Eigen::VectorXd operator()(const F& f, const Eigen::VectorXd& init, bool bounded) const
{
// Assert that the algorithm is non-gradient
// TO-DO: Add support for MLSL (Multi-Level Single-Linkage)
// TO-DO: Add better support for ISRES (Improved Stochastic Ranking Evolution Strategy)
// clang-format off
static_assert(Algorithm == nlopt::LN_COBYLA || Algorithm == nlopt::LN_BOBYQA ||
Algorithm == nlopt::LN_NEWUOA || Algorithm == nlopt::LN_NEWUOA_BOUND ||
Algorithm == nlopt::LN_PRAXIS || Algorithm == nlopt::LN_NELDERMEAD ||
Algorithm == nlopt::LN_SBPLX || Algorithm == nlopt::GN_DIRECT ||
Algorithm == nlopt::GN_DIRECT_L || Algorithm == nlopt::GN_DIRECT_L_RAND ||
Algorithm == nlopt::GN_DIRECT_NOSCAL || Algorithm == nlopt::GN_DIRECT_L_NOSCAL ||
Algorithm == nlopt::GN_DIRECT_L_RAND_NOSCAL || Algorithm == nlopt::GN_ORIG_DIRECT ||
Algorithm == nlopt::GN_ORIG_DIRECT_L || Algorithm == nlopt::GN_CRS2_LM ||
Algorithm == nlopt::GD_STOGO || Algorithm == nlopt::GD_STOGO_RAND ||
Algorithm == nlopt::GN_ISRES || Algorithm == nlopt::GN_ESCH, "NLOptNoGrad accepts gradient free nlopt algorithms only");
// clang-format on
int dim = init.size();
nlopt::opt opt(Algorithm, dim);
opt.set_max_objective(nlopt_func<F>, (void*)&f);
std::vector<double> x(dim);
Eigen::VectorXd::Map(&x[0], dim) = init;
opt.set_maxeval(Params::opt_nloptnograd::iterations());
if (bounded) {
opt.set_lower_bounds(std::vector<double>(dim, 0));
opt.set_upper_bounds(std::vector<double>(dim, 1));
}
double max;
opt.optimize(x, max);
return Eigen::VectorXd::Map(x.data(), x.size());
}
bool learn_variance(Eigen::VectorXd& var, const Eigen::VectorXd& q) {
if (adaptation_window())
estimator_.add_sample(q);
if (end_adaptation_window()) {
compute_next_window();
estimator_.sample_variance(var);
double n = static_cast<double>(estimator_.num_samples());
var = (n / (n + 5.0)) * var
+ 1e-3 * (5.0 / (n + 5.0)) * Eigen::VectorXd::Ones(var.size());
estimator_.restart();
++adapt_window_counter_;
return true;
}
++adapt_window_counter_;
return false;
}
void ObjectModelLine::optimizeModelCoefficients (const std::vector<int> &inliers,
const Eigen::VectorXd &model_coefficients,
Eigen::VectorXd &optimized_coefficients){
assert (model_coefficients.size () == 6);
if (inliers.size () == 0)
{
cout<<"[ObjectModelLine::optimizeModelCoefficients] Inliers vector empty! Returning the same coefficients";
optimized_coefficients = model_coefficients;
return;
}
assert (inliers.size () > 2);
optimized_coefficients.resize (6);
// Compute the 3x3 covariance matrix
Eigen::Vector4d centroid = Centroid3D::computeCentroid(this->inputPointCloud, inliers);
// compute3DCentroid (this->inputPointCloud, inliers, centroid);
Eigen::Matrix3d covariance_matrix;
// computeCovarianceMatrix (inputPointCloud, inliers, centroid, covariance_matrix);
covariance_matrix = Covariance3D::computeCovarianceMatrix (inputPointCloud, inliers, centroid);
optimized_coefficients[0] = centroid[0];
optimized_coefficients[1] = centroid[1];
optimized_coefficients[2] = centroid[2];
// Extract the eigenvalues and eigenvectors
//cloud_geometry::eigen_cov (covariance_matrix, eigen_values, eigen_vectors);
Eigen::SelfAdjointEigenSolver<Eigen::Matrix3d> ei_symm (covariance_matrix);
// EIGEN_ALIGN_MEMORY Eigen::Vector3d eigen_values = ei_symm.eigenvalues ();
EIGEN_ALIGN_MEMORY Eigen::Matrix3d eigen_vectors = ei_symm.eigenvectors ();
#ifdef EIGEN3
optimized_coefficients.tail<3> () = eigen_vectors.col (2).normalized ();
#else
optimized_coefficients.end<3> () = eigen_vectors.col (2).normalized ();
#endif
}
bool JointTrajGeneratorRML::insertSegments(
const Eigen::VectorXd &point,
const ros::Time &time,
TrajSegments &segments,
std::vector<size_t> &index_permutation) const
{
// Check the size of the jointspace command
if(point.size() == n_dof_) {
// Handle a position given as an Eigen vector
TrajSegment segment(n_dof_,true);
segment.start_time = time;
segment.goal_positions = point;
segments.clear();
segments.push_back(segment);
} else {
RTT::log(RTT::Debug) << "Received trajectory of invalid size." <<RTT::endlog();
return false;
}
return true;
}
UnifiedModel::UnifiedModel(const Eigen::MatrixXd& centers, const Eigen::MatrixXd& widths, const Eigen::MatrixXd& slopes, const Eigen::VectorXd& offsets, bool normalized_basis_functions, bool lines_pivot_at_max_activation)
{
int n_basis_functions = centers.rows();
#ifndef NDEBUG // Variables below are only required for asserts; check for NDEBUG to avoid warnings.
int n_dims = centers.cols();
#endif
assert(n_basis_functions==widths.rows());
assert(n_dims ==widths.cols());
assert(n_basis_functions==slopes.rows());
assert(n_dims ==slopes.cols());
assert(n_basis_functions==offsets.size());
centers_.resize(n_basis_functions);
covars_.resize(n_basis_functions);
slopes_.resize(n_basis_functions);
offsets_.resize(n_basis_functions);
priors_.resize(n_basis_functions);
for (int i=0; i<n_basis_functions; i++)
{
centers_[i] = centers.row(i);
covars_[i] = widths.row(i).asDiagonal();
covars_[i] = covars_[i].array().square();
slopes_[i] = slopes.row(i);
offsets_[i] = offsets[i];
priors_[i] = 1.0;
}
normalized_basis_functions_ = normalized_basis_functions;
lines_pivot_at_max_activation_ = lines_pivot_at_max_activation;
slopes_as_angles_ = false;
cosine_basis_functions_ = false;
initializeAllValuesVectorSize();
}
void TrajActionServer::command_joints(Eigen::VectorXd q_cmd) {
int njnts = q_cmd.size();
std_msgs::Float64 qval_msg;
qval_msg.data = q_cmd(0);
j1_pub_.publish(qval_msg);
if (njnts>1) {
qval_msg.data=q_cmd(1);
j2_pub_.publish(qval_msg);
// mimic this for pitch mechanism joints:
j2_1_pub_.publish(qval_msg);
j2_2_pub_.publish(qval_msg);
j2_5_pub_.publish(qval_msg);
// the following 2 joints follow w/ negative of j2
qval_msg.data= -q_cmd(1);
j2_3_pub_.publish(qval_msg);
j2_4_pub_.publish(qval_msg);
}
if (njnts>2) {
qval_msg.data=q_cmd(2);
j3_pub_.publish(qval_msg);
}
if (njnts>3) {
qval_msg.data=q_cmd(3);
j4_pub_.publish(qval_msg);
}
if (njnts>4) {
qval_msg.data=q_cmd(4);
j5_pub_.publish(qval_msg);
}
if (njnts>5) {
qval_msg.data=q_cmd(5);
j6_pub_.publish(qval_msg);
}
if (njnts>6) {
qval_msg.data=q_cmd(6);
j7_pub_.publish(qval_msg);
}
}
void VectorSum::updateHook()
{
// Reset the accumulator
sum_.setZero();
// Get the addends
bool has_new_data = false;
Eigen::VectorXd addend;
while(addends_in_.read( addend, false ) == RTT::NewData) {
if(addend.size() == dim_) {
sum_ += addend;
has_new_data = true;
} else {
RTT::log(RTT::Error) << "Input to VectorSum component does not have the correct dimension. All inputs should have dimension "<<dim_<<" but this input had dimension " << addend.size();
this->error();
}
}
// Write the sum
if(has_new_data) {
sum_out_.write( sum_ );
}
}
Eigen::VectorXd BlockSparseMatrix::operator* (const Eigen::VectorXd& rhs) const
{
CHECK(!mbCSRDirty);
int vectorLength = static_cast<int>(rhs.size());
double* rhsData = new double[vectorLength];
double* result = new double[vectorLength];
memcpy(rhsData, rhs.data(), vectorLength * sizeof(double));
char trans = 'n';
int numRows = mBlockHeight * mNumBlocksHeight;
#ifdef _MKL_IMPLEMENT
mkl_dcsrgemv(&trans, &numRows, const_cast<double*>(mCSREquivalent.GetValueData()), const_cast<int*>(mCSREquivalent.GetRowId()), const_cast<int*>(mCSREquivalent.GetColumnId()), rhsData, result);
#else
CHECK(0) << "_MKL_IMPLEMENT not defined!";
#endif
Eigen::VectorXd ret(vectorLength);
for (int i = 0; i < vectorLength; ++i)
ret[i] = result[i];
delete[] rhsData;
delete[] result;
return ret;
}
template <typename PointT> void
pcl::SampleConsensusModelCircle3D<PointT>::optimizeModelCoefficients (
const std::vector<int> &inliers,
const Eigen::VectorXf &model_coefficients,
Eigen::VectorXf &optimized_coefficients)
{
optimized_coefficients = model_coefficients;
// Needs a set of valid model coefficients
if (model_coefficients.size () != 7)
{
PCL_ERROR ("[pcl::SampleConsensusModelCircle3D::optimizeModelCoefficients] Invalid number of model coefficients given (%lu)!\n", model_coefficients.size ());
return;
}
// Need at least 3 samples
if (inliers.size () <= 3)
{
PCL_ERROR ("[pcl::SampleConsensusModelCircle3D::optimizeModelCoefficients] Not enough inliers found to support a model (%lu)! Returning the same coefficients.\n", inliers.size ());
return;
}
tmp_inliers_ = &inliers;
OptimizationFunctor functor (static_cast<int> (inliers.size ()), this);
Eigen::NumericalDiff<OptimizationFunctor> num_diff (functor);
Eigen::LevenbergMarquardt<Eigen::NumericalDiff<OptimizationFunctor>, double> lm (num_diff);
Eigen::VectorXd coeff;
int info = lm.minimize (coeff);
for (int i = 0; i < coeff.size (); ++i)
optimized_coefficients[i] = static_cast<float> (coeff[i]);
// Compute the L2 norm of the residuals
PCL_DEBUG ("[pcl::SampleConsensusModelCircle3D::optimizeModelCoefficients] LM solver finished with exit code %i, having a residual norm of %g. \nInitial solution: %g %g %g %g %g %g %g \nFinal solution: %g %g %g %g %g %g %g\n",
info, lm.fvec.norm (), model_coefficients[0], model_coefficients[1], model_coefficients[2], model_coefficients[3], model_coefficients[4], model_coefficients[5], model_coefficients[6], optimized_coefficients[0], optimized_coefficients[1], optimized_coefficients[2], optimized_coefficients[3], optimized_coefficients[4], optimized_coefficients[5], optimized_coefficients[6]);
}
Eigen::VectorXd operator()(const F& f, const Eigen::VectorXd& init, bool bounded) const
{
tools::par::init();
typedef std::pair<Eigen::VectorXd, double> pair_t;
auto body = [&](int i) {
// clang-format off
Eigen::VectorXd r_init = tools::random_vector(init.size());
Eigen::VectorXd v = Optimizer()(f, init, bounded);
double lik = opt::eval(f, v);
return std::make_pair(v, lik);
// clang-format on
};
auto comp = [](const pair_t& v1, const pair_t& v2) {
// clang-format off
return v1.second > v2.second;
// clang-format on
};
pair_t init_v = std::make_pair(init, -std::numeric_limits<float>::max());
auto m = tools::par::max(init_v, Params::opt_parallelrepeater::repeats(), body, comp);
return m.first;
};
double log_prob_grad(const M& model,
Eigen::VectorXd& params_r,
Eigen::VectorXd& gradient,
std::ostream* msgs = 0) {
using std::vector;
using stan::agrad::var;
Eigen::Matrix<var,Eigen::Dynamic,1> ad_params_r(params_r.size());
for (size_t i = 0; i < model.num_params_r(); ++i) {
stan::agrad::var var_i(params_r[i]);
ad_params_r[i] = var_i;
}
try {
var adLogProb
= model
.template log_prob<propto,
jacobian_adjust_transform>(ad_params_r, msgs);
double val = adLogProb.val();
stan::agrad::grad(adLogProb, ad_params_r, gradient);
return val;
} catch (std::exception &ex) {
stan::agrad::recover_memory();
throw;
}
}
IGL_INLINE Eigen::MatrixXd igl::rotate_vectors(
const Eigen::MatrixXd& V,
const Eigen::VectorXd& A,
const Eigen::MatrixXd& B1,
const Eigen::MatrixXd& B2)
{
Eigen::MatrixXd RV(V.rows(),V.cols());
for (unsigned i=0; i<V.rows();++i)
{
double norm = V.row(i).norm();
// project onto the tangent plane and convert to angle
double a = atan2(B2.row(i).dot(V.row(i)),B1.row(i).dot(V.row(i)));
// rotate
a += (A.size() == 1) ? A(0) : A(i);
// move it back to global coordinates
RV.row(i) = norm*cos(a) * B1.row(i) + norm*sin(a) * B2.row(i);
}
return RV;
}
// Fit a polynomial.
// Adapted from
// https://github.com/JuliaMath/Polynomials.jl/blob/master/src/Polynomials.jl#L676-L716
Eigen::VectorXd polyfit(Eigen::VectorXd xvals, Eigen::VectorXd yvals, int order)
{
assert(xvals.size() == yvals.size());
assert(order >= 1 && order <= xvals.size() - 1);
Eigen::MatrixXd A(xvals.size(), order + 1);
for (int i = 0; i < xvals.size(); i++)
{
A(i, 0) = 1.0;
}
for (int j = 0; j < xvals.size(); j++)
{
for (int i = 0; i < order; i++)
{
A(j, i + 1) = A(j, i) * xvals(j);
}
}
auto Q = A.householderQr();
auto result = Q.solve(yvals);
return result;
}
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();
}
//==============================================================================
TEST(World, Cloning)
{
// Create a list of skel files to test with
std::vector<std::string> fileList;
fileList.push_back(DART_DATA_PATH"skel/test/chainwhipa.skel");
fileList.push_back(DART_DATA_PATH"skel/test/single_pendulum.skel");
fileList.push_back(DART_DATA_PATH"skel/test/single_pendulum_euler_joint.skel");
fileList.push_back(DART_DATA_PATH"skel/test/single_pendulum_ball_joint.skel");
fileList.push_back(DART_DATA_PATH"skel/test/double_pendulum.skel");
fileList.push_back(DART_DATA_PATH"skel/test/double_pendulum_euler_joint.skel");
fileList.push_back(DART_DATA_PATH"skel/test/double_pendulum_ball_joint.skel");
fileList.push_back(DART_DATA_PATH"skel/test/serial_chain_revolute_joint.skel");
fileList.push_back(DART_DATA_PATH"skel/test/serial_chain_eulerxyz_joint.skel");
fileList.push_back(DART_DATA_PATH"skel/test/serial_chain_ball_joint.skel");
fileList.push_back(DART_DATA_PATH"skel/test/serial_chain_ball_joint_20.skel");
fileList.push_back(DART_DATA_PATH"skel/test/serial_chain_ball_joint_40.skel");
fileList.push_back(DART_DATA_PATH"skel/test/simple_tree_structure.skel");
fileList.push_back(DART_DATA_PATH"skel/test/simple_tree_structure_euler_joint.skel");
fileList.push_back(DART_DATA_PATH"skel/test/simple_tree_structure_ball_joint.skel");
fileList.push_back(DART_DATA_PATH"skel/test/tree_structure.skel");
fileList.push_back(DART_DATA_PATH"skel/test/tree_structure_euler_joint.skel");
fileList.push_back(DART_DATA_PATH"skel/test/tree_structure_ball_joint.skel");
fileList.push_back(DART_DATA_PATH"skel/fullbody1.skel");
std::vector<dart::simulation::WorldPtr> worlds;
for(size_t i=0; i<fileList.size(); ++i)
worlds.push_back(dart::utils::SkelParser::readWorld(fileList[i]));
for(size_t i=0; i<worlds.size(); ++i)
{
dart::simulation::WorldPtr original = worlds[i];
std::vector<dart::simulation::WorldPtr> clones;
clones.push_back(original);
for(size_t j=1; j<5; ++j)
clones.push_back(clones[j-1]->clone());
// Make sure all the Skeleton states match at the start
// TODO(MXG): This should be removed once state also gets copied over during a cloning
for(size_t j=1; j<clones.size(); ++j)
{
for(size_t k=0; k<original->getNumSkeletons(); ++k)
{
dart::dynamics::SkeletonPtr skel = original->getSkeleton(k);
dart::dynamics::SkeletonPtr clone = clones[j]->getSkeleton(k);
clone->setPositions(skel->getPositions());
clone->setVelocities(skel->getVelocities());
clone->setAccelerations(skel->getAccelerations());
clone->setForces(skel->getForces());
}
}
#ifndef NDEBUG // Debug mode
size_t numIterations = 3;
#else
size_t numIterations = 500;
#endif
for(size_t j=0; j<numIterations; ++j)
{
for(size_t k=0; k<original->getNumSkeletons(); ++k)
{
dart::dynamics::SkeletonPtr skel = original->getSkeleton(k);
// Generate a random command vector
Eigen::VectorXd commands = skel->getCommands();
for(int q=0; q<commands.size(); ++q)
commands[q] = random(-0.1, 0.1);
// Assign the command vector to each clone of the kth skeleton
for(size_t c=0; c<clones.size(); ++c)
{
dart::dynamics::SkeletonPtr skelClone = clones[c]->getSkeleton(k);
skelClone->setCommands(commands);
}
}
// Step each clone forward
for(size_t c=0; c<clones.size(); ++c)
clones[c]->step(false);
}
for(size_t c=0; c<clones.size(); ++c)
{
for(size_t k=0; k<original->getNumSkeletons(); ++k)
{
dart::dynamics::SkeletonPtr skel = original->getSkeleton(k);
dart::dynamics::SkeletonPtr clone = clones[c]->getSkeleton(k);
EXPECT_TRUE( equals(skel->getPositions(), clone->getPositions(), 0));
EXPECT_TRUE( equals(skel->getVelocities(), clone->getVelocities(), 0));
EXPECT_TRUE( equals(skel->getAccelerations(), clone->getAccelerations(), 0));
EXPECT_TRUE( equals(skel->getForces(), clone->getForces(), 0));
}
}
}
}
void TensorJTree::LearnSpectralParameters()
{
for (int i = 0; i < node_list->size(); ++i)
{
node_list->at(i)->MarkMultModes();
FindObservationPartitions(i);
}
for (int i = 0; i < node_list->size(); ++i)
{
node_list->at(i)->MarkObservableRepresentation();
}
for (int i = 0; i < node_list->size(); ++i)
{
cout << i;
cout << "\n";
node_list->at(i)->ComputeObservableRepresentation();
}
for (int i = 0; i < node_list->size(); ++i)
{
node_list->at(i)->FinalizeObservableRepresentation();
}
for (int i = 0; i < node_list->size(); ++i)
{
cout << i;
cout << "\n";
vector<double> big_forward_vec;
// big_forward_vec.reserve(10000);
Matrix big_back_matrix;
// big_back_matrix.Reserve(10000);
bool invModesExist = node_list->at(i)->InvModesExists();
if (invModesExist)
{
vector<Tensor*>& forward_list = node_list->at(i)->GetForwardList();
vector<Tensor*>& extra_list = node_list->at(i)->GetExtraList();
Tensor& X = node_list->at(i)->GetTransformTensor().GetTensor();
vector<int> result_dims = X.Dims();
assert(forward_list.size() == extra_list.size());
vector<int> inv_group_modes = node_list->at(i)->GetInvModeGroup();
vector<int> inv_modes = node_list->at(i)->GetInvModes();
for (int j = 0; j < forward_list.size(); ++j)
{
Tensor& forward_tensor = *(forward_list[j]);
Tensor& back_tensor = *(extra_list[j]);
if (j == 0)
{
Tensor::CreateLinearSystem(big_forward_vec, big_back_matrix, X, back_tensor, forward_tensor, inv_group_modes, inv_modes);
}
else
{
vector<double> forward_vec;
Matrix back_matrix;
Tensor::CreateLinearSystem(forward_vec, back_matrix, X, back_tensor, forward_tensor, inv_group_modes, inv_modes);
VectorPlus::Concat(big_forward_vec, forward_vec);
big_back_matrix.MatrixConcat(back_matrix);
}
}
Eigen::MatrixXd A(big_back_matrix.Dim(0), big_back_matrix.Dim(1));
for (int j = 0; j < big_back_matrix.Dim(0); ++j)
{
for (int k = 0; k < big_back_matrix.Dim(1); ++k)
{
A(j,k) = big_back_matrix.At(j,k);
}
}
Eigen::VectorXd b(big_forward_vec.size());
for (int j = 0; j < big_forward_vec.size(); ++j)
{
b(j) = big_forward_vec.at(j);
}
//cout << "yee";
Eigen::MatrixXd newA = A.transpose() * A;
Eigen::MatrixXd newb = A.transpose() * b;
Eigen::VectorXd res = newA.ldlt().solve(newb);
//cout << "yeeldlt solved";
//Eigen::VectorXd res = A.jacobiSvd(Eigen::ComputeThinU | Eigen::ComputeThinV).solve(b);
//cout << "yeesvdsolved";
// solve the linear system here
Tensor result_tensor(result_dims);
for (int j = 0; j < res.size(); ++j)
{
result_tensor.Set(j, res(j));
}
Tensor& curr_result = node_list->at(i)->GetTransformTensor().GetTensor();
// assert(Tensor::Diff(result_tensor, curr_result) < .0001);
node_list->at(i)->SetTransformTensor(result_tensor);
}
}
// average by computing template and see what happens
// hack it so we change the template
/* template_to_cliques = new vector<vector<int>*>();
for (int i = 0; i < NumCliques(); ++i)
{
template_to_cliques->push_back(new vector<int>(1,i));
} */
/*for (int i = 0; i < template_to_cliques->size(); ++i)
{
vector<int>& i_cliques = *(template_to_cliques->at(i));
vector<double> big_forward_vec;
Matrix big_back_matrix;
vector<int> result_dims;
bool invModesExist = node_list->at(i_cliques[0])->InvModesExists();
if (invModesExist)
{
for (int j = 0; j < i_cliques.size(); ++j)
{
if (node_list->at(i_cliques[0])->is_invalid())
continue;
Tensor& forward_tensor = node_list->at(i_cliques[j])->GetForwardTensor();
Tensor& back_tensor = node_list->at(i_cliques[j])->GetUExtraTensor();
Tensor& X = node_list->at(i_cliques[j])->GetTransformTensor().GetTensor();
vector<int>& inv_group_modes = node_list->at(i_cliques[j])->GetInvModeGroup();
vector<int>& inv_modes = node_list->at(i_cliques[j])->GetInvModes();
if (j == 0)
{
Tensor::CreateLinearSystem(big_forward_vec, big_back_matrix, X, back_tensor, forward_tensor, inv_group_modes, inv_modes);
result_dims = X.Dims();
}
else
{
vector<double> forward_vec;
Matrix back_matrix;
Tensor::CreateLinearSystem(forward_vec, back_matrix, X, back_tensor, forward_tensor, inv_group_modes, inv_modes);
VectorPlus::Concat(big_forward_vec, forward_vec);
big_back_matrix.MatrixConcat(back_matrix);
}
}
Eigen::MatrixXd A(big_back_matrix.Dim(0), big_back_matrix.Dim(1));
for (int i = 0; i < big_back_matrix.Dim(0); ++i)
{
for (int j = 0; j < big_back_matrix.Dim(1); ++j)
{
A(i,j) = big_back_matrix.At(i,j);
}
}
Eigen::VectorXd b(big_forward_vec.size());
for (int i = 0; i < big_forward_vec.size(); ++i)
{
b(i) = big_forward_vec.at(i);
}
Eigen::VectorXd res = A.jacobiSvd(Eigen::ComputeThinU | Eigen::ComputeThinV).solve(b);
// solve the linear system here
Tensor result_tensor(result_dims);
for (int i = 0; i < res.size(); ++i)
{
result_tensor.Set(i, res(i));
}
Tensor& curr_result = node_list->at(i_cliques[0])->GetTransformTensor().GetTensor();
// assert(Tensor::Diff(result_tensor, curr_result) < .0001);
for (int j = 0; j < i_cliques.size(); ++j)
{
node_list->at(i_cliques[j])->SetTransformTensor(result_tensor);
}
}
} */
/* for (int i = 0; i < template_to_cliques->size(); ++i)
{
vector<int>& i_cliques = *(template_to_cliques->at(i));
TensorCPT* avg_tensor = new TensorCPT(node_list->at(i_cliques[0])->GetTransformTensor());
for (int j = 1; j < i_cliques.size(); ++j)
{
TensorCPT::Add(*avg_tensor, node_list->at(i_cliques[j])->GetTransformTensor());
}
avg_tensor->Divide(i_cliques.size());
for (int j = 0; j < i_cliques.size(); ++j)
{
node_list->at(i_cliques[j])->SetTransformTensor(avg_tensor->GetTensor());
}
delete(avg_tensor);
} */
}
void TensorJTree::LearnTemplateSpectralParameters()
{
for (int i = 0; i < node_list->size(); ++i)
{
node_list->at(i)->MarkMultModes();
FindObservationPartitions(i);
}
for (int i = 0; i < node_list->size(); ++i)
{
node_list->at(i)->MarkObservableRepresentation();
}
for (int i = 0; i < node_list->size(); ++i)
{
cout << i;
cout << "\n";
node_list->at(i)->ComputeObservableRepresentation();
}
cout << "yeee";
cout << "\n";
for (int i = 0; i < node_list->size(); ++i)
{
cout << i;
cout << "\n";
node_list->at(i)->FinalizeTemplateObservableRepresentation();
}
cout << "yeee";
cout << "\n";
/* template_to_cliques = new vector<vector<int>*>();
for (int i = 0; i < NumCliques(); ++i)
{
template_to_cliques->push_back(new vector<int>(1,i));
} */
cout << "yeee";
cout << "\n";
for (int i = 0; i < template_to_cliques->size(); ++i)
{
vector<int>& i_cliques = *(template_to_cliques->at(i));
vector<double> big_forward_vec;
Matrix big_back_matrix;
vector<int> result_dims;
bool invModesExist = node_list->at(i_cliques[0])->InvModesExists();
if (invModesExist)
{
for (int j = 0; j < i_cliques.size(); ++j)
{
cout << j;
cout << "\n";
if (node_list->at(i_cliques[0])->is_invalid())
{
assert(0);
continue;
}
int index = i_cliques[j];
vector<Tensor*>& forward_list = node_list->at(index)->GetForwardList();
vector<Tensor*>& extra_list = node_list->at(index)->GetExtraList();
Tensor& X = node_list->at(index)->GetTransformTensor().GetTensor();
if (j == 0)
{
result_dims = X.Dims();
}
assert(forward_list.size() == extra_list.size());
vector<int> inv_group_modes = node_list->at(index)->GetInvModeGroup();
vector<int> inv_modes = node_list->at(index)->GetInvModes();
for (int k = 0; k < forward_list.size(); ++k)
{
Tensor& forward_tensor = *(forward_list[k]);
Tensor& back_tensor = *(extra_list[k]);
if (j == 0 && k == 0)
{
Tensor::CreateLinearSystem(big_forward_vec, big_back_matrix, X, back_tensor, forward_tensor, inv_group_modes, inv_modes);
}
else
{
vector<double> forward_vec;
Matrix back_matrix;
cout << "yeebeforesystem";
Tensor::CreateLinearSystem(forward_vec, back_matrix, X, back_tensor, forward_tensor, inv_group_modes, inv_modes);
cout << "yeeaftersystem";
VectorPlus::Concat(big_forward_vec, forward_vec);
big_back_matrix.MatrixConcat(back_matrix);
cout << "yeeafterconcat";
}
}
node_list->at(index)->DeleteForwardList();
node_list->at(index)->DeleteExtraList();
}
cout << big_back_matrix.Dim(0);
cout << "\n";
cout << big_back_matrix.Dim(1);
cout << "\n";
Eigen::MatrixXd A(big_back_matrix.Dim(0), big_back_matrix.Dim(1));
cout << "allocatedbigone";
for (int j = 0; j < big_back_matrix.Dim(0); ++j)
{
for (int k = 0; k < big_back_matrix.Dim(1); ++k)
{
(A)(j,k) = big_back_matrix.At(j,k);
}
}
Eigen::VectorXd b(big_forward_vec.size());
for (int j = 0; j < big_forward_vec.size(); ++j)
{
b(j) = big_forward_vec.at(j);
}
cout << "before solve";
cout << "\n";
Eigen::MatrixXd newA = A.transpose() * (A);
Eigen::MatrixXd newb = A.transpose() * b;
Eigen::VectorXd res = newA.ldlt().solve(newb);
cout << "after solve";
cout << "\n";
// solve the linear system here
Tensor result_tensor(result_dims);
for (int j = 0; j < res.size(); ++j)
{
result_tensor.Set(j, res(j));
}
Tensor& curr_result = node_list->at(i_cliques[0])->GetTransformTensor().GetTensor();
// assert(Tensor::Diff(result_tensor, curr_result) < .0001);
for (int j = 0; j < i_cliques.size(); ++j)
{
node_list->at(i_cliques[j])->SetTransformTensor(result_tensor);
}
}
}
}
TEST(McmcDiagEMetric, gradients) {
rng_t base_rng(0);
Eigen::VectorXd q = Eigen::VectorXd::Ones(11);
stan::mcmc::diag_e_point z(q.size());
z.q = q;
z.p.setOnes();
std::fstream data_stream(std::string("").c_str(), std::fstream::in);
stan::io::dump data_var_context(data_stream);
data_stream.close();
std::stringstream model_output, metric_output;
funnel_model_namespace::funnel_model model(data_var_context, &model_output);
stan::mcmc::diag_e_metric<funnel_model_namespace::funnel_model, rng_t> metric(model, &metric_output);
double epsilon = 1e-6;
metric.update(z);
Eigen::VectorXd g1 = metric.dtau_dq(z);
for (int i = 0; i < z.q.size(); ++i) {
double delta = 0;
z.q(i) += epsilon;
metric.update(z);
delta += metric.tau(z);
z.q(i) -= 2 * epsilon;
metric.update(z);
delta -= metric.tau(z);
z.q(i) += epsilon;
metric.update(z);
delta /= 2 * epsilon;
EXPECT_NEAR(delta, g1(i), epsilon);
}
Eigen::VectorXd g2 = metric.dtau_dp(z);
for (int i = 0; i < z.q.size(); ++i) {
double delta = 0;
z.p(i) += epsilon;
delta += metric.tau(z);
z.p(i) -= 2 * epsilon;
delta -= metric.tau(z);
z.p(i) += epsilon;
delta /= 2 * epsilon;
EXPECT_NEAR(delta, g2(i), epsilon);
}
Eigen::VectorXd g3 = metric.dphi_dq(z);
for (int i = 0; i < z.q.size(); ++i) {
double delta = 0;
z.q(i) += epsilon;
metric.update(z);
delta += metric.phi(z);
z.q(i) -= 2 * epsilon;
metric.update(z);
delta -= metric.phi(z);
z.q(i) += epsilon;
metric.update(z);
delta /= 2 * epsilon;
EXPECT_NEAR(delta, g3(i), epsilon);
}
EXPECT_EQ("", model_output.str());
EXPECT_EQ("", metric_output.str());
}
TEST(McmcUnitENuts, tree_boundary_test) {
rng_t base_rng(4839294);
stan::mcmc::unit_e_point z_init(3);
z_init.q(0) = 1;
z_init.q(1) = -1;
z_init.q(2) = 1;
z_init.p(0) = -1;
z_init.p(1) = 1;
z_init.p(2) = -1;
std::stringstream output;
stan::interface_callbacks::writer::stream_writer writer(output);
std::stringstream error_stream;
stan::interface_callbacks::writer::stream_writer error_writer(error_stream);
std::fstream empty_stream("", std::fstream::in);
stan::io::dump data_var_context(empty_stream);
typedef gauss3D_model_namespace::gauss3D_model model_t;
model_t model(data_var_context);
// Compute expected tree boundaries
typedef stan::mcmc::unit_e_metric<model_t, rng_t> metric_t;
metric_t metric(model);
stan::mcmc::expl_leapfrog<metric_t> unit_e_integrator;
double epsilon = 0.1;
stan::mcmc::unit_e_point z_test = z_init;
metric.init(z_test, writer, error_writer);
unit_e_integrator.evolve(z_test, metric, epsilon, writer, error_writer);
Eigen::VectorXd p_sharp_forward_1 = metric.dtau_dp(z_test);
unit_e_integrator.evolve(z_test, metric, epsilon, writer, error_writer);
Eigen::VectorXd p_sharp_forward_2 = metric.dtau_dp(z_test);
unit_e_integrator.evolve(z_test, metric, epsilon, writer, error_writer);
unit_e_integrator.evolve(z_test, metric, epsilon, writer, error_writer);
Eigen::VectorXd p_sharp_forward_3 = metric.dtau_dp(z_test);
unit_e_integrator.evolve(z_test, metric, epsilon, writer, error_writer);
unit_e_integrator.evolve(z_test, metric, epsilon, writer, error_writer);
unit_e_integrator.evolve(z_test, metric, epsilon, writer, error_writer);
unit_e_integrator.evolve(z_test, metric, epsilon, writer, error_writer);
Eigen::VectorXd p_sharp_forward_4 = metric.dtau_dp(z_test);
z_test = z_init;
metric.init(z_test, writer, error_writer);
unit_e_integrator.evolve(z_test, metric, -epsilon, writer, error_writer);
Eigen::VectorXd p_sharp_backward_1 = metric.dtau_dp(z_test);
unit_e_integrator.evolve(z_test, metric, -epsilon, writer, error_writer);
Eigen::VectorXd p_sharp_backward_2 = metric.dtau_dp(z_test);
unit_e_integrator.evolve(z_test, metric, -epsilon, writer, error_writer);
unit_e_integrator.evolve(z_test, metric, -epsilon, writer, error_writer);
Eigen::VectorXd p_sharp_backward_3 = metric.dtau_dp(z_test);
unit_e_integrator.evolve(z_test, metric, -epsilon, writer, error_writer);
unit_e_integrator.evolve(z_test, metric, -epsilon, writer, error_writer);
unit_e_integrator.evolve(z_test, metric, -epsilon, writer, error_writer);
unit_e_integrator.evolve(z_test, metric, -epsilon, writer, error_writer);
Eigen::VectorXd p_sharp_backward_4 = metric.dtau_dp(z_test);
// Check expected tree boundaries to those dynamically geneated by NUTS
stan::mcmc::unit_e_nuts<model_t, rng_t> sampler(model, base_rng);
sampler.set_nominal_stepsize(epsilon);
sampler.set_stepsize_jitter(0);
sampler.sample_stepsize();
stan::mcmc::ps_point z_propose = z_init;
Eigen::VectorXd p_sharp_left = Eigen::VectorXd::Zero(z_init.p.size());
Eigen::VectorXd p_sharp_right = Eigen::VectorXd::Zero(z_init.p.size());
Eigen::VectorXd rho = z_init.p;
double log_sum_weight = -std::numeric_limits<double>::infinity();
double H0 = -0.1;
int n_leapfrog = 0;
double sum_metro_prob = 0;
// Depth 0 forward
sampler.z() = z_init;
sampler.init_hamiltonian(writer, error_writer);
sampler.build_tree(0, z_propose,
p_sharp_left, p_sharp_right, rho,
H0, 1, n_leapfrog, log_sum_weight,
sum_metro_prob,
writer, error_writer);
for (int n = 0; n < rho.size(); ++n)
EXPECT_FLOAT_EQ(p_sharp_forward_1(n), p_sharp_left(n));
for (int n = 0; n < rho.size(); ++n)
EXPECT_FLOAT_EQ(p_sharp_forward_1(n), p_sharp_right(n));
// Depth 1 forward
sampler.z() = z_init;
sampler.init_hamiltonian(writer, error_writer);
sampler.build_tree(1, z_propose,
p_sharp_left, p_sharp_right, rho,
H0, 1, n_leapfrog, log_sum_weight,
sum_metro_prob,
writer, error_writer);
for (int n = 0; n < rho.size(); ++n)
EXPECT_FLOAT_EQ(p_sharp_forward_1(n), p_sharp_left(n));
for (int n = 0; n < rho.size(); ++n)
EXPECT_FLOAT_EQ(p_sharp_forward_2(n), p_sharp_right(n));
// Depth 2 forward
sampler.z() = z_init;
sampler.init_hamiltonian(writer, error_writer);
sampler.build_tree(2, z_propose,
p_sharp_left, p_sharp_right, rho,
H0, 1, n_leapfrog, log_sum_weight,
sum_metro_prob,
writer, error_writer);
for (int n = 0; n < rho.size(); ++n)
EXPECT_FLOAT_EQ(p_sharp_forward_1(n), p_sharp_left(n));
for (int n = 0; n < rho.size(); ++n)
EXPECT_FLOAT_EQ(p_sharp_forward_3(n), p_sharp_right(n));
// Depth 3 forward
sampler.z() = z_init;
sampler.init_hamiltonian(writer, error_writer);
sampler.build_tree(3, z_propose,
p_sharp_left, p_sharp_right, rho,
H0, 1, n_leapfrog, log_sum_weight,
sum_metro_prob,
writer, error_writer);
for (int n = 0; n < rho.size(); ++n)
EXPECT_FLOAT_EQ(p_sharp_forward_1(n), p_sharp_left(n));
for (int n = 0; n < rho.size(); ++n)
EXPECT_FLOAT_EQ(p_sharp_forward_4(n), p_sharp_right(n));
// Depth 0 backward
sampler.z() = z_init;
sampler.init_hamiltonian(writer, error_writer);
sampler.build_tree(0, z_propose,
p_sharp_left, p_sharp_right, rho,
H0, -1, n_leapfrog, log_sum_weight,
sum_metro_prob,
writer, error_writer);
for (int n = 0; n < rho.size(); ++n)
EXPECT_FLOAT_EQ(p_sharp_backward_1(n), p_sharp_left(n));
for (int n = 0; n < rho.size(); ++n)
EXPECT_FLOAT_EQ(p_sharp_backward_1(n), p_sharp_right(n));
// Depth 1 backward
sampler.z() = z_init;
sampler.init_hamiltonian(writer, error_writer);
sampler.build_tree(1, z_propose,
p_sharp_left, p_sharp_right, rho,
H0, -1, n_leapfrog, log_sum_weight,
sum_metro_prob,
writer, error_writer);
for (int n = 0; n < rho.size(); ++n)
EXPECT_FLOAT_EQ(p_sharp_backward_1(n), p_sharp_left(n));
for (int n = 0; n < rho.size(); ++n)
EXPECT_FLOAT_EQ(p_sharp_backward_2(n), p_sharp_right(n));
// Depth 2 backward
sampler.z() = z_init;
sampler.init_hamiltonian(writer, error_writer);
sampler.build_tree(2, z_propose,
p_sharp_left, p_sharp_right, rho,
H0, -1, n_leapfrog, log_sum_weight,
sum_metro_prob,
writer, error_writer);
for (int n = 0; n < rho.size(); ++n)
EXPECT_FLOAT_EQ(p_sharp_backward_1(n), p_sharp_left(n));
for (int n = 0; n < rho.size(); ++n)
EXPECT_FLOAT_EQ(p_sharp_backward_3(n), p_sharp_right(n));
// Depth 3 backward
sampler.z() = z_init;
sampler.init_hamiltonian(writer, error_writer);
sampler.build_tree(3, z_propose,
p_sharp_left, p_sharp_right, rho,
H0, -1, n_leapfrog, log_sum_weight,
sum_metro_prob,
writer, error_writer);
for (int n = 0; n < rho.size(); ++n)
EXPECT_FLOAT_EQ(p_sharp_backward_1(n), p_sharp_left(n));
for (int n = 0; n < rho.size(); ++n)
EXPECT_FLOAT_EQ(p_sharp_backward_4(n), p_sharp_right(n));
}
void ba81NormalQuad::layer::setStructure(Eigen::ArrayBase<T1> ¶m,
Eigen::MatrixBase<T2> &gmean, Eigen::MatrixBase<T3> &gcov)
{
abilitiesMap.clear();
std::string str = string_snprintf("layer:");
for (int ax=0; ax < gmean.rows(); ++ax) {
if (!abilitiesMask[ax]) continue;
abilitiesMap.push_back(ax);
str += " ";
str += quad->ig.factorNames[ax];
}
str += ":";
itemsMap.clear();
glItemsMap.resize(param.cols(), -1);
for (int ix=0, lx=0; ix < param.cols(); ++ix) {
if (!itemsMask[ix]) continue;
itemsMap.push_back(ix);
glItemsMap[ix] = lx++;
str += string_snprintf(" %d", ix);
}
str += "\n";
//mxLogBig(str);
dataColumns.clear();
dataColumns.reserve(numItems());
totalOutcomes = 0;
for (int ix=0; ix < numItems(); ++ix) {
int outcomes = quad->ig.itemOutcomes[ itemsMap[ix] ];
itemOutcomes.push_back(outcomes);
cumItemOutcomes.push_back(totalOutcomes);
totalOutcomes += outcomes;
dataColumns.push_back(quad->ig.dataColumns[ itemsMap[ix] ]);
}
Eigen::VectorXd mean;
Eigen::MatrixXd cov;
globalToLocalDist(gmean, gcov, mean, cov);
if (mean.size() == 0) {
numSpecific = 0;
primaryDims = 0;
maxDims = 1;
totalQuadPoints = 1;
totalPrimaryPoints = 1;
weightTableSize = 1;
return;
}
numSpecific = 0;
if (quad->ig.twotier) detectTwoTier(param, mean, cov);
if (numSpecific) quad->hasBifactorStructure = true;
primaryDims = cov.cols() - numSpecific;
maxDims = primaryDims + (numSpecific? 1 : 0);
totalQuadPoints = 1;
for (int dx=0; dx < maxDims; dx++) {
totalQuadPoints *= quad->gridSize;
}
totalPrimaryPoints = totalQuadPoints;
weightTableSize = totalQuadPoints;
if (numSpecific) {
totalPrimaryPoints /= quad->gridSize;
weightTableSize *= numSpecific;
}
}
//==============================================================================
void Function::evalGradient(const Eigen::VectorXd& _x, Eigen::VectorXd& _grad)
{
Eigen::Map<Eigen::VectorXd> tmpGrad(_grad.data(), _grad.size());
evalGradient(_x, tmpGrad);
}
Eigen::MatrixXd KalmanFilter::Propagate(Eigen::VectorXd x_hat_plus, Eigen::MatrixXd P_plus, double v_m, double w_m, Eigen::MatrixXd Q, double dt)
{
int n = x_hat_plus.size();
double ori = x_hat_plus(2);
Eigen::VectorXd x_hat_min(n);
Eigen::MatrixXd P_min(n,n);
Eigen::MatrixXd Set(n,n+1); //Set of state and covariance
Eigen::MatrixXd Phi_R(3,3);
Eigen::MatrixXd G(3,2);
Eigen::MatrixXd tempTrans;
//Propagate state (Robot and Landmark, no change in Landmark)
x_hat_min.head(3) << v_m*cos(ori),
v_m*sin(ori),
w_m;
x_hat_min.head(3) = x_hat_plus.head(3) + dt*x_hat_min.head(3);
x_hat_min.tail(n-3) = x_hat_plus.tail(n-3);
// Set up Phi_R and G
Phi_R << 1, 0, -dt*v_m*sin(ori),
0, 1, dt*v_m*cos(ori),
0, 0, 1;
G << -dt*cos(ori), 0,
-dt*sin(ori), 0,
0, -dt;
// Propagate Covariance
// P_RR
P_min.block(0,0,3,3) = Phi_R * P_plus.block(0,0,3,3) * Phi_R.transpose() + G * Q * G.transpose();
// P_RL
P_min.block(0,3,3,n-3) = Phi_R * P_plus.block(0,3,3,n-3);
// P_LR
tempTrans = P_min.block(0,3,3,n-3).transpose();
P_min.block(3,0,n-3,3) = tempTrans;
// P_LL are not affected by propagation.
P_min.block(3,3,n-3,n-3) = P_plus.block(3,3,n-3, n-3);
// Make sure the matrix is symmetric, may skip this option
tempTrans = 0.5 * (P_min + P_min.transpose());
P_min = tempTrans;
// Put State vector and Covariance into one matrix and return it.
// We can parse these out in the main function.
Set.block(0,0,n,1) = x_hat_min;
Set.block(0,1,n,n) = P_min;
return Set;
}
inline std::vector<double> eigenVectorToStdVector(const Eigen::VectorXd& v) {
std::vector<double> m(v.size());
for (int i = 0; i < v.size(); i++)
m[i] = v[i];
return m;
}
void Input::initMolecule() {
// Gather information necessary to build molecule_
// 1. number of atomic centers
int nuclei = int(geometry_.size() / 4);
// 2. position and charges of atomic centers
Eigen::Matrix3Xd centers = Eigen::Matrix3Xd::Zero(3, nuclei);
Eigen::VectorXd charges = Eigen::VectorXd::Zero(nuclei);
int j = 0;
for (int i = 0; i < nuclei; ++i) {
centers.col(i) =
(Eigen::Vector3d() << geometry_[j], geometry_[j + 1], geometry_[j + 2])
.finished();
charges(i) = geometry_[j + 3];
j += 4;
}
// 3. list of atoms and list of spheres
std::vector<Atom> radiiSet;
std::vector<Atom> atoms;
atoms.reserve(nuclei);
// FIXME Code duplication in function initMolecule in interface/Meddle.cpp
tie(radiiSetName_, radiiSet) = utils::bootstrapRadiiSet().create(radiiSet_);
for (int i = 0; i < charges.size(); ++i) {
int index = int(charges(i)) - 1;
atoms.push_back(radiiSet[index]);
if (scaling_)
atoms[i].radiusScaling = 1.2;
}
// Based on the creation mode (Implicit or Atoms)
// the spheres list might need postprocessing
if (mode_ == "IMPLICIT" || mode_ == "ATOMS") {
for (int i = 0; i < charges.size(); ++i) {
// Convert to Bohr and multiply by scaling factor (alpha)
double radius = atoms[i].radius * angstromToBohr() * atoms[i].radiusScaling;
spheres_.push_back(Sphere(centers.col(i), radius));
}
if (mode_ == "ATOMS") {
// Loop over the atomsInput array to get which atoms will have a user-given
// radius
for (size_t i = 0; i < atoms_.size(); ++i) {
int index =
atoms_[i] - 1; // -1 to go from human readable to machine readable
// Put the new Sphere in place of the implicit-generated one
spheres_[index] = Sphere(centers.col(index), radii_[i]);
}
}
}
// 4. masses
Eigen::VectorXd masses = Eigen::VectorXd::Zero(nuclei);
for (int i = 0; i < masses.size(); ++i) {
masses(i) = atoms[i].mass;
}
// 5. molecular point group
// FIXME currently hardcoded to C1
// OK, now get molecule_
molecule_ = Molecule(nuclei, charges, masses, centers, atoms, spheres_);
// Check that all atoms have a radius attached
std::vector<Atom>::const_iterator res =
std::find_if(atoms.begin(), atoms.end(), invalid);
if (res != atoms.end()) {
std::cout << molecule_ << std::endl;
PCMSOLVER_ERROR("Some atoms do not have a radius attached. Please specify a "
"radius for all atoms (see "
"http://pcmsolver.readthedocs.org/en/latest/users/input.html)!");
}
}
// more general version--arbitrary number of joints
bool TrajActionServer::update_trajectory(double traj_clock, trajectory_msgs::JointTrajectory trajectory, Eigen::VectorXd qvec_prev,
int &isegment, Eigen::VectorXd &qvec_new) {
trajectory_msgs::JointTrajectoryPoint trajectory_point_from, trajectory_point_to;
int njnts = qvec_prev.size();
cout<<"njnts for qvec_prev: "<<njnts<<endl;
Eigen::VectorXd qvec, qvec_to, delta_qvec, dqvec;
int nsegs = trajectory.points.size() - 1;
ROS_INFO("update_trajectory: nsegs = %d, isegment = %d",nsegs,isegment);
double t_subgoal;
//cout<<"traj_clock = "<<traj_clock<<endl;
if (isegment < nsegs) {
trajectory_point_to = trajectory.points[isegment + 1];
t_subgoal = trajectory_point_to.time_from_start.toSec();
cout<<"iseg = "<<isegment<<"; t_subgoal = "<<t_subgoal<<endl;
} else {
cout << "reached end of last segment" << endl;
trajectory_point_to = trajectory.points[nsegs];
t_subgoal = trajectory_point_to.time_from_start.toSec();
for (int i = 0; i < njnts; i++) {
qvec_new[i] = trajectory_point_to.positions[i];
}
cout << "final time: " << t_subgoal << endl;
return false;
}
cout<<"iseg = "<<isegment<<"; t_subgoal = "<<t_subgoal<<endl;
while ((t_subgoal < traj_clock)&&(isegment < nsegs)) {
cout<<"loop: iseg = "<<isegment<<"; t_subgoal = "<<t_subgoal<<endl;
isegment++;
if (isegment > nsegs - 1) {
//last point
trajectory_point_to = trajectory.points[nsegs];
cout<<"next traj pt #jnts = "<<trajectory_point_to.positions.size()<<endl;
for (int i = 0; i < njnts; i++) {
qvec_new[i] = trajectory_point_to.positions[i];
}
cout << "iseg>nsegs" << endl;
return false;
}
trajectory_point_to = trajectory.points[isegment + 1];
t_subgoal = trajectory_point_to.time_from_start.toSec();
}
//cout<<"t_subgoal = "<<t_subgoal<<endl;
//here if have a valid segment:
cout<<"njnts of trajectory_point_to: "<<trajectory_point_to.positions.size()<<endl;
qvec_to.resize(njnts);
for (int i = 0; i < njnts; i++) {
qvec_to[i] = trajectory_point_to.positions[i];
}
delta_qvec.resize(njnts);
delta_qvec = qvec_to - qvec_prev; //this far to go until next node;
double delta_time = t_subgoal - traj_clock;
if (delta_time < dt_traj) delta_time = dt_traj;
dqvec.resize(njnts);
dqvec = delta_qvec * dt_traj / delta_time;
qvec_new = qvec_prev + dqvec;
return true;
}
//==============================================================================
bool GradientDescentSolver::solve()
{
bool minimized = false;
bool satisfied = false;
std::shared_ptr<Problem> problem = mProperties.mProblem;
if(nullptr == problem)
{
dtwarn << "[GradientDescentSolver::solve] Attempting to solve a nullptr "
<< "problem! We will return false.\n";
return false;
}
double tol = std::abs(mProperties.mTolerance);
double gamma = mGradientP.mStepSize;
size_t dim = problem->getDimension();
if(dim == 0)
{
problem->setOptimalSolution(Eigen::VectorXd());
problem->setOptimumValue(0.0);
return true;
}
Eigen::VectorXd x = problem->getInitialGuess();
assert(x.size() == static_cast<int>(dim));
Eigen::VectorXd lastx = x;
Eigen::VectorXd dx(x.size());
Eigen::VectorXd grad(x.size());
mEqConstraintCostCache.resize(problem->getNumEqConstraints());
mIneqConstraintCostCache.resize(problem->getNumIneqConstraints());
mLastNumIterations = 0;
size_t attemptCount = 0;
do
{
size_t stepCount = 0;
do
{
++mLastNumIterations;
// Perturb the configuration if we have reached an iteration where we are
// supposed to perturb it.
if(mGradientP.mPerturbationStep > 0 && stepCount > 0
&& stepCount%mGradientP.mPerturbationStep == 0)
{
dx = x; // Seed the configuration randomizer with the current configuration
randomizeConfiguration(dx);
// Step the current configuration towards the randomized configuration
// proportionally to a randomized scaling factor
double scale = mGradientP.mMaxPerturbationFactor*mDistribution(mMT);
x += scale*(dx-x);
}
// Check if the equality constraints are satsified
satisfied = true;
for(size_t i=0; i<problem->getNumEqConstraints(); ++i)
{
mEqConstraintCostCache[i] = problem->getEqConstraint(i)->eval(x);
if(std::abs(mEqConstraintCostCache[i]) > tol)
satisfied = false;
}
// Check if the inequality constraints are satisfied
for(size_t i=0; i<problem->getNumIneqConstraints(); ++i)
{
mIneqConstraintCostCache[i] = problem->getIneqConstraint(i)->eval(x);
if(mIneqConstraintCostCache[i] > std::abs(tol))
satisfied = false;
}
Eigen::Map<Eigen::VectorXd> dxMap(dx.data(), dim);
Eigen::Map<Eigen::VectorXd> gradMap(grad.data(), dim);
// Compute the gradient of the objective, combined with the weighted
// gradients of the softened constraints
problem->getObjective()->evalGradient(x, dxMap);
for(int i=0; i < static_cast<int>(problem->getNumEqConstraints()); ++i)
{
if(std::abs(mEqConstraintCostCache[i]) < tol)
continue;
problem->getEqConstraint(i)->evalGradient(x, gradMap);
// Get the user-specified weight if available, otherwise use the default
// weight value
double weight = mGradientP.mEqConstraintWeights.size() > i?
mGradientP.mEqConstraintWeights[i] :
mGradientP.mDefaultConstraintWeight;
// We treat the constraint function as though we are minimizing its
// absolute value. We do not want to treat it as though we are
// minimizing its square, because that could adversely affect the
// curvature of its derivative.
dx += weight * grad * math::sign(mEqConstraintCostCache[i]);
}
for(int i=0; i < static_cast<int>(problem->getNumIneqConstraints()); ++i)
{
if(mIneqConstraintCostCache[i] < tol)
continue;
problem->getIneqConstraint(i)->evalGradient(x, gradMap);
// Get the user-specified weight if available, otherwise use the
// default weight value
double weight = mGradientP.mIneqConstraintWeights.size() > i?
mGradientP.mIneqConstraintWeights[i] :
mGradientP.mDefaultConstraintWeight;
dx += weight * grad;
}
x -= gamma*dx;
clampToBoundary(x);
if((x-lastx).norm() < tol)
minimized = true;
else
minimized = false;
lastx = x;
++stepCount;
if(nullptr != mProperties.mOutStream &&
mProperties.mIterationsPerPrint > 0 &&
stepCount%mProperties.mIterationsPerPrint == 0)
{
*mProperties.mOutStream
<< "[GradientDescentSolver] Progress (attempt #"
<< attemptCount << " | iteration #" << stepCount << ")\n"
<< "cost: " << problem->getObjective()->eval(x) << " | "
<< (minimized? "minimized | " : "not minimized | ")
<< (satisfied? "constraints satisfied | "
: "constraints unsatisfied | ")
<< "x: " << x.transpose() << "\n"
<< "grad: " << dx.transpose() << std::endl;
}
if(stepCount > mProperties.mNumMaxIterations)
break;
} while(!minimized || !satisfied);
if(!minimized || !satisfied)
{
++attemptCount;
if(mGradientP.mMaxAttempts > 0 && attemptCount >= mGradientP.mMaxAttempts)
break;
if(attemptCount-1 < problem->getSeeds().size())
{
x = problem->getSeed(attemptCount-1);
}
else
{
randomizeConfiguration(x);
}
}
} while(!minimized || !satisfied);
mLastConfig = x;
problem->setOptimalSolution(x);
problem->setOptimumValue(problem->getObjective()->eval(x));
return minimized && satisfied;
}
void multiTaskRecursiveLinearEstimator::setOutputErrorStandardDeviation(const Eigen::VectorXd &sigma_oe_input)
{
assert(sigma_oe.size() == m);
assert(sigma_oe_input.size() == m);
sigma_oe = sigma_oe_input;
}
double operator()(const Eigen::VectorXd & x1, const Eigen::VectorXd & x2) const {
assert(x1.size() == _ell.size());
double z = (x1 - x2).cwiseQuotient(_ell).squaredNorm();
return _sf2 * exp(-0.5 * z);
}
//==============================================================================
void NullFunction::evalGradient(const Eigen::VectorXd& _x,
Eigen::Map<Eigen::VectorXd> _grad)
{
_grad.resize(_x.size());
_grad.setZero();
}
void SubSystem::setParams(Eigen::VectorXd &xIn)
{
assert(xIn.size() == psize);
for (int i=0; i < psize; i++)
pvals[i] = xIn[i];
}