Network ConnectivityMeasures::pearsonsCorrelationCoeff(const MatrixXd& matData, const MatrixX3f& matVert) { Network finalNetwork("Pearson's Correlation Coefficient"); //Create nodes for(int i = 0; i < matData.rows(); ++i) { RowVectorXf rowVert = RowVectorXf::Zero(3); if(matVert.rows() != 0 && i < matVert.rows()) { rowVert(0) = matVert.row(i)(0); rowVert(1) = matVert.row(i)(1); rowVert(2) = matVert.row(i)(2); } finalNetwork << NetworkNode::SPtr(new NetworkNode(i, rowVert)); } //Create edges for(int i = 0; i < matData.rows(); ++i) { for(int j = i; j < matData.rows(); ++j) { double pearsonsCoeff = calcPearsonsCorrelationCoeff(matData.row(i), matData.row(j)); QSharedPointer<NetworkEdge> pEdge = QSharedPointer<NetworkEdge>(new NetworkEdge(finalNetwork.getNodes()[i], finalNetwork.getNodes()[j], pearsonsCoeff)); *finalNetwork.getNodeAt(i) << pEdge; finalNetwork << pEdge; } } return finalNetwork; }
Network ConnectivityMeasures::crossCorrelation(const MatrixXd& matData, const MatrixX3f& matVert) { Network finalNetwork("Cross Correlation"); //Create nodes for(int i = 0; i < matData.rows(); ++i) { RowVectorXf rowVert = RowVectorXf::Zero(3); if(matVert.rows() != 0 && i < matVert.rows()) { rowVert(0) = matVert.row(i)(0); rowVert(1) = matVert.row(i)(1); rowVert(2) = matVert.row(i)(2); } finalNetwork << NetworkNode::SPtr(new NetworkNode(i, rowVert)); } //Create edges for(int i = 0; i < matData.rows(); ++i) { for(int j = i; j < matData.rows(); ++j) { QPair<int,double> crossCorrPair = calcCrossCorrelation(matData.row(i), matData.row(j)); QSharedPointer<NetworkEdge> pEdge = QSharedPointer<NetworkEdge>(new NetworkEdge(finalNetwork.getNodes()[i], finalNetwork.getNodes()[j], crossCorrPair.second)); *finalNetwork.getNodeAt(i) << pEdge; finalNetwork << pEdge; } } // finalNetwork.scale(); // matDist /= matDist.maxCoeff(); return finalNetwork; }
MatrixX3f Surface::compute_normals(const MatrixX3f& rr, const MatrixX3i& tris) { printf("\tcomputing normals\n"); // first, compute triangle normals MatrixX3f r1(tris.rows(),3); MatrixX3f r2(tris.rows(),3); MatrixX3f r3(tris.rows(),3); for(qint32 i = 0; i < tris.rows(); ++i) { r1.row(i) = rr.row(tris(i, 0)); r2.row(i) = rr.row(tris(i, 1)); r3.row(i) = rr.row(tris(i, 2)); } MatrixX3f x = r2 - r1; MatrixX3f y = r3 - r1; MatrixX3f tri_nn(x.rows(),y.cols()); tri_nn.col(0) = x.col(1).cwiseProduct(y.col(2)) - x.col(2).cwiseProduct(y.col(1)); tri_nn.col(1) = x.col(2).cwiseProduct(y.col(0)) - x.col(0).cwiseProduct(y.col(2)); tri_nn.col(2) = x.col(0).cwiseProduct(y.col(1)) - x.col(1).cwiseProduct(y.col(0)); // Triangle normals and areas MatrixX3f tmp = tri_nn.cwiseProduct(tri_nn); VectorXf normSize = tmp.rowwise().sum(); normSize = normSize.cwiseSqrt(); for(qint32 i = 0; i < normSize.size(); ++i) if(normSize(i) != 0) tri_nn.row(i) /= normSize(i); MatrixX3f nn = MatrixX3f::Zero(rr.rows(), 3); for(qint32 p = 0; p < tris.rows(); ++p) { Vector3i verts = tris.row(p); for(qint32 j = 0; j < verts.size(); ++j) nn.row(verts(j)) = tri_nn.row(p); } tmp = nn.cwiseProduct(nn); normSize = tmp.rowwise().sum(); normSize = normSize.cwiseSqrt(); for(qint32 i = 0; i < normSize.size(); ++i) if(normSize(i) != 0) nn.row(i) /= normSize(i); return nn; }
void LabelView::initializeGL(QGLPainter *painter) { // in the constructor construct a builder on the stack QGLBuilder builder; float fac = 10.0f; builder << QGL::Faceted; m_pSceneNodeBrain = builder.currentNode(); builder.pushNode(); // Collor palette qint32 index; QSharedPointer<QGLMaterialCollection> palette = builder.sceneNode()->palette(); // register color palette within the root node // // Build each hemisphere in its separate node // for(qint32 h = 0; h < 2; ++h) { builder.newNode();//create new hemisphere node { MatrixX3i tris; MatrixX3f rr = m_surfSet[h].rr(); builder.pushNode(); // // Create each ROI in its own node // for(qint32 k = 0; k < m_qListLabels.size(); ++k) { //check if label hemi fits current hemi if(m_qListLabels[k].hemi != h) continue; //Ggenerate label tri information tris = m_qListLabels[k].selectTris(m_surfSet[h]); // add new ROI node when current ROI node is not empty if(builder.currentNode()->count() > 0) builder.newNode(); QGeometryData t_GeometryDataTri; MatrixXf t_TriCoords(3,3*tris.rows()); for(qint32 i = 0; i < tris.rows(); ++i) { t_TriCoords.col(i*3) = rr.row( tris(i,0) ).transpose(); t_TriCoords.col(i*3+1) = rr.row( tris(i,1) ).transpose(); t_TriCoords.col(i*3+2) = rr.row( tris(i,2) ).transpose(); } t_TriCoords *= fac; t_GeometryDataTri.appendVertexArray(QArray<QVector3D>::fromRawData( reinterpret_cast<const QVector3D*>(t_TriCoords.data()), t_TriCoords.cols() )); // // If triangles are available. // if (t_GeometryDataTri.count() > 0) { // // Add triangles to current node // builder.addTriangles(t_GeometryDataTri); // // Colorize ROI // QGLMaterial *t_pMaterialROI = new QGLMaterial(); int r, g, b; r = m_qListRGBAs[k][0]; g = m_qListRGBAs[k][1]; b = m_qListRGBAs[k][2]; t_pMaterialROI->setColor(QColor(r,g,b,200)); // t_pMaterialROI->setEmittedLight(QColor(100,100,100,255)); // t_pMaterialROI->setSpecularColor(QColor(10,10,10,20)); index = palette->addMaterial(t_pMaterialROI); builder.currentNode()->setMaterialIndex(index); } } } // Go one level up builder.popNode(); } // Go one level up builder.popNode(); // Optimze current scene for display and calculate lightning normals m_pSceneNode = builder.finalizedSceneNode(); m_pSceneNode->setParent(this); // // Create light models // m_pLightModel = new QGLLightModel(this); m_pLightModel->setAmbientSceneColor(Qt::white); m_pLightModel->setViewerPosition(QGLLightModel::LocalViewer); m_pLightModel = new QGLLightModel(this); m_pLightParametersScene = new QGLLightParameters(this); m_pLightParametersScene->setPosition(QVector3D(0.0f, 0.0f, 3.0f)); painter->setMainLight(m_pLightParametersScene); simCount = 0; // // Set stereo type // if (m_bStereo) { this->setStereoType(QGLView::RedCyanAnaglyph); camera()->setEyeSeparation(0.4f); m_pCameraFrontal->setEyeSeparation(0.1f); } }