void Deform::update_Ri()
{
Matrix3f Si;
MatrixXf Di;
Matrix3Xf Pi_Prime;
Matrix3Xf Pi;
for (int i = 0; i != P_Num; ++i) {
Di = MatrixXf::Zero(adj_list[i].size(), adj_list[i].size());
Pi_Prime.resize(3, adj_list[i].size());
Pi.resize(3, adj_list[i].size());
// if there is not any single unconnected point this for loop can have a more efficient representation
for (decltype(adj_list[i].size()) j = 0; j != adj_list[i].size(); ++j) {
Di(j, j) = Weight.coeffRef(i, adj_list[i][j]);
Pi.col(j) = P.col(i) - P.col(adj_list[i][j]);
Pi_Prime.col(j) = P_Prime.col(i) - P_Prime.col(adj_list[i][j]);
}
Si = Pi * Di * Pi_Prime.transpose();
Matrix3f Ui;
Vector3f Wi;
Matrix3f Vi;
wunderSVD3x3(Si, Ui, Wi, Vi);
R[i] = Vi * Ui.transpose();
if (R[i].determinant() < 0)
std::cout << "determinant is negative!" << std::endl;
}
}
void BrainView::genSurface()
{
if(m_SurfaceSet.size() == 0)
return;
if(m_pSceneNode)
{
delete m_pSceneNode;
m_pSceneNode = NULL;
}
// in the constructor construct a builder on the stack
QGLBuilder builder;
float fac = 100.0f; // too small vertices distances cause clipping errors --> 100 is a good value for freesurfer brain measures
builder << QGL::Smooth;//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
//
// get bounding box
//
calcBoundingBox();
//
// Build each surface in its separate node
//
QMap<qint32, Surface>::const_iterator it = m_SurfaceSet.data().constBegin();
for (it = m_SurfaceSet.data().begin(); it != m_SurfaceSet.data().end(); ++it)
{
builder.pushNode();
{
Matrix3Xf rr = it.value().rr().transpose();
//Centralize
for(qint32 i = 0; i < 3; ++i)
rr.row(i) = rr.row(i).array() - m_vecBoundingBoxCenter[i];
QGeometryData t_GeometryDataTri;
MatrixXf t_TriCoords = MatrixXf::Zero(3,3*(it.value().tris().rows()));
for(qint32 i = 0; i < it.value().tris().rows(); ++i)
for(qint32 j = 0; j < 3; ++j)
t_TriCoords.col(i*3+j) = rr.col( it.value().tris()(i,j) );
t_TriCoords *= fac;
t_GeometryDataTri.appendVertexArray(QArray<QVector3D>::fromRawData( reinterpret_cast<const QVector3D*>(t_TriCoords.data()), t_TriCoords.cols() ));
//
// Add triangles to current node
//
builder.addTriangles(t_GeometryDataTri);
//
// Colorize Surface
//
QGLMaterial *t_pMaterialROI = new QGLMaterial();
t_pMaterialROI->setColor(QColor(100,100,100,230));
index = palette->addMaterial(t_pMaterialROI);
builder.currentNode()->setMaterialIndex(index);
}
// Go one level up
builder.popNode();
}
m_bRenderPerVertex = false;
// Optimze current scene for display and calculate lightning normals
m_pSceneNode = builder.finalizedSceneNode();
m_pSceneNode->setParent(this);
}
void BrainView::genSurfacePerVertex()
{
if(m_SurfaceSet.size() == 0)
return;
if(m_pSceneNode)
{
delete m_pSceneNode;
m_pSceneNode = NULL;
}
// in the constructor construct a builder on the stack
QGLBuilder builder;
float fac = 100.0f; // too small vertices distances cause clipping errors --> 100 is a good value for freesurfer brain measures
builder << QGL::Smooth;//QGL::Faceted;
m_pSceneNodeBrain = builder.currentNode();
builder.pushNode();
//
// get bounding box
//
calcBoundingBox();
//
// Build each surface in its separate node
//
QMap<qint32, Surface>::const_iterator it = m_SurfaceSet.data().constBegin();
for (it = m_SurfaceSet.data().begin(); it != m_SurfaceSet.data().end(); ++it)
{
builder.pushNode();
{
Matrix3Xf rr = it.value().rr().transpose();
//Centralize
for(qint32 i = 0; i < 3; ++i)
rr.row(i) = rr.row(i).array() - (m_vecBoundingBoxCenter[i] + it.value().offset()[i]);
QGeometryData t_GeometryDataTri;
MatrixXf t_TriCoords = MatrixXf::Zero(3,3*(it.value().tris().rows()));
QArray<QColor4ub> cdata;
for(qint32 i = 0; i < it.value().tris().rows(); ++i)
{
for(qint32 j = 0; j < 3; ++j)
{
t_TriCoords.col(i*3+j) = rr.col( it.value().tris()(i,j) );
if(it.value().curv()[it.value().tris()(i,j)] >= 0)
cdata.append(QColor( 50, 50, 50, 230));//Sulci
else
cdata.append(QColor( 200, 200, 200, 230));//Gyri
}
}
t_TriCoords *= fac;
t_GeometryDataTri.appendVertexArray(QArray<QVector3D>::fromRawData( reinterpret_cast<const QVector3D*>(t_TriCoords.data()), t_TriCoords.cols() ));
t_GeometryDataTri.appendColorArray(cdata);
//
// Add triangles to current node
//
builder.addTriangles(t_GeometryDataTri);
}
// Go one level up
builder.popNode();
}
m_bRenderPerVertex = true;
// Optimze current scene for display and calculate lightning normals
m_pSceneNode = builder.finalizedSceneNode();
m_pSceneNode->setParent(this);
}