void FiberBundleReader::GenerateOutputInformation() { m_OutputCache = OutputType::New(); std::string ext = itksys::SystemTools::GetFilenameLastExtension(m_FileName); ext = itksys::SystemTools::LowerCase(ext); if ( m_FileName == "") { } else if (ext == ".fib") { try { TiXmlDocument doc( m_FileName ); doc.LoadFile(); TiXmlHandle hDoc(&doc); TiXmlElement* pElem; TiXmlHandle hRoot(0); pElem = hDoc.FirstChildElement().Element(); // save this for later hRoot = TiXmlHandle(pElem); pElem = hRoot.FirstChildElement(FiberBundleReader::XML_GEOMETRY).Element(); // read geometry mitk::Geometry3D::Pointer geometry = mitk::Geometry3D::New(); // read origin mitk::Point3D origin; double temp = 0; pElem->Attribute(FiberBundleReader::XML_ORIGIN_X, &temp); origin[0] = temp; pElem->Attribute(FiberBundleReader::XML_ORIGIN_Y, &temp); origin[1] = temp; pElem->Attribute(FiberBundleReader::XML_ORIGIN_Z, &temp); origin[2] = temp; geometry->SetOrigin(origin); // read spacing float spacing[3]; pElem->Attribute(FiberBundleReader::XML_SPACING_X, &temp); spacing[0] = temp; pElem->Attribute(FiberBundleReader::XML_SPACING_Y, &temp); spacing[1] = temp; pElem->Attribute(FiberBundleReader::XML_SPACING_Z, &temp); spacing[2] = temp; geometry->SetSpacing(spacing); // read transform vtkMatrix4x4* m = vtkMatrix4x4::New(); pElem->Attribute(FiberBundleReader::XML_MATRIX_XX, &temp); m->SetElement(0,0,temp); pElem->Attribute(FiberBundleReader::XML_MATRIX_XY, &temp); m->SetElement(1,0,temp); pElem->Attribute(FiberBundleReader::XML_MATRIX_XZ, &temp); m->SetElement(2,0,temp); pElem->Attribute(FiberBundleReader::XML_MATRIX_YX, &temp); m->SetElement(0,1,temp); pElem->Attribute(FiberBundleReader::XML_MATRIX_YY, &temp); m->SetElement(1,1,temp); pElem->Attribute(FiberBundleReader::XML_MATRIX_YZ, &temp); m->SetElement(2,1,temp); pElem->Attribute(FiberBundleReader::XML_MATRIX_ZX, &temp); m->SetElement(0,2,temp); pElem->Attribute(FiberBundleReader::XML_MATRIX_ZY, &temp); m->SetElement(1,2,temp); pElem->Attribute(FiberBundleReader::XML_MATRIX_ZZ, &temp); m->SetElement(2,2,temp); m->SetElement(0,3,origin[0]); m->SetElement(1,3,origin[1]); m->SetElement(2,3,origin[2]); m->SetElement(3,3,1); geometry->SetIndexToWorldTransformByVtkMatrix(m); // read bounds float bounds[] = {0, 0, 0, 0, 0, 0}; pElem->Attribute(FiberBundleReader::XML_SIZE_X, &temp); bounds[1] = temp; pElem->Attribute(FiberBundleReader::XML_SIZE_Y, &temp); bounds[3] = temp; pElem->Attribute(FiberBundleReader::XML_SIZE_Z, &temp); bounds[5] = temp; geometry->SetFloatBounds(bounds); // read bounds float bounds2[] = {0, 0, 0}; bounds2[0] = bounds[1]; bounds2[1] = bounds[3]; bounds2[2] = bounds[5]; m_OutputCache->SetBounds(bounds2); geometry->SetImageGeometry(true); m_OutputCache->SetGeometry(geometry); // generate tract container ContainerType::Pointer tractContainer = ContainerType::New(); int fiberID = 0; pElem = hRoot.FirstChildElement(FiberBundleReader::XML_FIBER_BUNDLE).FirstChild().Element(); for( pElem; pElem; pElem=pElem->NextSiblingElement()) { TiXmlElement* pElem2 = pElem->FirstChildElement(); ContainerTractType::Pointer tract = ContainerTractType::New(); for( pElem2; pElem2; pElem2=pElem2->NextSiblingElement()) { ContainerPointType point; pElem2->Attribute(FiberBundleReader::XML_POS_X, &temp); point[0] = temp; pElem2->Attribute(FiberBundleReader::XML_POS_Y, &temp); point[1] = temp; pElem2->Attribute(FiberBundleReader::XML_POS_Z, &temp); point[2] = temp; tract->InsertElement(tract->Size(), point); } pElem->Attribute(FiberBundleReader::XML_ID, &fiberID); tractContainer->CreateIndex(fiberID); tractContainer->SetElement(fiberID, tract); } m_OutputCache->addTractContainer(tractContainer); m_OutputCache->initFiberGroup(); MITK_INFO << "Fiber bundle read"; } catch(...) { MITK_INFO << "Could not read file "; } } else if (ext == ".vfib") { // generate tract container ContainerType::Pointer tractContainer = ContainerType::New(); mitk::Geometry3D::Pointer geometry = mitk::Geometry3D::New(); ///We create a Generic Reader to test de .vtk/ vtkDataReader *chooser=vtkDataReader::New(); chooser->SetFileName(m_FileName.c_str() ); if( chooser->IsFilePolyData()) { vtkPolyDataReader *reader = vtkPolyDataReader::New(); reader->SetFileName( m_FileName.c_str() ); reader->Update(); if ( reader->GetOutput() != NULL ) { vtkPolyData* output = reader->GetOutput(); output->ComputeBounds(); double bounds[3]; output->GetBounds(bounds); double center[3]; output->GetCenter(center); Point3D origin; origin.SetElement(0, -center[0]); origin.SetElement(1, -center[1]); origin.SetElement(2, -center[2]); MITK_INFO << origin; mitk::Surface::Pointer surf = mitk::Surface::New(); surf->SetVtkPolyData(output); mitk::Geometry3D* geom = surf->GetGeometry(); //geom->SetOrigin(origin); geom->SetImageGeometry(true); m_OutputCache->SetBounds(bounds); m_OutputCache->SetGeometry(geom); vtkCellArray* cells = output->GetLines(); cells->InitTraversal(); for (int i=0; i<output->GetNumberOfCells(); i++) { ContainerTractType::Pointer tract = ContainerTractType::New(); vtkCell* cell = output->GetCell(i); int p = cell->GetNumberOfPoints(); vtkPoints* points = cell->GetPoints(); for (int j=0; j<p; j++) { double p[3]; points->GetPoint(j, p); ContainerPointType point; point[0] = p[0]; point[1] = p[1]; point[2] = p[2]; tract->InsertElement(tract->Size(), point); } tractContainer->InsertElement(i, tract); } } reader->Delete(); } chooser->Delete(); m_OutputCache->addTractContainer(tractContainer); m_OutputCache->initFiberGroup(); MITK_INFO << "Fiber bundle read"; } }