double compute_max_step_from_singularities(const Eigen::MatrixXd& uv,
const Eigen::MatrixXi& F,
Eigen::MatrixXd& d) {
double max_step = INFINITY;
// The if statement is outside the for loops to avoid branching/ease parallelizing
if (uv.cols() == 2) {
for (int f = 0; f < F.rows(); f++) {
double min_positive_root = get_min_pos_root_2D(uv,F,d,f);
max_step = min(max_step, min_positive_root);
}
} else { // volumetric deformation
for (int f = 0; f < F.rows(); f++) {
double min_positive_root = get_min_pos_root_3D(uv,F,d,f);
max_step = min(max_step, min_positive_root);
}
}
return max_step;
}
/*
Train the classifier with the dataset of breastcancer patients from the
LibSVM Libary
*/
void TrainSVMClassifier_BreastCancerDataSet_shouldReturnTrue()
{
/* Declarating an featurematrixdataset, the first matrix
of the matrixpair is the trainingmatrix and the second one is the testmatrix.*/
std::pair<MatrixDoubleType,MatrixDoubleType> matrixDouble;
matrixDouble = convertCSVToMatrix<double>(GetTestDataFilePath("Classification/FeaturematrixBreastcancer.csv"),';',0.5,true);
m_TrainingMatrixX = matrixDouble.first;
m_TestXPredict = matrixDouble.second;
/* The declaration of the labelmatrixdataset is equivalent to the declaration
of the featurematrixdataset.*/
std::pair<MatrixIntType,MatrixIntType> matrixInt;
matrixInt = convertCSVToMatrix<int>(GetTestDataFilePath("Classification/LabelmatrixBreastcancer.csv"),';',0.5,false);
m_TrainingLabelMatrixY = matrixInt.first;
m_TestYPredict = matrixInt.second;
/* Setting of the SVM-Parameters*/
classifier = mitk::LibSVMClassifier::New();
classifier->SetGamma(1/(double)(m_TrainingMatrixX.cols()));
classifier->SetSvmType(0);
classifier->SetKernelType(2);
/* Train the classifier, by giving trainingdataset for the labels and features.
The result in an colunmvector of the labels.*/
classifier->Train(m_TrainingMatrixX,m_TrainingLabelMatrixY);
Eigen::MatrixXi classes = classifier->Predict(m_TestXPredict);
/* Testing the matching between the calculated colunmvector and the result
of the SVM */
unsigned int maxrows = classes.rows();
bool isYPredictVector = false;
int count = 0;
for(int i= 0; i < maxrows; i++){
if(classes(i,0) == m_TestYPredict(i,0)){
isYPredictVector = true;
count++;
}
}
MITK_INFO << 100*count/(double)(maxrows) << "%";
MITK_TEST_CONDITION(isIntervall<int>(m_TestYPredict,classes,75,100),"Testvalue is in range.");
}
bool BlockSparseMatrix::ConjugateGradientSolve(const Eigen::MatrixXd& rhs, Eigen::MatrixXd& sol)
{
return LltSolve(rhs, sol);
MatrixSolver* solver = new PCGSolver();
int numRows = rhs.rows();
int numCols = rhs.cols();
int num = numRows * numCols;
double* result = new double[num];
double* rhsData = new double[num];
int ithElem = 0;
for (int i = 0; i < numCols; ++i)
{
for (int j = 0; j < numRows; ++j)
{
rhsData[ithElem++] = rhs(j, i);
}
}
if (mbCSRDirty)
{
mCSREquivalent.ConvertFromBlockSparseMatrix(*this);
mbCSRDirty = false;
}
solver->SetMatrix(&mCSREquivalent);
solver->SetRHS(rhsData, numCols);
solver->Solve(result, true);
sol = Eigen::MatrixXd::Zero(numRows, numCols);
ithElem = 0;
for (int i = 0; i < numCols; ++i)
{
for (int j = 0; j < numRows; ++j)
{
sol(j, i) = result[ithElem++];
}
}
delete[] rhsData;
delete[] result;
delete solver;
return true;
}
// Derived from code by Yohann Solaro ( http://listengine.tuxfamily.org/lists.tuxfamily.org/eigen/2010/01/msg00187.html )
// see : http://en.wikipedia.org/wiki/Moore-Penrose_pseudoinverse#The_general_case_and_the_SVD_method
Eigen::MatrixXd pinv( const Eigen::MatrixXd &b, double rcond )
{
// TODO: Figure out why it wants fewer rows than columns
// if ( a.rows()<a.cols() )
// return false;
bool flip = false;
Eigen::MatrixXd a;
if( a.rows() < a.cols() )
{
a = b.transpose();
flip = true;
}
else
a = b;
// SVD
Eigen::JacobiSVD<Eigen::MatrixXd> svdA;
svdA.compute( a, Eigen::ComputeFullU | Eigen::ComputeThinV );
Eigen::JacobiSVD<Eigen::MatrixXd>::SingularValuesType vSingular = svdA.singularValues();
// Build a diagonal matrix with the Inverted Singular values
// The pseudo inverted singular matrix is easy to compute :
// is formed by replacing every nonzero entry by its reciprocal (inversing).
Eigen::VectorXd vPseudoInvertedSingular( svdA.matrixV().cols() );
for (int iRow=0; iRow<vSingular.rows(); iRow++)
{
if ( fabs(vSingular(iRow)) <= rcond )
{
vPseudoInvertedSingular(iRow)=0.;
}
else
vPseudoInvertedSingular(iRow)=1./vSingular(iRow);
}
// A little optimization here
Eigen::MatrixXd mAdjointU = svdA.matrixU().adjoint().block( 0, 0, vSingular.rows(), svdA.matrixU().adjoint().cols() );
// Pseudo-Inversion : V * S * U'
Eigen::MatrixXd a_pinv = (svdA.matrixV() * vPseudoInvertedSingular.asDiagonal()) * mAdjointU;
if( flip )
{
a = a.transpose();
a_pinv = a_pinv.transpose();
}
return a_pinv;
}
IGL_INLINE void igl::n_polyvector_general(const Eigen::MatrixXd &V,
const Eigen::MatrixXi &F,
const Eigen::VectorXi& b,
const Eigen::MatrixXd& bc,
const Eigen::VectorXi &I,
Eigen::MatrixXd &output)
{
Eigen::VectorXi isConstrained = Eigen::VectorXi::Constant(F.rows(),0);
Eigen::MatrixXd cfW = Eigen::MatrixXd::Constant(F.rows(),bc.cols(),0);
for(unsigned i=0; i<b.size();++i)
{
isConstrained(b(i)) = 1;
cfW.row(b(i)) << bc.row(i);
}
int n = I.rows();
igl::GeneralPolyVectorFieldFinder<Eigen::MatrixXd, Eigen::MatrixXi> pvff(V,F,n);
pvff.solve(isConstrained, cfW, I, output);
}
//! Function to read the amplitudes and fundamental argument multiplers for tidal corrections
std::pair< Eigen::MatrixXd, Eigen::MatrixXd > readAmplitudesAndFundamentalArgumentMultipliers(
const std::string amplitudesFile,
const std::string fundamentalArgumentMultipliersFile,
const double minimumAmplitude )
{
// Read amplitudes and fundamental argument multipliers into matrices.
Eigen::MatrixXd amplitudesRaw = input_output::readMatrixFromFile( amplitudesFile );
Eigen::MatrixXd fundamentalArgumentMultipliersRaw = input_output::readMatrixFromFile( fundamentalArgumentMultipliersFile );
// Check whether amplitudes and fundamental argument multipliers matrices have same number of rows
if( amplitudesRaw.rows( ) != fundamentalArgumentMultipliersRaw.rows( ) )
{
throw std::runtime_error( "Amplitude and argument multipler files contain unequal set of entries" );
}
// Check whether number of columns in fundamental argument multiplier matrix is equal to 6.
if( fundamentalArgumentMultipliersRaw.cols( ) != 6 )
{
throw std::runtime_error( "Number of columns in fundamental argument multipler matrix not equal to 6" );
}
// If acceptance amplitude is larger than 0.0 check RSS of amplitudes for each entry.
Eigen::MatrixXd fundamentalArgumentMultipliers, amplitudes;
if( minimumAmplitude > 0.0 )
{
// Filter raw data and remove entries with RSS amplitude that is too low
std::pair< Eigen::MatrixXd, Eigen::MatrixXd > filteredData =
filterRawDataForAmplitudes( fundamentalArgumentMultipliersRaw, amplitudesRaw, minimumAmplitude );
amplitudes = filteredData.first;
fundamentalArgumentMultipliers = filteredData.second;
}
// If all amplitudes are to be expected, raw data is same as return data.
else
{
amplitudes = amplitudesRaw;
fundamentalArgumentMultipliers = fundamentalArgumentMultipliersRaw;
}
// return amplitudes and fundamental argument multipliers.
return std::pair< Eigen::MatrixXd, Eigen::MatrixXd >( amplitudes, fundamentalArgumentMultipliers );
}
void RBMTestCase::inputGradient()
{
OpenANN::OutputInfo info;
info.dimensions.push_back(3);
OpenANN::RBM layer(3, 2, 1, 0.01, 0.0, true);
LayerAdapter opt(layer, info);
Eigen::MatrixXd X = Eigen::MatrixXd::Random(2, 3);
Eigen::MatrixXd Y = Eigen::MatrixXd::Random(2, 2);
opt.trainingSet(X, Y);
Eigen::MatrixXd gradient = opt.inputGradient();
ASSERT_EQUALS(gradient.rows(), 2);
Eigen::MatrixXd estimatedGradient = OpenANN::FiniteDifferences::
inputGradient(X, Y, opt);
ASSERT_EQUALS(estimatedGradient.rows(), 2);
for(int j = 0; j < gradient.rows(); j++)
for(int i = 0; i < gradient.cols(); i++)
ASSERT_EQUALS_DELTA(gradient(j, i), estimatedGradient(j, i), 1e-10);
}
//------------------------------------------------------------------------------
void LocalAssembler::assemble_exterior_facet(Eigen::MatrixXd& A,
UFC& ufc,
const std::vector<double>& vertex_coordinates,
const ufc::cell& ufc_cell,
const Cell& cell,
const Facet& facet,
const std::size_t local_facet,
const MeshFunction<std::size_t>* domains)
{
// Skip if there are no exterior facet integrals
if (!ufc.form.has_exterior_facet_integrals())
return;
// Extract default exterior facet integral
ufc::exterior_facet_integral* integral
= ufc.default_exterior_facet_integral.get();
// Get integral for sub domain (if any)
if (domains && !domains->empty())
integral = ufc.get_exterior_facet_integral((*domains)[facet]);
// Skip integral if zero
if (!integral)
return;
// Update to current cell
ufc.update(cell, vertex_coordinates, ufc_cell,
integral->enabled_coefficients());
// Tabulate exterior facet tensor
integral->tabulate_tensor(ufc.A.data(),
ufc.w(),
vertex_coordinates.data(),
local_facet,
ufc_cell.orientation);
// Stuff a_ufc.A into A
const std::size_t M = A.rows();
const std::size_t N = A.cols();
for (std::size_t i = 0; i < M; i++)
for (std::size_t j = 0; j < N; j++)
A(i, j) += ufc.A[N*i + j];
}
void BranchList::smoothBranchPositions()
{
for (int i = 0; i < mBranches.size(); i++)
{
Eigen::MatrixXd positions = mBranches[i]->getPositions();
int numberOfInputPoints = positions.cols();
int controlPointFactor = 5;
int numberOfControlPoints = numberOfInputPoints / controlPointFactor;
vtkCardinalSplinePtr splineX = vtkSmartPointer<vtkCardinalSpline>::New();
vtkCardinalSplinePtr splineY = vtkSmartPointer<vtkCardinalSpline>::New();
vtkCardinalSplinePtr splineZ = vtkSmartPointer<vtkCardinalSpline>::New();
if (numberOfControlPoints >= 2)
{
//add control points to spline
for(int j=0; j<numberOfControlPoints; j++)
{
int indexP = (j*numberOfInputPoints)/numberOfControlPoints;
splineX->AddPoint(indexP,positions(0,indexP));
splineY->AddPoint(indexP,positions(1,indexP));
splineZ->AddPoint(indexP,positions(2,indexP));
}
//Always add the last point to complete spline
splineX->AddPoint(numberOfInputPoints-1,positions(0,numberOfInputPoints-1));
splineY->AddPoint(numberOfInputPoints-1,positions(1,numberOfInputPoints-1));
splineZ->AddPoint(numberOfInputPoints-1,positions(2,numberOfInputPoints-1));
//evaluate spline - get smoothed positions
Eigen::MatrixXd smoothingResult(3 , numberOfInputPoints);
for(int j=0; j<numberOfInputPoints; j++)
{
double splineParameter = j;
smoothingResult(0,j) = splineX->Evaluate(splineParameter);
smoothingResult(1,j) = splineY->Evaluate(splineParameter);
smoothingResult(2,j) = splineZ->Evaluate(splineParameter);
}
mBranches[i]->setPositions(smoothingResult);
}
}
}
//! Initialize atmosphere table reader.
void TabulatedAtmosphere::initialize( const std::string& atmosphereTableFile )
{
// Locally store the atmosphere table file name.
atmosphereTableFile_ = atmosphereTableFile;
Eigen::MatrixXd containerOfAtmosphereTableFileData
= input_output::readMatrixFromFile( atmosphereTableFile_, " \t", "%" );
// Check whether data is present in the file.
if ( containerOfAtmosphereTableFileData.rows( ) < 1
|| containerOfAtmosphereTableFileData.cols( ) < 1 )
{
std::cerr << "The atmosphere table file is empty." << std::endl;
std::cerr << atmosphereTableFile_ << std::endl;
}
// Initialize vectors.
altitudeData_.resize( containerOfAtmosphereTableFileData.rows( ) );
densityData_.resize( containerOfAtmosphereTableFileData.rows( ) );
pressureData_.resize( containerOfAtmosphereTableFileData.rows( ) );
temperatureData_.resize( containerOfAtmosphereTableFileData.rows( ) );
// Loop through all the strings stored in the container and store the data
// in the right Eigen::VectorXd.
for ( int i = 0; i < containerOfAtmosphereTableFileData.rows( ); i++ )
{
altitudeData_[ i ] = containerOfAtmosphereTableFileData( i, 0 );
densityData_[ i ] = containerOfAtmosphereTableFileData( i, 1 );
pressureData_[ i ] = containerOfAtmosphereTableFileData( i, 2 );
temperatureData_[ i ] = containerOfAtmosphereTableFileData( i, 3 );
}
using namespace interpolators;
cubicSplineInterpolationForDensity_
= boost::make_shared< CubicSplineInterpolatorDouble >( altitudeData_, densityData_ );
cubicSplineInterpolationForPressure_
= boost::make_shared< CubicSplineInterpolatorDouble >( altitudeData_, pressureData_ );
cubicSplineInterpolationForTemperature_
= boost::make_shared< CubicSplineInterpolatorDouble >(
altitudeData_, temperatureData_ );
}
bool pre_draw(igl::opengl::glfw::Viewer & viewer)
{
using namespace Eigen;
using namespace std;
if(viewer.core.is_animating)
{
// Interpolate pose and identity
RotationList anim_pose(pose.size());
for(int e = 0;e<pose.size();e++)
{
anim_pose[e] = pose[e].slerp(anim_t,Quaterniond::Identity());
}
// Propagate relative rotations via FK to retrieve absolute transformations
RotationList vQ;
vector<Vector3d> vT;
igl::forward_kinematics(C,BE,P,anim_pose,vQ,vT);
const int dim = C.cols();
MatrixXd T(BE.rows()*(dim+1),dim);
for(int e = 0;e<BE.rows();e++)
{
Affine3d a = Affine3d::Identity();
a.translate(vT[e]);
a.rotate(vQ[e]);
T.block(e*(dim+1),0,dim+1,dim) =
a.matrix().transpose().block(0,0,dim+1,dim);
}
// Compute deformation via LBS as matrix multiplication
U = M*T;
// Also deform skeleton edges
MatrixXd CT;
MatrixXi BET;
igl::deform_skeleton(C,BE,T,CT,BET);
viewer.data().set_vertices(U);
viewer.data().set_edges(CT,BET,sea_green);
viewer.data().compute_normals();
anim_t += anim_t_dir;
anim_t_dir *= (anim_t>=1.0 || anim_t<=0.0?-1.0:1.0);
}
return false;
}
IGL_INLINE void igl::ViewerData::add_points(const Eigen::MatrixXd& P, const Eigen::MatrixXd& C)
{
Eigen::MatrixXd P_temp;
// If P only has two columns, pad with a column of zeros
if (P.cols() == 2)
{
P_temp = Eigen::MatrixXd::Zero(P.rows(),3);
P_temp.block(0,0,P.rows(),2) = P;
}
else
P_temp = P;
int lastid = points.rows();
points.conservativeResize(points.rows() + P_temp.rows(),6);
for (unsigned i=0; i<P_temp.rows(); ++i)
points.row(lastid+i) << P_temp.row(i), i<C.rows() ? C.row(i) : C.row(C.rows()-1);
dirty |= DIRTY_OVERLAY_POINTS;
}
// Trying to assign from matrix to noOfPoints
void mitk::LibSVMClassifier::ReadXValues(LibSVM::svm_problem * problem, LibSVM::svm_node** xSpace, const Eigen::MatrixXd &X)
{
auto noOfPoints = static_cast<int>(X.rows());
auto features = static_cast<int>(X.cols());
problem->x = static_cast<LibSVM::svm_node **>(malloc(sizeof(LibSVM::svm_node *) * noOfPoints));
(*xSpace) = static_cast<LibSVM::svm_node *> (malloc(sizeof(LibSVM::svm_node) * noOfPoints * (features+1)));
for (int row = 0; row < noOfPoints; ++row)
{
for (int col = 0; col < features; ++col)
{
(*xSpace)[row*features + col].index = col;
(*xSpace)[row*features + col].value = X(row,col);
}
(*xSpace)[row*features + features].index = -1;
problem->x[row] = &((*xSpace)[row*features]);
}
}
bool init_weights(
const Eigen::MatrixXd & V,
const Eigen::MatrixXi & F,
const Eigen::MatrixXd & C,
const Eigen::MatrixXi & BE,
Eigen::MatrixXd & W)
{
using namespace igl;
using namespace Eigen;
// Mesh with samples on skeleton
// New vertices of tet mesh, V prefaces VV
MatrixXd VV;
MatrixXi TT,FF,CE;
VectorXi P;
if(!mesh_with_skeleton(V,F,C,P,BE,CE,10,VV,TT,FF))
{
return false;
}
// List of boundary indices (aka fixed value indices into VV)
VectorXi b;
// List of boundary conditions of each weight function
MatrixXd bc;
if(!boundary_conditions(VV,TT,C,P,BE,CE,b,bc))
{
return false;
}
// compute BBW
// Default bbw data and flags
BBWData bbw_data;
bbw_data.active_set_params.max_iter = 4;
// Weights matrix
if(!bbw(VV,TT,b,bc,bbw_data,W))
{
return false;
}
// Normalize weights to sum to one
normalize_row_sums(W,W);
W.conservativeResize(V.rows(),W.cols());
return true;
}
double accuracy( const Eigen::MatrixXd& X, const Eigen::VectorXd& y, const Eigen::VectorXd& theta ) {
const unsigned N = X.rows(), K = X.cols();
// Eigen:::VectorXd p;
// p.resize(N, 0); p.setZero();
double correct = 0.0;
Eigen::VectorXd xtheta = X*theta;
Eigen::VectorXd predicted;
maths::Sigmoid()( predicted, xtheta );
std::cout << predicted << std::endl;
for ( size_t i = 0; i < N; ++i ) {
int p = predicted[i]> 0.5 ? 1 : 0;
// printf("%d, %d, %f\n", )
if ( p == y(i,0) ) ++correct;
}
return correct / N;
}
void setMatrix(PETScMatrix& m, Eigen::MatrixXd const& tmp)
{
using IndexType = PETScMatrix::IndexType;
auto const rows = tmp.rows();
auto const cols = tmp.cols();
assert(rows == m.getNumberOfRows() && cols == m.getNumberOfColumns());
m.setZero();
std::vector<IndexType> row_idcs(rows);
std::vector<IndexType> col_idcs(cols);
std::iota(row_idcs.begin(), row_idcs.end(), 0);
std::iota(col_idcs.begin(), col_idcs.end(), 0);
// PETSc wants row-major
Eigen::Matrix<double, Eigen::Dynamic, Eigen::Dynamic, Eigen::RowMajor> tmp_ = tmp;
m.add(row_idcs, col_idcs, tmp_);
}
double computePlaneToPlaneHomographyError(
const Eigen::MatrixXd &points1,
const Eigen::MatrixXd &points2,
const Eigen::MatrixXd &H,
Eigen::VectorXd &error
)
{
double sum = 0;
unsigned int nPoints = points1.cols();
error.resize( nPoints );
for( unsigned int i = 0; i < nPoints; i++ )
{
Eigen::Vector3d p1 = H * points1.col(i).homogeneous();
Eigen::Vector3d p2 = points2.col(i).homogeneous();
p1 /= p1[2];
double err = (p1 - p2).norm();
sum += error[i] = err * err;
}
return sum / double( nPoints );
}
void PCATestCase::dimensionalityReduction()
{
OpenANN::RandomNumberGenerator rng;
const int N = 100;
const int D = 5;
Eigen::MatrixXd X(N, D);
rng.fillNormalDistribution(X);
// Strong correlation
Eigen::MatrixXd A = Eigen::MatrixXd::Identity(D, D) * 0.5 +
Eigen::MatrixXd::Ones(D, D);
Eigen::MatrixXd Xt = X * A.transpose();
// Dimensionality reduction
OpenANN::PCA pca(1);
pca.fit(Xt);
Eigen::MatrixXd Y = pca.transform(Xt);
ASSERT_EQUALS(Y.rows(), N);
ASSERT_EQUALS(Y.cols(), 1);
ASSERT_EQUALS(pca.explainedVarianceRatio().rows(), 1);
ASSERT(pca.explainedVarianceRatio().sum() > 0.9);
}
//==============================================================================
Eigen::VectorXd Spline::evaluatePolynomial(
const Eigen::MatrixXd& _coefficients, double _t, int _derivative)
{
const auto numOutputs = _coefficients.rows();
const auto numCoeffs = _coefficients.cols();
const auto timeVector
= common::SplineProblem<>::createTimeVector(_t, _derivative, numCoeffs);
const auto derivativeMatrix
= common::SplineProblem<>::createCoefficientMatrix(numCoeffs);
const auto derivativeVector = derivativeMatrix.row(_derivative);
const auto evaluationVector
= derivativeVector.cwiseProduct(timeVector.transpose());
Eigen::VectorXd outputVector(numOutputs);
for (int ioutput = 0; ioutput < numOutputs; ++ioutput)
outputVector[ioutput] = _coefficients.row(ioutput).dot(evaluationVector);
return outputVector;
}
Eigen::VectorXd BicZ_j_cpp(Eigen::MatrixXd X,Eigen::MatrixXd Z,Eigen::VectorXd Bic_vide_vect,Eigen::VectorXd BicOld,double methode,int j)
{
int size=X.cols();
int sizerow = X.rows();
Eigen::VectorXd BicRes(size);
Eigen::MatrixXd mat_var_a_droite;
int k;
//debut de la boucle colonne de Z
BicRes=BicOld;
//colonne de Z sur laquelle on va travailler (variable a gauche)
Eigen::VectorXd colZ=Z.block(0,j,size,1);
int newsize=colZ.sum();
//si la somme de la colonne=0 alors on appelle mixmod
if(newsize==0)
{
BicRes(j)=Bic_vide_vect(j);
}
else
{
//calcul du nouveau BIC
mat_var_a_droite.resize(sizerow,newsize);
k=0;
//on echerche l'emplacement des 1 dans le vecteur colonne (variables a droite)
for(int p=0;p<size;p++)
{
if (colZ(p)==1)
{
//on regroupe les variables a droite dans une matrice
mat_var_a_droite.block(0,k,sizerow,1)=X.block(0,p,sizerow,1);
k=k+1;
}//fin if
}//fin for j
//calcul de son BIC en appellant OLS (les parametres sont : Y=X[,colonne],X=X[,matrice des variables à droite])
BicRes(j)=BicLoc_cpp(mat_var_a_droite,X.block(0,j,sizerow,1),"T",methode);
}//fin else
return BicRes;
}
// Helpers that draws the most common meshes
IGL_INLINE void igl::ViewerData::set_mesh(const Eigen::MatrixXd& _V, const Eigen::MatrixXi& _F)
{
using namespace std;
Eigen::MatrixXd V_temp;
// If V only has two columns, pad with a column of zeros
if (_V.cols() == 2)
{
V_temp = Eigen::MatrixXd::Zero(_V.rows(),3);
V_temp.block(0,0,_V.rows(),2) = _V;
}
else
V_temp = _V;
if (V.rows() == 0 && F.rows() == 0)
{
clear();
V = V_temp;
F = _F;
compute_normals();
uniform_colors(Eigen::Vector3d(51.0/255.0,43.0/255.0,33.3/255.0),
Eigen::Vector3d(255.0/255.0,228.0/255.0,58.0/255.0),
Eigen::Vector3d(255.0/255.0,235.0/255.0,80.0/255.0));
grid_texture();
}
else
{
if (_V.rows() == V.rows() && _F.rows() == F.rows())
{
V = V_temp;
F = _F;
}
else
cerr << "ERROR (set_mesh): The new mesh has a different number of vertices/faces. Please clear the mesh before plotting.";
}
dirty |= DIRTY_FACE | DIRTY_POSITION;
}
void ODELCPSolver::transferToODEFormulation(const Eigen::MatrixXd& _A,
const Eigen::VectorXd& _b,
Eigen::MatrixXd* _AOut,
Eigen::VectorXd* _bOut,
int _numDir,
int _numContacts) {
int numOtherConstrs = _A.rows() - _numContacts * (2 + _numDir);
int n = _numContacts * 3 + numOtherConstrs;
Eigen::MatrixXd AIntermediate = Eigen::MatrixXd::Zero(n, _A.cols());
*_AOut = Eigen::MatrixXd::Zero(n, n);
*_bOut = Eigen::VectorXd::Zero(n);
int offset = _numDir / 4;
for (int i = 0; i < _numContacts; ++i) {
AIntermediate.row(i) = _A.row(i);
(*_bOut)[i] = _b[i];
AIntermediate.row(_numContacts + i * 2 + 0) =
_A.row(_numContacts + i * _numDir + 0);
AIntermediate.row(_numContacts + i * 2 + 1) =
_A.row(_numContacts + i * _numDir + offset);
(*_bOut)[_numContacts + i * 2 + 0] = _b[_numContacts + i * _numDir + 0];
(*_bOut)[_numContacts + i * 2 + 1] = _b[_numContacts + i * _numDir
+ offset];
}
for (int i = 0; i < numOtherConstrs; i++) {
AIntermediate.row(_numContacts * 3 + i) =
_A.row(_numContacts * (_numDir + 2) + i);
(*_bOut)[_numContacts * 3 + i] = _b[_numContacts * (_numDir + 2) + i];
}
for (int i = 0; i < _numContacts; ++i) {
_AOut->col(i) = AIntermediate.col(i);
_AOut->col(_numContacts + i * 2 + 0) =
AIntermediate.col(_numContacts + i * _numDir + 0);
_AOut->col(_numContacts + i * 2 + 1) =
AIntermediate.col(_numContacts + i * _numDir + offset);
}
for (int i = 0; i < numOtherConstrs; i++)
_AOut->col(_numContacts * 3 + i) =
AIntermediate.col(_numContacts * (_numDir + 2) + i);
}
void evaluateSVDSPQRSolver(const Eigen::MatrixXd& A, const Eigen::VectorXd& b,
const Eigen::VectorXd& x, double tol = 1e-9) {
cholmod_common cholmod;
cholmod_l_start(&cholmod);
cholmod_sparse* A_CS = aslam::calibration::eigenDenseToCholmodSparseCopy(A,
&cholmod);
cholmod_dense b_CD;
aslam::calibration::eigenDenseToCholmodDenseView(b, &b_CD);
Eigen::VectorXd x_est;
aslam::calibration::LinearSolver linearSolver;
for (std::ptrdiff_t i = 1; i < A.cols(); ++i) {
// double before = aslam::calibration::Timestamp::now();
linearSolver.solve(A_CS, &b_CD, i, x_est);
// double after = aslam::calibration::Timestamp::now();
double error = (b - A * x_est).norm();
// std::cout << std::fixed << std::setprecision(18) << "noscale: " << "error: "
// << error << " est_diff: " << (x - x_est).norm() << " time: "
// << after - before << std::endl;
ASSERT_NEAR(error, 0, tol);
linearSolver.getOptions().columnScaling = true;
// before = aslam::calibration::Timestamp::now();
linearSolver.solve(A_CS, &b_CD, i, x_est);
// after = aslam::calibration::Timestamp::now();
error = (b - A * x_est).norm();
// std::cout << std::fixed << std::setprecision(18) << "onscale: " << "error: "
// << error << " est_diff: " << (x - x_est).norm() << " time: "
// << after - before << std::endl;
linearSolver.getOptions().columnScaling = false;
ASSERT_NEAR(error, 0, tol);
// std::cout << "SVD rank: " << linearSolver.getSVDRank() << std::endl;
// std::cout << "SVD rank deficiency: " << linearSolver.getSVDRankDeficiency()
// << std::endl;
// std::cout << "QR rank: " << linearSolver.getQRRank() << std::endl;
// std::cout << "QR rank deficiency: "
// << linearSolver.getQRRankDeficiency() << std::endl;
// std::cout << "SV gap: " << linearSolver.getSvGap() << std::endl;
}
cholmod_l_free_sparse(&A_CS, &cholmod);
cholmod_l_finish(&cholmod);
}
Evrot::Evrot(Eigen::MatrixXd& X, int method):
mMethod(method),
mNumDims(X.cols()),
mNumData(X.rows()),
mNumAngles((int)(mNumDims*(mNumDims-1)/2)), // get the number of angles
ik(Eigen::VectorXi(mNumAngles)),
jk(Eigen::VectorXi(mNumAngles)),
mX(X),
mClusters(std::vector<std::vector<int> >(mNumDims)) //allocate clusters vector
{
// build index mapping (to index upper triangle)
int k = 0;
for( int i=0; i<mNumDims-1; i++ ){
for( int j=i+1; j<=mNumDims-1; j++ ){
ik[k] = i;
jk[k] = j;
k++;
}
}
evrot();
}
IGL_INLINE void igl::ViewerData::set_edges(
const Eigen::MatrixXd& P,
const Eigen::MatrixXi& E,
const Eigen::MatrixXd& C)
{
using namespace Eigen;
lines.resize(E.rows(),9);
assert(C.cols() == 3);
for(int e = 0;e<E.rows();e++)
{
RowVector3d color;
if(C.size() == 3)
{
color<<C;
}else if(C.rows() == E.rows())
{
color<<C.row(e);
}
lines.row(e)<< P.row(E(e,0)), P.row(E(e,1)), color;
}
dirty |= DIRTY_OVERLAY_LINES;
}
std::tuple<Eigen::MatrixXd, Eigen::MatrixXd>
lu_no_pivoting(const Eigen::MatrixXd & A)
{
Eigen::MatrixXd Acopy = A;
int n = Acopy.rows();
assert(n == Acopy.cols());
Eigen::MatrixXd L(n,n);
Eigen::MatrixXd U(n,n);
L.triangularView<Eigen::StrictlyUpper>().setZero();
U.triangularView<Eigen::StrictlyLower>().setZero();
for (int k=0; k<n-1; k++) {
lu_helper(k, n, &Acopy, &L, &U);
}
L(n-1,n-1) = 1;
U(n-1,n-1) = Acopy(n-1,n-1);
return std::make_tuple(L,U);
}
void MassRegistration::show(std::vector<Eigen::MatrixXd> Xv, bool save, std::string filename, bool stop){
viewer->removeAllPointClouds();
srand(0);
for(unsigned int xi = 0; xi < Xv.size(); xi++){
Eigen::MatrixXd X = Xv[xi];
pcl::PointCloud<pcl::PointXYZRGBNormal>::Ptr cloud (new pcl::PointCloud<pcl::PointXYZRGBNormal>);
int r = 256*(1+(rand()%4))/4 - 1;//255*((xi+1) & 1);
int g = 256*(1+(rand()%4))/4 - 1;//255*((xi+1) & 1);
int b = 256*(1+(rand()%4))/4 - 1;//255*(xi & 1);
unsigned int nr_data = X.cols();
cloud->points.clear();
for(unsigned int i = 0; i < nr_data; i++){
pcl::PointXYZRGBNormal p;
p.x = X(0,i);
p.y = X(1,i);
p.z = X(2,i);
p.b = r;
p.g = g;
p.r = b;
cloud->points.push_back(p);
}
char buf [1024];
sprintf(buf,"cloud%i",xi);
viewer->addPointCloud<pcl::PointXYZRGBNormal> (cloud, pcl::visualization::PointCloudColorHandlerRGBField<pcl::PointXYZRGBNormal>(cloud), buf);
}
if(!save){
viewer->spin();
}else{
viewer->spinOnce();
}
//void pcl::visualization::PCLVisualizerInteractorStyle::saveScreenshot ( const std::string & file )
if(save){
printf("saving: %s\n",filename.c_str());
viewer->saveScreenshot(filename);
}
viewer->removeAllPointClouds();
}
Balloon::Balloon(double r, double dt, Eigen::MatrixXd positions, Eigen::MatrixXi faces)
:
ParticleObject(r)
{
m_radius = r;
m_step = dt;
m_positions = positions;
m_speeds = Eigen::MatrixXd::Zero(positions.rows(), positions.cols());
m_forces = Eigen::MatrixXd::Zero(m_positions.rows(), m_positions.cols());
m_num_point = m_positions.rows();
m_mass = m_mass_all / (double)m_num_point;
c = 2.0*sqrt(m_mass*k)/3.0;
m_faces = faces;
m_faceactive = Eigen::VectorXi::Zero(m_faces.rows());
for(int i=0; i<m_faceactive.rows(); i++)
{
m_faceactive(i) = 1;
}
igl::adjacency_list(m_faces, m_adjacency_list);
igl::triangle_triangle_adjacency(m_positions, m_faces, m_facetoface);
std::vector<std::vector<int>> tmp_list;
igl::vertex_triangle_adjacency(m_positions, m_faces, m_vertextoface, tmp_list);
initEdges();
computeNormals();
calcAveRadius();
m_threshold_ratio = Eigen::VectorXd::Ones(m_edges.rows()) * threshold_ratio;
// for(int i=0; i<m_positions.rows(); i++){
// // std::cout << "adjacent to " << i << ": " << m_adjacency_list[i].size() << std::endl;
// }
// for(int i=0; i<m_positions.rows(); i++){
// // std::cout << "normal " << i << ": " << m_normals.norm() << std::endl;
// }
}
QPair<Eigen::MatrixXd, QList<int> > Epidetect::prepareData(Eigen::MatrixXd mat)
{
MatrixXd trimmedMatrix;
QList<int> stimLocations;
QStringList badChs = m_pFiffInfo->bads;
QStringList chNames = m_pFiffInfo->ch_names;
trimmedMatrix.resize(mat.rows()- badChs.size(), mat.cols());
int j = 0;
for (int i=0 ; i < mat.rows(); i++)
{
QString type = m_pFiffInfo->channel_type(i);
if (type == "stim")
stimLocations << i;
if (!(badChs.contains(chNames[i])))
{
if ((type != "stim") && (type != "ecg") && (type != "eeg"))
{
trimmedMatrix.row(j) = mat.row(i);
j++;
}
}
}
qSort(stimLocations);
trimmedMatrix.conservativeResize(j,trimmedMatrix.cols());
QPair<MatrixXd, QList<int> > out;
out.first = trimmedMatrix;
out.second = stimLocations;
return out;
}
//==============================================================================
void Spline::addSegment(
const Eigen::MatrixXd& _coefficients,
double _duration,
const statespace::StateSpace::State* _startState)
{
if (_duration <= 0.)
throw std::invalid_argument("Duration must be positive.");
if (static_cast<std::size_t>(_coefficients.rows())
!= mStateSpace->getDimension())
throw std::invalid_argument("Incorrect number of dimensions.");
if (_coefficients.cols() < 1)
throw std::invalid_argument("At least one coefficient is required.");
PolynomialSegment segment;
segment.mCoefficients = _coefficients;
segment.mDuration = _duration;
segment.mStartState = mStateSpace->allocateState();
mStateSpace->copyState(_startState, segment.mStartState);
mSegments.emplace_back(std::move(segment));
}