/**
* Generates an artificial topographyGrid of size numRows x numCols if no
* topographic data is available. Results are dumped into topographyGrid.
* @param topographyGrid A pointer to a zero-initialized Grid of size
* numRows x numCols.
* @param numRows The desired number of non-border rows in the resulting matrix.
* @param numCols The desired number of non-border cols in the resulting matrix.
*/
void simulatetopographyGrid(Grid* topographyGrid, int numRows, int numCols) {
Eigen::VectorXd refx = refx.LinSpaced(numCols, -2*M_PI, 2*M_PI);
Eigen::VectorXd refy = refx.LinSpaced(numRows, -2*M_PI, 2*M_PI);
Eigen::MatrixXd X = refx.replicate(1, numRows);
X.transposeInPlace();
Eigen::MatrixXd Y = refy.replicate(1, numCols);
// Eigen can only deal with two matrices at a time,
// so split the computation:
// topographyGrid = sin(X) * sin(Y) * abs(X) * abs(Y) -pi
Eigen::MatrixXd absXY = X.cwiseAbs().cwiseProduct(Y.cwiseAbs());
Eigen::MatrixXd sins = X.array().sin().cwiseProduct(Y.array().sin());
Eigen::MatrixXd temp;
temp.resize(numRows, numCols);
temp = absXY.cwiseProduct(sins);
// All this work to create a matrix of pi...
Eigen::MatrixXd pi;
pi.resize(numRows, numCols);
pi.setConstant(M_PI);
temp = temp - pi;
// And the final result.
topographyGrid->data.block(border, border, numRows, numCols) =
temp.block(0, 0, numRows, numCols);
// Ignore positive values.
topographyGrid->data =
topographyGrid->data.unaryExpr(std::ptr_fun(validateDepth));
topographyGrid->clearNA();
}
TEST(decimate,hemisphere)
{
// Load a hemisphere centered at the origin. For each original vertex compute
// its "perfect normal" (i.e., its position treated as unit vectors).
// Decimate the model and using the birth indices of the output vertices grab
// their original "perfect normals" and compare them to their current
// positions treated as unit vectors. If vertices have not moved much, then
// these should be similar (mostly this is checking if the birth indices are
// sane).
Eigen::MatrixXd V,U;
Eigen::MatrixXi F,G;
Eigen::VectorXi J,I;
// Load example mesh: GetParam() will be name of mesh file
test_common::load_mesh("hemisphere.obj", V, F);
// Perfect normals from positions
Eigen::MatrixXd NV = V.rowwise().normalized();
// Remove half of the faces
igl::decimate(V,F,F.rows()/2,U,G,J,I);
// Expect that all normals still point in same direction as original
Eigen::MatrixXd NU = U.rowwise().normalized();
Eigen::MatrixXd NVI;
igl::slice(NV,I,1,NVI);
ASSERT_EQ(NVI.rows(),NU.rows());
ASSERT_EQ(NVI.cols(),NU.cols());
// Dot product
Eigen::VectorXd D = (NU.array()*NVI.array()).rowwise().sum();
Eigen::VectorXd O = Eigen::VectorXd::Ones(D.rows());
// 0.2 chosen to succeed on 256 face hemisphere.obj reduced to 128 faces
test_common::assert_near(D,O,0.02);
}
/*Predicts where the tracked bounding box will be in the next frame*/
Eigen::Vector4d bb_predict(Eigen::VectorXd const & bb0,
Eigen::MatrixXd const & pt0, Eigen::MatrixXd const & pt1) {
Eigen::MatrixXd of(pt1.rows(), pt1.cols());
of = pt1.array() - pt0.array();
double dx = median(of.row(0));
double dy = median(of.row(1));
unsigned int matCols = pt0.cols(), pos = 0, len = (matCols * (matCols - 1))
/ 2;
Eigen::RowVectorXd d1(len);
Eigen::RowVectorXd d2(len);
//calculate euclidean distance
for (unsigned int h = 0; h < matCols - 1; h++)
for (unsigned int j = h + 1; j < matCols; j++, pos++) {
d1(pos) = sqrt(((pt0(0, h) - pt0(0, j)) * (pt0(0, h) - pt0(0, j)))
+ ((pt0(1, h) - pt0(1, j)) * (pt0(1, h) - pt0(1, j))));
d2(pos) = sqrt(((pt1(0, h) - pt1(0, j)) * (pt1(0, h) - pt1(0, j)))
+ ((pt1(1, h) - pt1(1, j)) * (pt1(1, h) - pt1(1, j))));
}
Eigen::RowVectorXd ds(len);
//calculate mean value
ds = d2.array() / d1.array();
double s = median(ds);
double s1 = (0.5 * (s - 1) * bb_width(bb0));
double s2 = (0.5 * (s - 1) * bb_height(bb0));
Eigen::Vector4d bb1;
//
bb1(0) = bb0(0) - s1 + dx;
bb1(1) = bb0(1) - s2 + dy;
bb1(2) = bb0(2) + s1 + dx;
bb1(3) = bb0(3) + s2 + dy;
return bb1;
}
// Great circle distance, up to a constant of proportionality equal to 2*R
// where R is the earth's radius
Eigen::MatrixXd greatcirc_dist(const Eigen::MatrixXd &X, const Eigen::MatrixXd &Y) {
int nr = X.rows();
int nc = Y.rows();
Eigen::MatrixXd lon1 = X.col(0).replicate(1,nc) * pi_180;
Eigen::MatrixXd lat1 = X.col(1).replicate(1,nc) * pi_180;
Eigen::MatrixXd lon2 = Y.col(0).transpose().replicate(nr,1) * pi_180;
Eigen::MatrixXd lat2 = Y.col(1).transpose().replicate(nr,1) * pi_180;
Eigen::MatrixXd dlon = 0.5*(lon2 - lon1);
Eigen::MatrixXd dlat = 0.5*(lat2 - lat1);
Eigen::MatrixXd a = dlat.array().sin().square().matrix() +
(dlon.array().sin().square() * lat1.array().cos() * lat2.array().cos()).matrix();
Eigen::MatrixXd c = (a.array()<1.0).select(a.array().sqrt(),Eigen::MatrixXd::Ones(nr,nc)).array().asin();
return (c); // Instead of (2*R*c) where R = 6378137 is the Earth's radius.
}
// Compute the average contour, by calling compute_contour_vals repeatedly
//
// [[Rcpp::export]]
Eigen::MatrixXd rcppstandardize_rates(const Eigen::VectorXd &tiles, const Eigen::VectorXd &rates,
const Eigen::VectorXd &xseed, const Eigen::VectorXd &yseed,
const Eigen::MatrixXd &marks, const Eigen::VectorXd &nmrks,
const std::string &distm) {
bool use_weighted_mean = true;
int nxmrks = nmrks(0);
int nymrks = nmrks(1);
Eigen::MatrixXd Zvals = Eigen::MatrixXd::Zero(nymrks,nxmrks);
Eigen::MatrixXd zvals = Eigen::MatrixXd::Zero(nymrks,nxmrks);
int niters = tiles.size();
for ( int i = 0, pos = 0 ; i < niters ; i++ ) {
int now_tiles = (int)tiles(i);
Eigen::VectorXd now_rates = rates.segment(pos,now_tiles);
Eigen::VectorXd now_xseed = xseed.segment(pos,now_tiles);
Eigen::VectorXd now_yseed = yseed.segment(pos,now_tiles);
Eigen::MatrixXd now_seeds(now_tiles, 2);
now_seeds << now_xseed,now_yseed;
if (use_weighted_mean) {
compute_contour_vals(zvals,marks,now_rates,now_seeds,distm);
zvals = zvals.array() - zvals.mean();
} else {
now_rates = now_rates.array() - now_rates.mean();
compute_contour_vals(zvals,marks,now_rates,now_seeds,distm);
}
Zvals += zvals;
pos += now_tiles;
}
// Do not divide by niters here but in 'average.eems.contours' instead
// Zvals = Zvals.array() / niters;
return Zvals.transpose();
}
Eigen::MatrixXd RtHPIS::magnetic_dipole(Eigen::MatrixXd pos, Eigen::MatrixXd pnt, Eigen::MatrixXd ori) {
double u0 = 1e-7;
int nchan;
Eigen::MatrixXd r, r2, r5, x, y, z, mx, my, mz, Tx, Ty, Tz, lf, temp;
nchan = pnt.rows();
// Shift the magnetometers so that the dipole is in the origin
pnt.array().col(0) -= pos(0);pnt.array().col(1) -= pos(1);pnt.array().col(2) -= pos(2);
r = pnt.array().square().rowwise().sum().sqrt();
r2 = r5 = x = y = z = mx = my = mz = Tx = Ty = Tz = lf = Eigen::MatrixXd::Zero(nchan,3);
for(int i = 0;i < nchan;i++) {
r2.row(i).array().fill(pow(r(i),2));
r5.row(i).array().fill(pow(r(i),5));
}
for(int i = 0;i < nchan;i++) {
x.row(i).array().fill(pnt(i,0));
y.row(i).array().fill(pnt(i,1));
z.row(i).array().fill(pnt(i,2));
}
mx.col(0).array().fill(1);my.col(1).array().fill(1);mz.col(2).array().fill(1);
Tx = 3 * x.cwiseProduct(pnt) - mx.cwiseProduct(r2);
Ty = 3 * y.cwiseProduct(pnt) - my.cwiseProduct(r2);
Tz = 3 * z.cwiseProduct(pnt) - mz.cwiseProduct(r2);
for(int i = 0;i < nchan;i++) {
lf(i,0) = Tx.row(i).dot(ori.row(i));
lf(i,1) = Ty.row(i).dot(ori.row(i));
lf(i,2) = Tz.row(i).dot(ori.row(i));
}
for(int i = 0;i < nchan;i++) {
for(int j = 0;j < 3;j++) {
lf(i,j) = u0 * lf(i,j)/(4 * M_PI * r5(i,j));
}
}
return lf;
}
int FeatureTransformationEstimator::consensus3D(Eigen::MatrixXd P, Eigen::MatrixXd Q, Eigen::Isometry3d T, double thresh, Eigen::Array<bool, 1, Eigen::Dynamic> &consensusSet)
{
int consensus = 0;
P = T * P.colwise().homogeneous();
Eigen::MatrixXd norms = (P - Q).colwise().norm();
consensusSet = norms.array() < thresh;
consensus = consensusSet.count();
return consensus;
}
int main(int argc, char * argv[])
{
using namespace Eigen;
using namespace std;
using namespace igl;
VectorXd D;
if(!read_triangle_mesh("../shared/beetle.off",V,F))
{
cout<<"failed to load mesh"<<endl;
}
twod = V.col(2).minCoeff()==V.col(2).maxCoeff();
bbd = (V.colwise().maxCoeff()-V.colwise().minCoeff()).norm();
SparseMatrix<double> L,M;
cotmatrix(V,F,L);
L = (-L).eval();
massmatrix(V,F,MASSMATRIX_TYPE_DEFAULT,M);
const size_t k = 5;
if(!eigs(L,M,k+1,EIGS_TYPE_SM,U,D))
{
cout<<"failed."<<endl;
}
U = ((U.array()-U.minCoeff())/(U.maxCoeff()-U.minCoeff())).eval();
igl::viewer::Viewer viewer;
viewer.callback_key_down = [&](igl::viewer::Viewer & viewer,unsigned char key,int)->bool
{
switch(key)
{
default:
return false;
case ' ':
{
U = U.rightCols(k).eval();
// Rescale eigen vectors for visualization
VectorXd Z =
bbd*0.5*U.col(c);
Eigen::MatrixXd C;
igl::parula(U.col(c).eval(),false,C);
c = (c+1)%U.cols();
if(twod)
{
V.col(2) = Z;
}
viewer.data.set_mesh(V,F);
viewer.data.compute_normals();
viewer.data.set_colors(C);
return true;
}
}
};
viewer.callback_key_down(viewer,' ',0);
viewer.core.show_lines = false;
viewer.launch();
}
void scaleData(Eigen::MatrixXd& data, double min, double max)
{
if(min >= max)
throw OpenANNException("Scaling failed: max has to be greater than min!");
const double minData = data.minCoeff();
const double maxData = data.maxCoeff();
const double dataRange = maxData - minData;
const double desiredRange = max - min;
const double scaling = desiredRange / dataRange;
data = data.array() * scaling + (min - minData * scaling);
}
normal_fullrank operator/=(const normal_fullrank& rhs) {
static const char* function =
"stan::variational::normal_fullrank::operator/=";
stan::math::check_size_match(function,
"Dimension of lhs", dimension_,
"Dimension of rhs", rhs.dimension());
mu_.array() /= rhs.mu().array();
L_chol_.array() /= rhs.L_chol().array();
return *this;
}
IGL_INLINE void igl::ViewerData::set_colors(const Eigen::MatrixXd &C)
{
using namespace std;
using namespace Eigen;
// Ambient color should be darker color
const auto ambient = [](const MatrixXd & C)->MatrixXd
{
return 0.1*C;
};
// Specular color should be a less saturated and darker color: dampened
// highlights
const auto specular = [](const MatrixXd & C)->MatrixXd
{
const double grey = 0.3;
return grey+0.1*(C.array()-grey);
};
if (C.rows() == 1)
{
for (unsigned i=0;i<V_material_diffuse.rows();++i)
{
V_material_diffuse.row(i) = C.row(0);
}
V_material_ambient = ambient(V_material_diffuse);
V_material_specular = specular(V_material_diffuse);
for (unsigned i=0;i<F_material_diffuse.rows();++i)
{
F_material_diffuse.row(i) = C.row(0);
}
F_material_ambient = ambient(F_material_diffuse);
F_material_specular = specular(F_material_diffuse);
}
else if (C.rows() == V.rows())
{
set_face_based(false);
V_material_diffuse = C;
V_material_ambient = ambient(V_material_diffuse);
V_material_specular = specular(V_material_diffuse);
}
else if (C.rows() == F.rows())
{
set_face_based(true);
F_material_diffuse = C;
F_material_ambient = ambient(F_material_diffuse);
F_material_specular = specular(F_material_diffuse);
}
else
cerr << "ERROR (set_colors): Please provide a single color, or a color per face or per vertex.";
dirty |= DIRTY_DIFFUSE;
}
void test_linear_ring()
{
trace.beginBlock("linear ring");
const Domain domain(Point(-5,-5), Point(5,5));
typedef DiscreteExteriorCalculus<1, 2, EigenLinearAlgebraBackend> Calculus;
Calculus calculus;
calculus.initKSpace<Domain>(domain);
for (int kk=-8; kk<10; kk++) calculus.insertSCell( calculus.myKSpace.sCell(Point(-8,kk), kk%2 == 0 ? Calculus::KSpace::POS : Calculus::KSpace::NEG) );
for (int kk=-8; kk<10; kk++) calculus.insertSCell( calculus.myKSpace.sCell(Point(kk,10), kk%2 == 0 ? Calculus::KSpace::POS : Calculus::KSpace::NEG) );
for (int kk=10; kk>-8; kk--) calculus.insertSCell( calculus.myKSpace.sCell(Point(10,kk)) );
for (int kk=10; kk>-8; kk--) calculus.insertSCell( calculus.myKSpace.sCell(Point(kk,-8)) );
calculus.updateIndexes();
{
trace.info() << calculus << endl;
Board2D board;
board << domain;
board << calculus;
board.saveSVG("ring_structure.svg");
}
const Calculus::PrimalDerivative0 d0 = calculus.derivative<0, PRIMAL>();
display_operator_info("d0", d0);
const Calculus::PrimalHodge0 h0 = calculus.hodge<0, PRIMAL>();
display_operator_info("h0", h0);
const Calculus::DualDerivative0 d0p = calculus.derivative<0, DUAL>();
display_operator_info("d0p", d0p);
const Calculus::PrimalHodge1 h1 = calculus.hodge<1, PRIMAL>();
display_operator_info("h1", h1);
const Calculus::PrimalIdentity0 laplace = calculus.laplace<PRIMAL>();
display_operator_info("laplace", laplace);
const int laplace_size = calculus.kFormLength(0, PRIMAL);
const Eigen::MatrixXd laplace_dense(laplace.myContainer);
for (int ii=0; ii<laplace_size; ii++)
FATAL_ERROR( laplace_dense(ii,ii) == 2 );
FATAL_ERROR( laplace_dense.array().rowwise().sum().abs().sum() == 0 );
FATAL_ERROR( laplace_dense.transpose() == laplace_dense );
trace.endBlock();
}
void object::test<6>()
{
for (int i = 0;i<10;i++)
{
int dim = rand()%1000+2;
int samplenum1 = rand()%1000+100;
int samplenum2 = rand()%1000+100;
Eigen::MatrixXd ha = Eigen::MatrixXd::Random(dim,samplenum1);
Eigen::MatrixXd hb = Eigen::MatrixXd::Random(dim,samplenum2);
Eigen::VectorXd haa = (ha.array()*ha.array()).colwise().sum();
Eigen::VectorXd hbb = (hb.array()*hb.array()).colwise().sum();
Eigen::MatrixXd hdist = -2*ha.transpose()*hb;
hdist.colwise() += haa;
hdist.rowwise() += hbb.transpose();
Matrix<double> ga(ha),gb(hb);
Matrix<double> gdist = -2*ga.transpose()*gb;
Vector<double> gaa = (ga.array()*ga.array()).colwise().sum();
Vector<double> gbb = (gb.array()*gb.array()).colwise().sum();
gdist.colwise() += gaa;
gdist.rowwise() += gbb;
ensure(check_diff(hdist,gdist));
}
}
dipError RtHPIS::dipfitError(Eigen::MatrixXd pos, Eigen::MatrixXd data, struct sens sensors)
{
// Variable Declaration
struct dipError e;
Eigen::MatrixXd lf, dif;
// Compute lead field for a magnetic dipole in infinite vacuum
lf = ft_compute_leadfield(pos, sensors);
e.moment = pinv(lf) * data;
dif = data - lf * e.moment;
e.error = dif.array().square().sum()/data.array().square().sum();
return e;
}
void KMeansTestCase::clustering()
{
const int N = 1000;
const int D = 10;
Eigen::MatrixXd X(N, D);
OpenANN::RandomNumberGenerator rng;
rng.fillNormalDistribution(X);
OpenANN::KMeans kmeans(D, 5);
const int batchSize = 200;
double averageDistToCenter = std::numeric_limits<double>::max();
for(int i = 0; i < N/batchSize; i++)
{
// Data points will be closer to centers after each update
Eigen::MatrixXd Y = kmeans.fitPartial(X.block(i*batchSize, 0, batchSize, D)).transform(X);
const double newDistance = Y.array().rowwise().maxCoeff().sum();
ASSERT(newDistance < averageDistToCenter);
averageDistToCenter = newDistance;
}
}
int FeatureTransformationEstimator::consensusReprojection(Eigen::MatrixXd P, Eigen::MatrixXd Q, Eigen::Isometry3d T, double thresh, Eigen::Array<bool, 1, Eigen::Dynamic> &consensusSet)
{
Eigen::MatrixXd Pproj(2, P.cols());
Eigen::MatrixXd Qproj(2, P.cols());
for (int i = 0; i < P.cols(); i++) {
Eigen::Vector3d PT = T * P.col(i).homogeneous();
Pproj(0,i) = pnp.uc + pnp.fu * PT(0) / PT(2);
Pproj(1,i) = pnp.vc + pnp.fv * PT(1) / PT(2);
Qproj(0,i) = pnp.uc + pnp.fu * Q(0,i) / Q(2,i);
Qproj(1,i) = pnp.vc + pnp.fv * Q(1,i) / Q(2,i);
}
int consensus = 0;
Eigen::MatrixXd norms = (Pproj - Qproj).colwise().norm();
consensusSet = norms.array() < thresh;
consensus = consensusSet.count();
return consensus;
}
normal_fullrank operator+=(double scalar) {
mu_.array() += scalar;
L_chol_.array() += scalar;
return *this;
}
int main(int argc, char *argv[])
{
using namespace Eigen;
using namespace std;
// Load a mesh in OFF format
igl::readOFF("../shared/cow.off", V, F);
// Compute Laplace-Beltrami operator: #V by #V
igl::cotmatrix(V,F,L);
// Alternative construction of same Laplacian
SparseMatrix<double> G,K;
// Gradient/Divergence
igl::grad(V,F,G);
// Diagonal per-triangle "mass matrix"
VectorXd dblA;
igl::doublearea(V,F,dblA);
// Place areas along diagonal #dim times
const auto & T = 1.*(dblA.replicate(3,1)*0.5).asDiagonal();
// Laplacian K built as discrete divergence of gradient or equivalently
// discrete Dirichelet energy Hessian
K = -G.transpose() * T * G;
cout<<"|K-L|: "<<(K-L).norm()<<endl;
const auto &key_down = [](igl::Viewer &viewer,unsigned char key,int mod)->bool
{
switch(key)
{
case 'r':
case 'R':
U = V;
break;
case ' ':
{
// Recompute just mass matrix on each step
SparseMatrix<double> M;
igl::massmatrix(U,F,igl::MASSMATRIX_TYPE_BARYCENTRIC,M);
// Solve (M-delta*L) U = M*U
const auto & S = (M - 0.001*L);
Eigen::SimplicialLLT<Eigen::SparseMatrix<double > > solver(S);
assert(solver.info() == Eigen::Success);
U = solver.solve(M*U).eval();
// Compute centroid and subtract (also important for numerics)
VectorXd dblA;
igl::doublearea(U,F,dblA);
double area = 0.5*dblA.sum();
MatrixXd BC;
igl::barycenter(U,F,BC);
RowVector3d centroid(0,0,0);
for(int i = 0;i<BC.rows();i++)
{
centroid += 0.5*dblA(i)/area*BC.row(i);
}
U.rowwise() -= centroid;
// Normalize to unit surface area (important for numerics)
U.array() /= sqrt(area);
break;
}
default:
return false;
}
// Send new positions, update normals, recenter
viewer.data.set_vertices(U);
viewer.data.compute_normals();
viewer.core.align_camera_center(U,F);
return true;
};
// Use original normals as pseudo-colors
MatrixXd N;
igl::per_vertex_normals(V,F,N);
MatrixXd C = N.rowwise().normalized().array()*0.5+0.5;
// Initialize smoothing with base mesh
U = V;
viewer.data.set_mesh(U, F);
viewer.data.set_colors(C);
viewer.callback_key_down = key_down;
cout<<"Press [space] to smooth."<<endl;;
cout<<"Press [r] to reset."<<endl;;
return viewer.launch();
}
void run ()
{
auto input_header = Header::open (argument[0]);
Header output_header (input_header);
output_header.datatype() = DataType::from_command_line (DataType::from<float> ());
// Linear
transform_type linear_transform;
bool linear = false;
auto opt = get_options ("linear");
if (opt.size()) {
linear = true;
linear_transform = load_transform (opt[0][0]);
} else {
linear_transform.setIdentity();
}
// Replace
const bool replace = get_options ("replace").size();
if (replace && !linear) {
INFO ("no linear is supplied so replace with the default (identity) transform");
linear = true;
}
// Template
opt = get_options ("template");
Header template_header;
if (opt.size()) {
if (replace)
throw Exception ("you cannot use the -replace option with the -template option");
template_header = Header::open (opt[0][0]);
for (size_t i = 0; i < 3; ++i) {
output_header.size(i) = template_header.size(i);
output_header.spacing(i) = template_header.spacing(i);
}
output_header.transform() = template_header.transform();
add_line (output_header.keyval()["comments"], std::string ("regridded to template image \"" + template_header.name() + "\""));
}
// Warp 5D warp
// TODO add reference to warp format documentation
opt = get_options ("warp_full");
Image<default_type> warp;
if (opt.size()) {
warp = Image<default_type>::open (opt[0][0]).with_direct_io();
if (warp.ndim() != 5)
throw Exception ("the input -warp_full image must be a 5D file.");
if (warp.size(3) != 3)
throw Exception ("the input -warp_full image must have 3 volumes (x,y,z) in the 4th dimension.");
if (warp.size(4) != 4)
throw Exception ("the input -warp_full image must have 4 volumes in the 5th dimension.");
if (linear)
throw Exception ("the -warp_full option cannot be applied in combination with -linear since the "
"linear transform is already included in the warp header");
}
// Warp from image1 or image2
int from = 1;
opt = get_options ("from");
if (opt.size()) {
from = opt[0][0];
if (!warp.valid())
WARN ("-from option ignored since no 5D warp was input");
}
// Warp deformation field
opt = get_options ("warp");
if (opt.size()) {
if (warp.valid())
throw Exception ("only one warp field can be input with either -warp or -warp_mid");
warp = Image<default_type>::open (opt[0][0]).with_direct_io (Stride::contiguous_along_axis(3));
if (warp.ndim() != 4)
throw Exception ("the input -warp file must be a 4D deformation field");
if (warp.size(3) != 3)
throw Exception ("the input -warp file must have 3 volumes in the 4th dimension (x,y,z positions)");
}
// Inverse
const bool inverse = get_options ("inverse").size();
if (inverse) {
if (!(linear || warp.valid()))
throw Exception ("no linear or warp transformation provided for option '-inverse'");
if (warp.valid())
if (warp.ndim() == 4)
throw Exception ("cannot apply -inverse with the input -warp_df deformation field.");
linear_transform = linear_transform.inverse();
}
// Half
const bool half = get_options ("half").size();
if (half) {
if (!(linear))
throw Exception ("no linear transformation provided for option '-half'");
{
Eigen::Matrix<default_type, 4, 4> temp;
temp.row(3) << 0, 0, 0, 1.0;
temp.topLeftCorner(3,4) = linear_transform.matrix().topLeftCorner(3,4);
linear_transform.matrix() = temp.sqrt().topLeftCorner(3,4);
}
}
// Flip
opt = get_options ("flip");
if (opt.size()) {
std::vector<int> axes = opt[0][0];
transform_type flip;
flip.setIdentity();
for (size_t i = 0; i < axes.size(); ++i) {
if (axes[i] < 0 || axes[i] > 2)
throw Exception ("axes supplied to -flip are out of bounds (" + std::string (opt[0][0]) + ")");
flip(axes[i],3) += flip(axes[i],axes[i]) * input_header.spacing(axes[i]) * (input_header.size(axes[i])-1);
flip(axes[i], axes[i]) *= -1.0;
}
if (!replace)
flip = input_header.transform() * flip * input_header.transform().inverse();
linear_transform = linear_transform * flip;
linear = true;
}
Stride::List stride = Stride::get (input_header);
// Detect FOD image for reorientation
opt = get_options ("noreorientation");
bool fod_reorientation = false;
Eigen::MatrixXd directions_cartesian;
if (!opt.size() && (linear || warp.valid() || template_header.valid()) && input_header.ndim() == 4 &&
input_header.size(3) >= 6 &&
input_header.size(3) == (int) Math::SH::NforL (Math::SH::LforN (input_header.size(3)))) {
CONSOLE ("SH series detected, performing apodised PSF reorientation");
fod_reorientation = true;
Eigen::MatrixXd directions_az_el;
opt = get_options ("directions");
if (opt.size())
directions_az_el = load_matrix (opt[0][0]);
else
directions_az_el = DWI::Directions::electrostatic_repulsion_300();
Math::SH::spherical2cartesian (directions_az_el, directions_cartesian);
// load with SH coeffients contiguous in RAM
stride = Stride::contiguous_along_axis (3, input_header);
}
// Modulate FODs
bool modulate = false;
if (get_options ("modulate").size()) {
modulate = true;
if (!fod_reorientation)
throw Exception ("modulation can only be performed with FOD reorientation");
}
// Rotate/Flip gradient directions if present
if (linear && input_header.ndim() == 4 && !warp && !fod_reorientation) {
try {
auto grad = DWI::get_DW_scheme (input_header);
if (input_header.size(3) == (ssize_t) grad.rows()) {
INFO ("DW gradients detected and will be reoriented");
Eigen::MatrixXd rotation = linear_transform.linear();
Eigen::MatrixXd test = rotation.transpose() * rotation;
test = test.array() / test.diagonal().mean();
if (!test.isIdentity (0.001))
WARN ("the input linear transform contains shear or anisotropic scaling and "
"therefore should not be used to reorient diffusion gradients");
if (replace)
rotation = linear_transform.linear() * input_header.transform().linear().inverse();
for (ssize_t n = 0; n < grad.rows(); ++n) {
Eigen::Vector3 grad_vector = grad.block<1,3>(n,0);
grad.block<1,3>(n,0) = rotation * grad_vector;
}
DWI::set_DW_scheme (output_header, grad);
}
}
catch (Exception& e) {
e.display (2);
}
}
// Interpolator
int interp = 2; // cubic
opt = get_options ("interp");
if (opt.size()) {
interp = opt[0][0];
if (!warp && !template_header)
WARN ("interpolator choice ignored since the input image will not be regridded");
}
// Out of bounds value
float out_of_bounds_value = 0.0;
opt = get_options ("nan");
if (opt.size()) {
out_of_bounds_value = NAN;
if (!warp && !template_header)
WARN ("Out of bounds value ignored since the input image will not be regridded");
}
auto input = input_header.get_image<float>().with_direct_io (stride);
// Reslice the image onto template
if (template_header.valid() && !warp) {
INFO ("image will be regridded");
if (get_options ("midway_space").size()) {
INFO("regridding to midway space");
std::vector<Header> headers;
headers.push_back(input_header);
headers.push_back(template_header);
std::vector<Eigen::Transform<default_type, 3, Eigen::Projective>> void_trafo;
auto padding = Eigen::Matrix<double, 4, 1>(1.0, 1.0, 1.0, 1.0);
int subsampling = 1;
auto midway_header = compute_minimum_average_header (headers, subsampling, padding, void_trafo);
for (size_t i = 0; i < 3; ++i) {
output_header.size(i) = midway_header.size(i);
output_header.spacing(i) = midway_header.spacing(i);
}
output_header.transform() = midway_header.transform();
}
if (interp == 0)
output_header.datatype() = DataType::from_command_line (input_header.datatype());
auto output = Image<float>::create (argument[1], output_header).with_direct_io();
switch (interp) {
case 0:
Filter::reslice<Interp::Nearest> (input, output, linear_transform, Adapter::AutoOverSample, out_of_bounds_value);
break;
case 1:
Filter::reslice<Interp::Linear> (input, output, linear_transform, Adapter::AutoOverSample, out_of_bounds_value);
break;
case 2:
Filter::reslice<Interp::Cubic> (input, output, linear_transform, Adapter::AutoOverSample, out_of_bounds_value);
break;
case 3:
Filter::reslice<Interp::Sinc> (input, output, linear_transform, Adapter::AutoOverSample, out_of_bounds_value);
break;
default:
assert (0);
break;
}
if (fod_reorientation)
Registration::Transform::reorient ("reorienting", output, output, linear_transform, directions_cartesian.transpose(), modulate);
} else if (warp.valid()) {
if (replace)
throw Exception ("you cannot use the -replace option with the -warp or -warp_df option");
if (!template_header) {
for (size_t i = 0; i < 3; ++i) {
output_header.size(i) = warp.size(i);
output_header.spacing(i) = warp.spacing(i);
}
output_header.transform() = warp.transform();
add_line (output_header.keyval()["comments"], std::string ("resliced using warp image \"" + warp.name() + "\""));
}
auto output = Image<float>::create(argument[1], output_header).with_direct_io();
if (warp.ndim() == 5) {
Image<default_type> warp_deform;
// Warp to the midway space defined by the warp grid
if (get_options ("midway_space").size()) {
warp_deform = Registration::Warp::compute_midway_deformation (warp, from);
// Use the full transform to warp from the image image to the template
} else {
warp_deform = Registration::Warp::compute_full_deformation (warp, template_header, from);
}
apply_warp (input, output, warp_deform, interp, out_of_bounds_value);
if (fod_reorientation)
Registration::Transform::reorient_warp ("reorienting", output, warp_deform, directions_cartesian.transpose(), modulate);
// Compose and apply input linear and 4D deformation field
} else if (warp.ndim() == 4 && linear) {
auto warp_composed = Image<default_type>::scratch (warp);
Registration::Warp::compose_linear_deformation (linear_transform, warp, warp_composed);
apply_warp (input, output, warp_composed, interp, out_of_bounds_value);
if (fod_reorientation)
Registration::Transform::reorient_warp ("reorienting", output, warp_composed, directions_cartesian.transpose(), modulate);
// Apply 4D deformation field only
} else {
apply_warp (input, output, warp, interp, out_of_bounds_value);
if (fod_reorientation)
Registration::Transform::reorient_warp ("reorienting", output, warp, directions_cartesian.transpose(), modulate);
}
// No reslicing required, so just modify the header and do a straight copy of the data
} else {
if (get_options ("midway").size())
throw Exception ("midway option given but no template image defined");
INFO ("image will not be regridded");
Eigen::MatrixXd rotation = linear_transform.linear();
Eigen::MatrixXd temp = rotation.transpose() * rotation;
if (!temp.isIdentity (0.001))
WARN("the input linear transform is not orthonormal and therefore applying this without the -template"
"option will mean the output header transform will also be not orthonormal");
add_line (output_header.keyval()["comments"], std::string ("transform modified"));
if (replace)
output_header.transform() = linear_transform;
else
output_header.transform() = linear_transform.inverse() * output_header.transform();
auto output = Image<float>::create (argument[1], output_header).with_direct_io();
copy_with_progress (input, output);
if (fod_reorientation) {
transform_type transform = linear_transform;
if (replace)
transform = linear_transform * output_header.transform().inverse();
Registration::Transform::reorient ("reorienting", output, output, transform, directions_cartesian.transpose());
}
}
}
void Dmp::analyticalSolution(const VectorXd& ts, MatrixXd& xs, MatrixXd& xds, Eigen::MatrixXd& forcing_terms, Eigen::MatrixXd& fa_outputs) const
{
int n_time_steps = ts.size();
// INTEGRATE SYSTEMS ANALYTICALLY AS MUCH AS POSSIBLE
// Integrate phase
MatrixXd xs_phase;
MatrixXd xds_phase;
phase_system_->analyticalSolution(ts,xs_phase,xds_phase);
// Compute gating term
MatrixXd xs_gating;
MatrixXd xds_gating;
gating_system_->analyticalSolution(ts,xs_gating,xds_gating);
// Compute the output of the function approximator
fa_outputs.resize(ts.size(),dim_orig());
fa_outputs.fill(0.0);
//if (isTrained())
computeFunctionApproximatorOutput(xs_phase, fa_outputs);
MatrixXd xs_gating_rep = xs_gating.replicate(1,fa_outputs.cols());
MatrixXd g_minus_y0_rep = (attractor_state()-initial_state()).transpose().replicate(n_time_steps,1);
forcing_terms = fa_outputs.array()*xs_gating_rep.array(); // zzz *g_minus_y0_rep.array();
MatrixXd xs_goal, xds_goal;
// Get current delayed goal
if (goal_system_==NULL)
{
// If there is no dynamical system for the delayed goal, the goal is
// simply the attractor state
xs_goal = attractor_state().transpose().replicate(n_time_steps,1);
// with zero change
xds_goal = MatrixXd::Zero(n_time_steps,dim_orig());
}
else
{
// Integrate goal system and get current goal state
goal_system_->analyticalSolution(ts,xs_goal,xds_goal);
}
xs.resize(n_time_steps,dim());
xds.resize(n_time_steps,dim());
int T = n_time_steps;
xs.GOALM(T) = xs_goal; xds.GOALM(T) = xds_goal;
xs.PHASEM(T) = xs_phase; xds.PHASEM(T) = xds_phase;
xs.GATINGM(T) = xs_gating; xds.GATINGM(T) = xds_gating;
// THE REST CANNOT BE DONE ANALYTICALLY
// Reset the dynamical system, and get the first state
double damping = spring_system_->damping_coefficient();
SpringDamperSystem localspring_system_(tau(),initial_state(),attractor_state(),damping);
// Set first attractor state
localspring_system_.set_attractor_state(xs_goal.row(0));
// Start integrating spring damper system
int dim_spring = localspring_system_.dim();
VectorXd x_spring(dim_spring), xd_spring(dim_spring); // zzz Why are these needed?
int t0 = 0;
localspring_system_.integrateStart(x_spring, xd_spring);
xs.row(t0).SPRING = x_spring;
xds.row(t0).SPRING = xd_spring;
// Add forcing term to the acceleration of the spring state
xds.SPRINGM_Z(1) = xds.SPRINGM_Z(1) + forcing_terms.row(t0)/tau();
for (int tt=1; tt<n_time_steps; tt++)
{
double dt = ts[tt]-ts[tt-1];
// Euler integration
xs.row(tt).SPRING = xs.row(tt-1).SPRING + dt*xds.row(tt-1).SPRING;
// Set the attractor state of the spring system
localspring_system_.set_attractor_state(xs.row(tt).GOAL);
// Integrate spring damper system
localspring_system_.differentialEquation(xs.row(tt).SPRING, xd_spring);
xds.row(tt).SPRING = xd_spring;
// Add forcing term to the acceleration of the spring state
xds.row(tt).SPRING_Z = xds.row(tt).SPRING_Z + forcing_terms.row(tt)/tau();
// Compute y component from z
xds.row(tt).SPRING_Y = xs.row(tt).SPRING_Z/tau();
}
}
void display()
{
using namespace Eigen;
using namespace igl;
using namespace std;
if(!trackball_on && tot_num_samples < 10000)
{
if(S.size() == 0)
{
S.resize(V.rows());
S.setZero();
}
VectorXd Si;
const int num_samples = 20;
ambient_occlusion(ei,V,N,num_samples,Si);
S *= (double)tot_num_samples;
S += Si*(double)num_samples;
tot_num_samples += num_samples;
S /= (double)tot_num_samples;
}
// Convert to 1-intensity
C.conservativeResize(S.rows(),3);
if(ao_on)
{
C<<S,S,S;
C.array() = (1.0-ao_factor*C.array());
}else
{
C.setConstant(1.0);
}
if(ao_normalize)
{
C.col(0) *= ((double)C.rows())/C.col(0).sum();
C.col(1) *= ((double)C.rows())/C.col(1).sum();
C.col(2) *= ((double)C.rows())/C.col(2).sum();
}
C.col(0) *= color(0);
C.col(1) *= color(1);
C.col(2) *= color(2);
glClearColor(back[0],back[1],back[2],0);
glClear(GL_COLOR_BUFFER_BIT | GL_DEPTH_BUFFER_BIT);
// All smooth points
glEnable( GL_POINT_SMOOTH );
glDisable(GL_LIGHTING);
if(lights_on)
{
lights();
}
push_scene();
glEnable(GL_DEPTH_TEST);
glDepthFunc(GL_LEQUAL);
glEnable(GL_NORMALIZE);
glEnable(GL_COLOR_MATERIAL);
glColorMaterial(GL_FRONT_AND_BACK,GL_AMBIENT_AND_DIFFUSE);
push_object();
// Draw the model
// Set material properties
glEnable(GL_COLOR_MATERIAL);
draw_mesh(V,F,N,C);
pop_object();
// Draw a nice floor
glPushMatrix();
const double floor_offset =
-2./bbd*(V.col(1).maxCoeff()-mid(1));
glTranslated(0,floor_offset,0);
const float GREY[4] = {0.5,0.5,0.6,1.0};
const float DARK_GREY[4] = {0.2,0.2,0.3,1.0};
draw_floor(GREY,DARK_GREY);
glPopMatrix();
pop_scene();
report_gl_error();
TwDraw();
glutSwapBuffers();
glutPostRedisplay();
}
inline Real stdDev(const Eigen::MatrixXd& input){
return ::sqrt(((Eigen::MatrixXd)((input.array()-input.sum()/input.rows()).pow(2.0))).sum()/(input.rows()-1));
}
normal_fullrank sqrt() const {
return normal_fullrank(Eigen::VectorXd(mu_.array().sqrt()),
Eigen::MatrixXd(L_chol_.array().sqrt()));
}