame->setVisible(false); switch (index) { case 0: break; case 1: m_Controls->m_BallWidget2->setVisible(true); m_Controls->m_Comp4FractionFrame->setVisible(true); break; case 2: m_Controls->m_AstrosticksWidget2->setVisible(true); m_Controls->m_Comp4FractionFrame->setVisible(true); break; case 3: m_Controls->m_DotWidget2->setVisible(true); m_Controls->m_Comp4FractionFrame->setVisible(true); break; case 4: m_Controls->m_PrototypeWidget4->setVisible(true); m_Controls->m_Comp4FractionFrame->setVisible(true); break; } } void QmitkFiberfoxView::OnConstantRadius(int value) { if (value>0 && m_Controls->m_RealTimeFibers->isChecked()) GenerateFibers(); } void QmitkFiberfoxView::OnAddMotion(int value) { if (value>0) m_Controls->m_MotionArtifactFrame->setVisible(true); else m_Controls->m_MotionArtifactFrame->setVisible(false); } void QmitkFiberfoxView::OnAddAliasing(int value) { if (value>0) m_Controls->m_AliasingFrame->setVisible(true); else m_Controls->m_AliasingFrame->setVisible(false); } void QmitkFiberfoxView::OnAddSpikes(int value) { if (value>0) m_Controls->m_SpikeFrame->setVisible(true); else m_Controls->m_SpikeFrame->setVisible(false); } void QmitkFiberfoxView::OnAddEddy(int value) { if (value>0) m_Controls->m_EddyFrame->setVisible(true); else m_Controls->m_EddyFrame->setVisible(false); } void QmitkFiberfoxView::OnAddDistortions(int value) { if (value>0) m_Controls->m_DistortionsFrame->setVisible(true); else m_Controls->m_DistortionsFrame->setVisible(false); } void QmitkFiberfoxView::OnAddGhosts(int value) { if (value>0) m_Controls->m_GhostFrame->setVisible(true); else m_Controls->m_GhostFrame->setVisible(false); } void QmitkFiberfoxView::OnAddNoise(int value) { if (value>0) m_Controls->m_NoiseFrame->setVisible(true); else m_Controls->m_NoiseFrame->setVisible(false); } void QmitkFiberfoxView::OnDistributionChanged(int value) { if (value==1) m_Controls->m_VarianceBox->setVisible(true); else m_Controls->m_VarianceBox->setVisible(false); if (m_Controls->m_RealTimeFibers->isChecked()) GenerateFibers(); } void QmitkFiberfoxView::OnVarianceChanged(double) { if (m_Controls->m_RealTimeFibers->isChecked()) GenerateFibers(); } void QmitkFiberfoxView::OnFiberDensityChanged(int) { if (m_Controls->m_RealTimeFibers->isChecked()) GenerateFibers(); } void QmitkFiberfoxView::OnFiberSamplingChanged(double) { if (m_Controls->m_RealTimeFibers->isChecked()) GenerateFibers(); } void QmitkFiberfoxView::OnTensionChanged(double) { if (m_Controls->m_RealTimeFibers->isChecked()) GenerateFibers(); } void QmitkFiberfoxView::OnContinuityChanged(double) { if (m_Controls->m_RealTimeFibers->isChecked()) GenerateFibers(); } void QmitkFiberfoxView::OnBiasChanged(double) { if (m_Controls->m_RealTimeFibers->isChecked()) GenerateFibers(); } void QmitkFiberfoxView::AlignOnGrid() { for (unsigned int i=0; i(m_SelectedFiducials.at(i)->GetData()); mitk::Point3D wc0 = pe->GetWorldControlPoint(0); mitk::DataStorage::SetOfObjects::ConstPointer parentFibs = GetDataStorage()->GetSources(m_SelectedFiducials.at(i)); for( mitk::DataStorage::SetOfObjects::const_iterator it = parentFibs->begin(); it != parentFibs->end(); ++it ) { mitk::DataNode::Pointer pFibNode = *it; if ( pFibNode.IsNotNull() && dynamic_cast(pFibNode->GetData()) ) { mitk::DataStorage::SetOfObjects::ConstPointer parentImgs = GetDataStorage()->GetSources(pFibNode); for( mitk::DataStorage::SetOfObjects::const_iterator it2 = parentImgs->begin(); it2 != parentImgs->end(); ++it2 ) { mitk::DataNode::Pointer pImgNode = *it2; if ( pImgNode.IsNotNull() && dynamic_cast(pImgNode->GetData()) ) { mitk::Image::Pointer img = dynamic_cast(pImgNode->GetData()); mitk::BaseGeometry::Pointer geom = img->GetGeometry(); itk::Index<3> idx; geom->WorldToIndex(wc0, idx); mitk::Point3D cIdx; cIdx[0]=idx[0]; cIdx[1]=idx[1]; cIdx[2]=idx[2]; mitk::Point3D world; geom->IndexToWorld(cIdx,world); mitk::Vector3D trans = world - wc0; pe->GetGeometry()->Translate(trans); break; } } break; } } } for(unsigned int i=0; iGetSources(fibNode); for( mitk::DataStorage::SetOfObjects::const_iterator it = sources->begin(); it != sources->end(); ++it ) { mitk::DataNode::Pointer imgNode = *it; if ( imgNode.IsNotNull() && dynamic_cast(imgNode->GetData()) ) { mitk::DataStorage::SetOfObjects::ConstPointer derivations = GetDataStorage()->GetDerivations(fibNode); for( mitk::DataStorage::SetOfObjects::const_iterator it2 = derivations->begin(); it2 != derivations->end(); ++it2 ) { mitk::DataNode::Pointer fiducialNode = *it2; if ( fiducialNode.IsNotNull() && dynamic_cast(fiducialNode->GetData()) ) { mitk::PlanarEllipse::Pointer pe = dynamic_cast(fiducialNode->GetData()); mitk::Point3D wc0 = pe->GetWorldControlPoint(0); mitk::Image::Pointer img = dynamic_cast(imgNode->GetData()); mitk::BaseGeometry::Pointer geom = img->GetGeometry(); itk::Index<3> idx; geom->WorldToIndex(wc0, idx); mitk::Point3D cIdx; cIdx[0]=idx[0]; cIdx[1]=idx[1]; cIdx[2]=idx[2]; mitk::Point3D world; geom->IndexToWorld(cIdx,world); mitk::Vector3D trans = world - wc0; pe->GetGeometry()->Translate(trans); } } break; } } } for(unsigned int i=0; i(m_SelectedImages.at(i)->GetData()); mitk::DataStorage::SetOfObjects::ConstPointer derivations = GetDataStorage()->GetDerivations(m_SelectedImages.at(i)); for( mitk::DataStorage::SetOfObjects::const_iterator it = derivations->begin(); it != derivations->end(); ++it ) { mitk::DataNode::Pointer fibNode = *it; if ( fibNode.IsNotNull() && dynamic_cast(fibNode->GetData()) ) { mitk::DataStorage::SetOfObjects::ConstPointer derivations2 = GetDataStorage()->GetDerivations(fibNode); for( mitk::DataStorage::SetOfObjects::const_iterator it2 = derivations2->begin(); it2 != derivations2->end(); ++it2 ) { mitk::DataNode::Pointer fiducialNode = *it2; if ( fiducialNode.IsNotNull() && dynamic_cast(fiducialNode->GetData()) ) { mitk::PlanarEllipse::Pointer pe = dynamic_cast(fiducialNode->GetData()); mitk::Point3D wc0 = pe->GetWorldControlPoint(0); mitk::BaseGeometry::Pointer geom = img->GetGeometry(); itk::Index<3> idx; geom->WorldToIndex(wc0, idx); mitk::Point3D cIdx; cIdx[0]=idx[0]; cIdx[1]=idx[1]; cIdx[2]=idx[2]; mitk::Point3D world; geom->IndexToWorld(cIdx,world); mitk::Vector3D trans = world - wc0; pe->GetGeometry()->Translate(trans); } } } } } mitk::RenderingManager::GetInstance()->RequestUpdateAll(); if (m_Controls->m_RealTimeFibers->isChecked()) GenerateFibers(); } void QmitkFiberfoxView::OnFlipButton() { if (m_SelectedFiducial.IsNull()) return; std::map::iterator it = m_DataNodeToPlanarFigureData.find(m_SelectedFiducial.GetPointer()); if( it != m_DataNodeToPlanarFigureData.end() ) { QmitkPlanarFigureData& data = it->second; data.m_Flipped += 1; data.m_Flipped %= 2; } if (m_Controls->m_RealTimeFibers->isChecked()) GenerateFibers(); } QmitkFiberfoxView::GradientListType QmitkFiberfoxView::GenerateHalfShell(int NPoints) { NPoints *= 2; GradientListType pointshell; int numB0 = NPoints/20; if (numB0==0) numB0=1; GradientType g; g.Fill(0.0); for (int i=0; i theta; theta.set_size(NPoints); vnl_vector phi; phi.set_size(NPoints); double C = sqrt(4*M_PI); phi(0) = 0.0; phi(NPoints-1) = 0.0; for(int i=0; i0 && i std::vector > QmitkFiberfoxView::MakeGradientList() { std::vector > retval; vnl_matrix_fixed* U = itk::PointShell >::DistributePointShell(); // Add 0 vector for B0 int numB0 = ndirs/10; if (numB0==0) numB0=1; itk::Vector v; v.Fill(0.0); for (int i=0; i v; v[0] = U->get(0,i); v[1] = U->get(1,i); v[2] = U->get(2,i); retval.push_back(v); } return retval; } void QmitkFiberfoxView::OnAddBundle() { if (m_SelectedImage.IsNull()) return; mitk::DataStorage::SetOfObjects::ConstPointer children = GetDataStorage()->GetDerivations(m_SelectedImage); mitk::FiberBundleX::Pointer bundle = mitk::FiberBundleX::New(); mitk::DataNode::Pointer node = mitk::DataNode::New(); node->SetData( bundle ); QString name = QString("Bundle_%1").arg(children->size()); node->SetName(name.toStdString()); m_SelectedBundles.push_back(node); UpdateGui(); GetDataStorage()->Add(node, m_SelectedImage); } void QmitkFiberfoxView::OnDrawROI() { if (m_SelectedBundles.empty()) OnAddBundle(); if (m_SelectedBundles.empty()) return; mitk::DataStorage::SetOfObjects::ConstPointer children = GetDataStorage()->GetDerivations(m_SelectedBundles.at(0)); mitk::PlanarEllipse::Pointer figure = mitk::PlanarEllipse::New(); mitk::DataNode::Pointer node = mitk::DataNode::New(); node->SetData( figure ); node->SetBoolProperty("planarfigure.3drendering", true); QList nodes = this->GetDataManagerSelection(); for( int i=0; iSetSelected(false); m_SelectedFiducial = node; QString name = QString("Fiducial_%1").arg(children->size()); node->SetName(name.toStdString()); node->SetSelected(true); this->DisableCrosshairNavigation(); mitk::PlanarFigureInteractor::Pointer figureInteractor = dynamic_cast(node->GetDataInteractor().GetPointer()); if(figureInteractor.IsNull()) { figureInteractor = mitk::PlanarFigureInteractor::New(); us::Module* planarFigureModule = us::ModuleRegistry::GetModule( "MitkPlanarFigure" ); figureInteractor->LoadStateMachine("PlanarFigureInteraction.xml", planarFigureModule ); figureInteractor->SetEventConfig( "PlanarFigureConfig.xml", planarFigureModule ); figureInteractor->SetDataNode( node ); } UpdateGui(); GetDataStorage()->Add(node, m_SelectedBundles.at(0)); } bool CompareLayer(mitk::DataNode::Pointer i,mitk::DataNode::Pointer j) { int li = -1; i->GetPropertyValue("layer", li); int lj = -1; j->GetPropertyValue("layer", lj); return liGetSources(m_SelectedFiducial); for( mitk::DataStorage::SetOfObjects::const_iterator it = parents->begin(); it != parents->end(); ++it ) if(dynamic_cast((*it)->GetData())) m_SelectedBundles.push_back(*it); if (m_SelectedBundles.empty()) return; } FiberfoxParameters parameters = UpdateImageParameters(); for (unsigned int i=0; iGetDerivations(m_SelectedBundles.at(i)); std::vector< mitk::DataNode::Pointer > childVector; for( mitk::DataStorage::SetOfObjects::const_iterator it = children->begin(); it != children->end(); ++it ) childVector.push_back(*it); sort(childVector.begin(), childVector.end(), CompareLayer); vector< mitk::PlanarEllipse::Pointer > fib; vector< unsigned int > flip; float radius = 1; int count = 0; for( std::vector< mitk::DataNode::Pointer >::const_iterator it = childVector.begin(); it != childVector.end(); ++it ) { mitk::DataNode::Pointer node = *it; if ( node.IsNotNull() && dynamic_cast(node->GetData()) ) { mitk::PlanarEllipse* ellipse = dynamic_cast(node->GetData()); if (m_Controls->m_ConstantRadiusBox->isChecked()) { ellipse->SetTreatAsCircle(true); mitk::Point2D c = ellipse->GetControlPoint(0); mitk::Point2D p = ellipse->GetControlPoint(1); mitk::Vector2D v = p-c; if (count==0) { radius = v.GetVnlVector().magnitude(); ellipse->SetControlPoint(1, p); ellipse->Modified(); } else { v.Normalize(); v *= radius; ellipse->SetControlPoint(1, c+v); ellipse->Modified(); } } fib.push_back(ellipse); std::map::iterator it = m_DataNodeToPlanarFigureData.find(node.GetPointer()); if( it != m_DataNodeToPlanarFigureData.end() ) { QmitkPlanarFigureData& data = it->second; flip.push_back(data.m_Flipped); } else flip.push_back(0); } count++; } if (fib.size()>1) { parameters.m_FiberGen.m_Fiducials.push_back(fib); parameters.m_FiberGen.m_FlipList.push_back(flip); } else if (fib.size()>0) m_SelectedBundles.at(i)->SetData( mitk::FiberBundleX::New() ); mitk::RenderingManager::GetInstance()->RequestUpdateAll(); } itk::FibersFromPlanarFiguresFilter::Pointer filter = itk::FibersFromPlanarFiguresFilter::New(); filter->SetParameters(parameters.m_FiberGen); filter->Update(); vector< mitk::FiberBundleX::Pointer > fiberBundles = filter->GetFiberBundles(); for (unsigned int i=0; iSetData( fiberBundles.at(i) ); if (fiberBundles.at(i)->GetNumFibers()>50000) m_SelectedBundles.at(i)->SetVisibility(false); } mitk::RenderingManager::GetInstance()->RequestUpdateAll(); } void QmitkFiberfoxView::GenerateImage() { if (m_Controls->m_FiberBundleComboBox->GetSelectedNode().IsNull() && m_Controls->m_TemplateComboBox->GetSelectedNode().IsNull()) { mitk::Image::Pointer image = mitk::ImageGenerator::GenerateGradientImage( m_Controls->m_SizeX->value(), m_Controls->m_SizeY->value(), m_Controls->m_SizeZ->value(), m_Controls->m_SpacingX->value(), m_Controls->m_SpacingY->value(), m_Controls->m_SpacingZ->value()); mitk::DataNode::Pointer node = mitk::DataNode::New(); node->SetData( image ); node->SetName("Dummy"); unsigned int window = m_Controls->m_SizeX->value()*m_Controls->m_SizeY->value()*m_Controls->m_SizeZ->value(); unsigned int level = window/2; mitk::LevelWindow lw; lw.SetLevelWindow(level, window); node->SetProperty( "levelwindow", mitk::LevelWindowProperty::New( lw ) ); GetDataStorage()->Add(node); m_SelectedImage = node; mitk::BaseData::Pointer basedata = node->GetData(); if (basedata.IsNotNull()) { mitk::RenderingManager::GetInstance()->InitializeViews( basedata->GetTimeGeometry(), mitk::RenderingManager::REQUEST_UPDATE_ALL, true ); mitk::RenderingManager::GetInstance()->RequestUpdateAll(); } UpdateGui(); } else if (m_Controls->m_FiberBundleComboBox->GetSelectedNode().IsNotNull()) SimulateImageFromFibers(m_Controls->m_FiberBundleComboBox->GetSelectedNode()); else if ( m_Controls->m_TemplateComboBox->GetSelectedNode().IsNotNull() ) SimulateForExistingDwi(m_Controls->m_TemplateComboBox->GetSelectedNode()); } void QmitkFiberfoxView::SimulateForExistingDwi(mitk::DataNode* imageNode) { bool isDiffusionImage( mitk::DiffusionPropertyHelper::IsDiffusionWeightedImage( dynamic_cast(imageNode->GetData())) ); if ( !isDiffusionImage ) { return; } FiberfoxParameters parameters = UpdateImageParameters(); if (parameters.m_NoiseModel==NULL && parameters.m_SignalGen.m_Spikes==0 && parameters.m_SignalGen.m_FrequencyMap.IsNull() && parameters.m_SignalGen.m_KspaceLineOffset<=0.000001 && !parameters.m_SignalGen.m_DoAddGibbsRinging && !(parameters.m_SignalGen.m_EddyStrength>0) && parameters.m_SignalGen.m_CroppingFactor>0.999) { QMessageBox::information( NULL, "Simulation cancelled", "No valid artifact enabled! Motion artifacts and relaxation effects can NOT be added to an existing diffusion weighted image."); return; } mitk::Image::Pointer diffImg = dynamic_cast(imageNode->GetData()); ItkDwiType::Pointer itkVectorImagePointer = ItkDwiType::New(); mitk::CastToItkImage(diffImg, itkVectorImagePointer); m_ArtifactsToDwiFilter = itk::AddArtifactsToDwiImageFilter< short >::New(); m_ArtifactsToDwiFilter->SetInput(itkVectorImagePointer); parameters.m_Misc.m_ParentNode = imageNode; m_ArtifactsToDwiFilter->SetParameters(parameters); m_Worker.m_FilterType = 1; m_Thread.start(QThread::LowestPriority); } void QmitkFiberfoxView::SimulateImageFromFibers(mitk::DataNode* fiberNode) { mitk::FiberBundleX::Pointer fiberBundle = dynamic_cast(fiberNode->GetData()); if (fiberBundle->GetNumFibers()<=0) return; FiberfoxParameters parameters = UpdateImageParameters(); m_TractsToDwiFilter = itk::TractsToDWIImageFilter< short >::New(); parameters.m_Misc.m_ParentNode = fiberNode; if (m_Controls->m_TemplateComboBox->GetSelectedNode().IsNotNull() && mitk::DiffusionPropertyHelper::IsDiffusionWeightedImage( dynamic_cast(m_Controls->m_TemplateComboBox->GetSelectedNode()->GetData()))) { bool first = true; bool ok = true; mitk::Image::Pointer diffImg = dynamic_cast(m_Controls->m_TemplateComboBox->GetSelectedNode()->GetData()); itk::Image< itk::DiffusionTensor3D< double >, 3 >::Pointer tensorImage = NULL; const int shOrder = 2; typedef itk::AnalyticalDiffusionQballReconstructionImageFilter QballFilterType; QballFilterType::CoefficientImageType::Pointer itkFeatureImage = NULL; ItkDoubleImgType::Pointer adcImage = NULL; for (unsigned int i=0; i* model = NULL; if (i* >(parameters.m_FiberModelList.at(i)); else model = dynamic_cast< mitk::RawShModel<>* >(parameters.m_NonFiberModelList.at(i-parameters.m_FiberModelList.size())); if (model!=0 && model->GetNumberOfKernels()<=0) { if (first==true) { ItkDwiType::Pointer itkVectorImagePointer = ItkDwiType::New(); mitk::CastToItkImage(diffImg, itkVectorImagePointer); typedef itk::DiffusionTensor3DReconstructionImageFilter< short, short, double > TensorReconstructionImageFilterType; TensorReconstructionImageFilterType::Pointer filter = TensorReconstructionImageFilterType::New(); filter->SetGradientImage( static_cast( diffImg->GetProperty(mitk::DiffusionPropertyHelper::GRADIENTCONTAINERPROPERTYNAME.c_str()).GetPointer() )->GetGradientDirectionsContainer(), itkVectorImagePointer ); filter->SetBValue( static_cast(diffImg->GetProperty(mitk::DiffusionPropertyHelper::REFERENCEBVALUEPROPERTYNAME.c_str()).GetPointer() )->GetValue() ); filter->Update(); tensorImage = filter->GetOutput(); const int NumCoeffs = (shOrder*shOrder + shOrder + 2)/2 + shOrder; QballFilterType::Pointer qballfilter = QballFilterType::New(); qballfilter->SetGradientImage( static_cast( diffImg->GetProperty(mitk::DiffusionPropertyHelper::GRADIENTCONTAINERPROPERTYNAME.c_str()).GetPointer() )->GetGradientDirectionsContainer(), itkVectorImagePointer ); qballfilter->SetBValue( static_cast(diffImg->GetProperty(mitk::DiffusionPropertyHelper::REFERENCEBVALUEPROPERTYNAME.c_str()).GetPointer() )->GetValue() ); qballfilter->SetLambda(0.006); qballfilter->SetNormalizationMethod(QballFilterType::QBAR_RAW_SIGNAL); qballfilter->Update(); itkFeatureImage = qballfilter->GetCoefficientImage(); itk::AdcImageFilter< short, double >::Pointer adcFilter = itk::AdcImageFilter< short, double >::New(); adcFilter->SetInput( itkVectorImagePointer ); adcFilter->SetGradientDirections( static_cast( diffImg->GetProperty(mitk::DiffusionPropertyHelper::GRADIENTCONTAINERPROPERTYNAME.c_str()).GetPointer() )->GetGradientDirectionsContainer() ); adcFilter->SetB_value( static_cast(diffImg->GetProperty(mitk::DiffusionPropertyHelper::REFERENCEBVALUEPROPERTYNAME.c_str()).GetPointer() )->GetValue() ); adcFilter->Update(); adcImage = adcFilter->GetOutput(); } ok = model->SampleKernels(diffImg, parameters.m_SignalGen.m_MaskImage, tensorImage, itkFeatureImage, adcImage); if (!ok) break; } } if (!ok) { QMessageBox::information( NULL, "Simulation cancelled", "No valid prototype signals could be sampled."); return; } } else if ( m_Controls->m_Compartment1Box->currentIndex()==3 || m_Controls->m_Compartment3Box->currentIndex()==3 || m_Controls->m_Compartment4Box->currentIndex()==4 ) { QMessageBox::information( NULL, "Simulation cancelled", "Prototype signal but no diffusion-weighted image selected to sample signal from."); return; } m_TractsToDwiFilter->SetParameters(parameters); m_TractsToDwiFilter->SetFiberBundle(fiberBundle); m_Worker.m_FilterType = 0; m_Thread.start(QThread::LowestPriority); } void QmitkFiberfoxView::ApplyTransform() { vector< mitk::DataNode::Pointer > selectedBundles; for(unsigned int i=0; iGetDerivations(m_SelectedImages.at(i)); for( mitk::DataStorage::SetOfObjects::const_iterator it = derivations->begin(); it != derivations->end(); ++it ) { mitk::DataNode::Pointer fibNode = *it; if ( fibNode.IsNotNull() && dynamic_cast(fibNode->GetData()) ) selectedBundles.push_back(fibNode); } } if (selectedBundles.empty()) selectedBundles = m_SelectedBundles2; if (!selectedBundles.empty()) { for (std::vector::const_iterator it = selectedBundles.begin(); it!=selectedBundles.end(); ++it) { mitk::FiberBundleX::Pointer fib = dynamic_cast((*it)->GetData()); fib->RotateAroundAxis(m_Controls->m_XrotBox->value(), m_Controls->m_YrotBox->value(), m_Controls->m_ZrotBox->value()); fib->TranslateFibers(m_Controls->m_XtransBox->value(), m_Controls->m_YtransBox->value(), m_Controls->m_ZtransBox->value()); fib->ScaleFibers(m_Controls->m_XscaleBox->value(), m_Controls->m_YscaleBox->value(), m_Controls->m_ZscaleBox->value()); // handle child fiducials if (m_Controls->m_IncludeFiducials->isChecked()) { mitk::DataStorage::SetOfObjects::ConstPointer derivations = GetDataStorage()->GetDerivations(*it); for( mitk::DataStorage::SetOfObjects::const_iterator it2 = derivations->begin(); it2 != derivations->end(); ++it2 ) { mitk::DataNode::Pointer fiducialNode = *it2; if ( fiducialNode.IsNotNull() && dynamic_cast(fiducialNode->GetData()) ) { mitk::PlanarEllipse* pe = dynamic_cast(fiducialNode->GetData()); mitk::BaseGeometry* geom = pe->GetGeometry(); // translate mitk::Vector3D world; world[0] = m_Controls->m_XtransBox->value(); world[1] = m_Controls->m_YtransBox->value(); world[2] = m_Controls->m_ZtransBox->value(); geom->Translate(world); // calculate rotation matrix double x = m_Controls->m_XrotBox->value()*M_PI/180; double y = m_Controls->m_YrotBox->value()*M_PI/180; double z = m_Controls->m_ZrotBox->value()*M_PI/180; itk::Matrix< double, 3, 3 > rotX; rotX.SetIdentity(); rotX[1][1] = cos(x); rotX[2][2] = rotX[1][1]; rotX[1][2] = -sin(x); rotX[2][1] = -rotX[1][2]; itk::Matrix< double, 3, 3 > rotY; rotY.SetIdentity(); rotY[0][0] = cos(y); rotY[2][2] = rotY[0][0]; rotY[0][2] = sin(y); rotY[2][0] = -rotY[0][2]; itk::Matrix< double, 3, 3 > rotZ; rotZ.SetIdentity(); rotZ[0][0] = cos(z); rotZ[1][1] = rotZ[0][0]; rotZ[0][1] = -sin(z); rotZ[1][0] = -rotZ[0][1]; itk::Matrix< double, 3, 3 > rot = rotZ*rotY*rotX; // transform control point coordinate into geometry translation geom->SetOrigin(pe->GetWorldControlPoint(0)); mitk::Point2D cp; cp.Fill(0.0); pe->SetControlPoint(0, cp); // rotate fiducial geom->GetIndexToWorldTransform()->SetMatrix(rot*geom->GetIndexToWorldTransform()->GetMatrix()); // implicit translation mitk::Vector3D trans; trans[0] = geom->GetOrigin()[0]-fib->GetGeometry()->GetCenter()[0]; trans[1] = geom->GetOrigin()[1]-fib->GetGeometry()->GetCenter()[1]; trans[2] = geom->GetOrigin()[2]-fib->GetGeometry()->GetCenter()[2]; mitk::Vector3D newWc = rot*trans; newWc = newWc-trans; geom->Translate(newWc); pe->Modified(); } } } } } else { for (unsigned int i=0; i(m_SelectedFiducials.at(i)->GetData()); mitk::BaseGeometry* geom = pe->GetGeometry(); // translate mitk::Vector3D world; world[0] = m_Controls->m_XtransBox->value(); world[1] = m_Controls->m_YtransBox->value(); world[2] = m_Controls->m_ZtransBox->value(); geom->Translate(world); // calculate rotation matrix double x = m_Controls->m_XrotBox->value()*M_PI/180; double y = m_Controls->m_YrotBox->value()*M_PI/180; double z = m_Controls->m_ZrotBox->value()*M_PI/180; itk::Matrix< double, 3, 3 > rotX; rotX.SetIdentity(); rotX[1][1] = cos(x); rotX[2][2] = rotX[1][1]; rotX[1][2] = -sin(x); rotX[2][1] = -rotX[1][2]; itk::Matrix< double, 3, 3 > rotY; rotY.SetIdentity(); rotY[0][0] = cos(y); rotY[2][2] = rotY[0][0]; rotY[0][2] = sin(y); rotY[2][0] = -rotY[0][2]; itk::Matrix< double, 3, 3 > rotZ; rotZ.SetIdentity(); rotZ[0][0] = cos(z); rotZ[1][1] = rotZ[0][0]; rotZ[0][1] = -sin(z); rotZ[1][0] = -rotZ[0][1]; itk::Matrix< double, 3, 3 > rot = rotZ*rotY*rotX; // transform control point coordinate into geometry translation geom->SetOrigin(pe->GetWorldControlPoint(0)); mitk::Point2D cp; cp.Fill(0.0); pe->SetControlPoint(0, cp); // rotate fiducial geom->GetIndexToWorldTransform()->SetMatrix(rot*geom->GetIndexToWorldTransform()->GetMatrix()); pe->Modified(); } if (m_Controls->m_RealTimeFibers->isChecked()) GenerateFibers(); } mitk::RenderingManager::GetInstance()->RequestUpdateAll(); } void QmitkFiberfoxView::CopyBundles() { if ( m_SelectedBundles.size()<1 ){ QMessageBox::information( NULL, "Warning", "Select at least one fiber bundle!"); MITK_WARN("QmitkFiberFoxView") << "Select at least one fiber bundle!"; return; } for (std::vector::const_iterator it = m_SelectedBundles.begin(); it!=m_SelectedBundles.end(); ++it) { // find parent image mitk::DataNode::Pointer parentNode; mitk::DataStorage::SetOfObjects::ConstPointer parentImgs = GetDataStorage()->GetSources(*it); for( mitk::DataStorage::SetOfObjects::const_iterator it2 = parentImgs->begin(); it2 != parentImgs->end(); ++it2 ) { mitk::DataNode::Pointer pImgNode = *it2; if ( pImgNode.IsNotNull() && dynamic_cast(pImgNode->GetData()) ) { parentNode = pImgNode; break; } } mitk::FiberBundleX::Pointer fib = dynamic_cast((*it)->GetData()); mitk::FiberBundleX::Pointer newBundle = fib->GetDeepCopy(); QString name((*it)->GetName().c_str()); name += "_copy"; mitk::DataNode::Pointer fbNode = mitk::DataNode::New(); fbNode->SetData(newBundle); fbNode->SetName(name.toStdString()); fbNode->SetVisibility(true); if (parentNode.IsNotNull()) GetDataStorage()->Add(fbNode, parentNode); else GetDataStorage()->Add(fbNode); // copy child fiducials if (m_Controls->m_IncludeFiducials->isChecked()) { mitk::DataStorage::SetOfObjects::ConstPointer derivations = GetDataStorage()->GetDerivations(*it); for( mitk::DataStorage::SetOfObjects::const_iterator it2 = derivations->begin(); it2 != derivations->end(); ++it2 ) { mitk::DataNode::Pointer fiducialNode = *it2; if ( fiducialNode.IsNotNull() && dynamic_cast(fiducialNode->GetData()) ) { mitk::PlanarEllipse::Pointer pe = dynamic_cast(fiducialNode->GetData())->Clone(); mitk::DataNode::Pointer newNode = mitk::DataNode::New(); newNode->SetData(pe); newNode->SetName(fiducialNode->GetName()); newNode->SetBoolProperty("planarfigure.3drendering", true); GetDataStorage()->Add(newNode, fbNode); } } } } mitk::RenderingManager::GetInstance()->RequestUpdateAll(); } void QmitkFiberfoxView::JoinBundles() { if ( m_SelectedBundles.size()<2 ){ QMessageBox::information( NULL, "Warning", "Select at least two fiber bundles!"); MITK_WARN("QmitkFiberFoxView") << "Select at least two fiber bundles!"; return; } std::vector::const_iterator it = m_SelectedBundles.begin(); mitk::FiberBundleX::Pointer newBundle = dynamic_cast((*it)->GetData()); QString name(""); name += QString((*it)->GetName().c_str()); ++it; for (; it!=m_SelectedBundles.end(); ++it) { newBundle = newBundle->AddBundle(dynamic_cast((*it)->GetData())); name += "+"+QString((*it)->GetName().c_str()); } mitk::DataNode::Pointer fbNode = mitk::DataNode::New(); fbNode->SetData(newBundle); fbNode->SetName(name.toStdString()); fbNode->SetVisibility(true); GetDataStorage()->Add(fbNode); mitk::RenderingManager::GetInstance()->RequestUpdateAll(); } void QmitkFiberfoxView::UpdateGui() { m_Controls->m_GeometryFrame->setEnabled(true); m_Controls->m_GeometryMessage->setVisible(false); m_Controls->m_DiffusionPropsMessage->setVisible(false); m_Controls->m_FiberGenMessage->setVisible(true); m_Controls->m_TransformBundlesButton->setEnabled(false); m_Controls->m_CopyBundlesButton->setEnabled(false); m_Controls->m_GenerateFibersButton->setEnabled(false); m_Controls->m_FlipButton->setEnabled(false); m_Controls->m_CircleButton->setEnabled(false); m_Controls->m_BvalueBox->setEnabled(true); m_Controls->m_NumGradientsBox->setEnabled(true); m_Controls->m_JoinBundlesButton->setEnabled(false); m_Controls->m_AlignOnGrid->setEnabled(false); // Fiber generation gui if (m_SelectedFiducial.IsNotNull()) { m_Controls->m_TransformBundlesButton->setEnabled(true); m_Controls->m_FlipButton->setEnabled(true); m_Controls->m_AlignOnGrid->setEnabled(true); } if (m_SelectedImage.IsNotNull() || !m_SelectedBundles.empty()) { m_Controls->m_CircleButton->setEnabled(true); m_Controls->m_FiberGenMessage->setVisible(false); } if (m_SelectedImage.IsNotNull() && !m_SelectedBundles.empty()) m_Controls->m_AlignOnGrid->setEnabled(true); if (!m_SelectedBundles.empty()) { m_Controls->m_TransformBundlesButton->setEnabled(true); m_Controls->m_CopyBundlesButton->setEnabled(true); m_Controls->m_GenerateFibersButton->setEnabled(true); if (m_SelectedBundles.size()>1) m_Controls->m_JoinBundlesButton->setEnabled(true); } // Signal generation gui if (m_Controls->m_MaskComboBox->GetSelectedNode().IsNotNull() || m_Controls->m_TemplateComboBox->GetSelectedNode().IsNotNull()) { m_Controls->m_GeometryMessage->setVisible(true); m_Controls->m_GeometryFrame->setEnabled(false); } if (m_Controls->m_TemplateComboBox->GetSelectedNode().IsNotNull() && mitk::DiffusionPropertyHelper::IsDiffusionWeightedImage( dynamic_cast(m_Controls->m_TemplateComboBox->GetSelectedNode()->GetData()))) { m_Controls->m_DiffusionPropsMessage->setVisible(true); m_Controls->m_BvalueBox->setEnabled(false); m_Controls->m_NumGradientsBox->setEnabled(false); m_Controls->m_GeometryMessage->setVisible(true); m_Controls->m_GeometryFrame->setEnabled(false); } } void QmitkFiberfoxView::OnSelectionChanged( berry::IWorkbenchPart::Pointer, const QList& nodes ) { m_SelectedBundles2.clear(); m_SelectedImages.clear(); m_SelectedFiducials.clear(); m_SelectedFiducial = NULL; m_SelectedBundles.clear(); m_SelectedImage = NULL; // iterate all selected objects, adjust warning visibility for( int i=0; i(node->GetData())); // } // if ( node.IsNotNull() && isDiffusionImage ) // { // m_SelectedDWI = node; // m_SelectedImage = node; // m_SelectedImages.push_back(node); // } if( node.IsNotNull() && dynamic_cast(node->GetData()) ) { m_SelectedImages.push_back(node); m_SelectedImage = node; } else if ( node.IsNotNull() && dynamic_cast(node->GetData()) ) { m_SelectedBundles2.push_back(node); if (m_Controls->m_RealTimeFibers->isChecked()) { m_SelectedBundles.push_back(node); mitk::FiberBundleX::Pointer newFib = dynamic_cast(node->GetData()); if (newFib->GetNumFibers()!=m_Controls->m_FiberDensityBox->value()) GenerateFibers(); } else m_SelectedBundles.push_back(node); } else if ( node.IsNotNull() && dynamic_cast(node->GetData()) ) { m_SelectedFiducials.push_back(node); m_SelectedFiducial = node; m_SelectedBundles.clear(); mitk::DataStorage::SetOfObjects::ConstPointer parents = GetDataStorage()->GetSources(node); for( mitk::DataStorage::SetOfObjects::const_iterator it = parents->begin(); it != parents->end(); ++it ) { mitk::DataNode::Pointer pNode = *it; if ( pNode.IsNotNull() && dynamic_cast(pNode->GetData()) ) m_SelectedBundles.push_back(pNode); } } } UpdateGui(); } void QmitkFiberfoxView::EnableCrosshairNavigation() { MITK_DEBUG << "EnableCrosshairNavigation"; // enable the crosshair navigation if (mitk::ILinkedRenderWindowPart* linkedRenderWindow = dynamic_cast(this->GetRenderWindowPart())) { MITK_DEBUG << "enabling linked navigation"; linkedRenderWindow->EnableLinkedNavigation(true); // linkedRenderWindow->EnableSlicingPlanes(true); } if (m_Controls->m_RealTimeFibers->isChecked()) GenerateFibers(); } void QmitkFiberfoxView::DisableCrosshairNavigation() { MITK_DEBUG << "DisableCrosshairNavigation"; // disable the crosshair navigation during the drawing if (mitk::ILinkedRenderWindowPart* linkedRenderWindow = dynamic_cast(this->GetRenderWindowPart())) { MITK_DEBUG << "disabling linked navigation"; linkedRenderWindow->EnableLinkedNavigation(false); // linkedRenderWindow->EnableSlicingPlanes(false); } } void QmitkFiberfoxView::NodeRemoved(const mitk::DataNode* node) { mitk::DataNode* nonConstNode = const_cast(node); std::map::iterator it = m_DataNodeToPlanarFigureData.find(nonConstNode); if (dynamic_cast(node->GetData())) { m_SelectedBundles.clear(); m_SelectedBundles2.clear(); } else if (dynamic_cast(node->GetData())) m_SelectedImages.clear(); if( it != m_DataNodeToPlanarFigureData.end() ) { QmitkPlanarFigureData& data = it->second; // remove observers data.m_Figure->RemoveObserver( data.m_EndPlacementObserverTag ); data.m_Figure->RemoveObserver( data.m_SelectObserverTag ); data.m_Figure->RemoveObserver( data.m_StartInteractionObserverTag ); data.m_Figure->RemoveObserver( data.m_EndInteractionObserverTag ); m_DataNodeToPlanarFigureData.erase( it ); } } void QmitkFiberfoxView::NodeAdded( const mitk::DataNode* node ) { // add observer for selection in renderwindow mitk::PlanarFigure* figure = dynamic_cast(node->GetData()); bool isPositionMarker (false); node->GetBoolProperty("isContourMarker", isPositionMarker); if( figure && !isPositionMarker ) { MITK_DEBUG << "figure added. will add interactor if needed."; mitk::PlanarFigureInteractor::Pointer figureInteractor = dynamic_cast(node->GetDataInteractor().GetPointer()); mitk::DataNode* nonConstNode = const_cast( node ); if(figureInteractor.IsNull()) { figureInteractor = mitk::PlanarFigureInteractor::New(); us::Module* planarFigureModule = us::ModuleRegistry::GetModule( "MitkPlanarFigure" ); figureInteractor->LoadStateMachine("PlanarFigureInteraction.xml", planarFigureModule ); figureInteractor->SetEventConfig( "PlanarFigureConfig.xml", planarFigureModule ); figureInteractor->SetDataNode( nonConstNode ); } MITK_DEBUG << "will now add observers for planarfigure"; QmitkPlanarFigureData data; data.m_Figure = figure; // // add observer for event when figure has been placed typedef itk::SimpleMemberCommand< QmitkFiberfoxView > SimpleCommandType; // SimpleCommandType::Pointer initializationCommand = SimpleCommandType::New(); // initializationCommand->SetCallbackFunction( this, &QmitkFiberfoxView::PlanarFigureInitialized ); // data.m_EndPlacementObserverTag = figure->AddObserver( mitk::EndPlacementPlanarFigureEvent(), initializationCommand ); // add observer for event when figure is picked (selected) typedef itk::MemberCommand< QmitkFiberfoxView > MemberCommandType; MemberCommandType::Pointer selectCommand = MemberCommandType::New(); selectCommand->SetCallbackFunction( this, &QmitkFiberfoxView::PlanarFigureSelected ); data.m_SelectObserverTag = figure->AddObserver( mitk::SelectPlanarFigureEvent(), selectCommand ); // add observer for event when interaction with figure starts SimpleCommandType::Pointer startInteractionCommand = SimpleCommandType::New(); startInteractionCommand->SetCallbackFunction( this, &QmitkFiberfoxView::DisableCrosshairNavigation); data.m_StartInteractionObserverTag = figure->AddObserver( mitk::StartInteractionPlanarFigureEvent(), startInteractionCommand ); // add observer for event when interaction with figure starts SimpleCommandType::Pointer endInteractionCommand = SimpleCommandType::New(); endInteractionCommand->SetCallbackFunction( this, &QmitkFiberfoxView::EnableCrosshairNavigation); data.m_EndInteractionObserverTag = figure->AddObserver( mitk::EndInteractionPlanarFigureEvent(), endInteractionCommand ); m_DataNodeToPlanarFigureData[nonConstNode] = data; } } void QmitkFiberfoxView::PlanarFigureSelected( itk::Object* object, const itk::EventObject& ) { mitk::TNodePredicateDataType::Pointer isPf = mitk::TNodePredicateDataType::New(); mitk::DataStorage::SetOfObjects::ConstPointer allPfs = this->GetDataStorage()->GetSubset( isPf ); for ( mitk::DataStorage::SetOfObjects::const_iterator it = allPfs->begin(); it!=allPfs->end(); ++it) { mitk::DataNode* node = *it; if( node->GetData() == object ) { node->SetSelected(true); m_SelectedFiducial = node; } else node->SetSelected(false); } UpdateGui(); this->RequestRenderWindowUpdate(); } void QmitkFiberfoxView::SetFocus() { m_Controls->m_CircleButton->setFocus(); } void QmitkFiberfoxView::SetOutputPath() { // SELECT FOLDER DIALOG string outputPath = QFileDialog::getExistingDirectory(NULL, "Save images to...", QString(outputPath.c_str())).toStdString(); if (outputPath.empty()) m_Controls->m_SavePathEdit->setText("-"); else { outputPath += "/"; m_Controls->m_SavePathEdit->setText(QString(outputPath.c_str())); } }