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JointMechanicsTool.cpp
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JointMechanicsTool.cpp
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/* -------------------------------------------------------------------------- *
* JointMechanicsTool.cpp *
* -------------------------------------------------------------------------- *
* Author(s): Colin Smith *
* *
* Licensed under the Apache License, Version 2.0 (the "License"); you may *
* not use this file except in compliance with the License. You may obtain a *
* copy of the License at http://www.apache.org/licenses/LICENSE-2.0. *
* *
* Unless required by applicable law or agreed to in writing, software *
* distributed under the License is distributed on an "AS IS" BASIS, *
* WITHOUT WARRANTIES OR CONDITIONS OF ANY KIND, either express or implied. *
* See the License for the specific language governing permissions and *
* limitations under the License. *
* -------------------------------------------------------------------------- */
#include <OpenSim/Simulation/Model/Model.h>
#include "JointMechanicsTool.h"
#include "VTPFileAdapter.h"
#include "H5Cpp.h"
#include "hdf5_hl.h"
#include "Smith2018ArticularContactForce.h"
#include "HelperFunctions.h"
#include "Blankevoort1991Ligament.h"
#include <OpenSim/Analyses/StatesReporter.h>
#include <OpenSim/Common/STOFileAdapter.h>
#include <OpenSim/Common/GCVSpline.h>
#include <OpenSim/Common/CSVFileAdapter.h>
using namespace OpenSim;
JointMechanicsTool::JointMechanicsTool() : Object()
{
setNull();
constructProperties();
_directoryOfSetupFile = "";
}
JointMechanicsTool::JointMechanicsTool(std::string settings_file) :
Object(settings_file) {
constructProperties();
updateFromXMLDocument();
loadModel(settings_file);
_directoryOfSetupFile = IO::getParentDirectory(settings_file);
IO::chDir(_directoryOfSetupFile);
}
JointMechanicsTool::JointMechanicsTool(Model *aModel,
std::string states_file, std::string results_dir) :
JointMechanicsTool()
{
if(aModel==NULL) return;
setModel(*aModel);
set_states_file(states_file);
set_results_directory(results_dir);
}
void JointMechanicsTool::setNull()
{
setAuthors("Colin Smith");
}
void JointMechanicsTool::constructProperties()
{
Array<std::string> defaultListAll;
defaultListAll.append("all");
Array<std::string> defaultListNone;
defaultListNone.append("none");
constructProperty_model_file("");
constructProperty_states_file("");
constructProperty_results_directory(".");
constructProperty_results_file_basename("");
constructProperty_start_time(-1);
constructProperty_stop_time(-1);
constructProperty_resample_step_size(-1);
constructProperty_normalize_to_cycle(false);
constructProperty_lowpass_filter_frequency(-1);
constructProperty_print_processed_kinematics(false);
constructProperty_contacts(defaultListAll);
constructProperty_contact_outputs(defaultListAll);
constructProperty_contact_mesh_properties(defaultListNone);
constructProperty_ligaments(defaultListAll);
constructProperty_ligament_outputs(defaultListAll);
constructProperty_muscles(defaultListNone);
constructProperty_muscle_outputs(defaultListNone);
constructProperty_attached_geometry_bodies(defaultListNone);
constructProperty_output_origin("ground");
constructProperty_output_frame("ground");
constructProperty_write_vtp_files(true);
constructProperty_vtp_file_format("binary");
constructProperty_write_h5_file(true);
constructProperty_h5_states_data(true);
constructProperty_h5_kinematics_data(true);
constructProperty_AnalysisSet(AnalysisSet());
}
void JointMechanicsTool::setModel(Model& aModel)
{
_model = &aModel;
set_model_file(_model->getDocumentFileName());
}
void JointMechanicsTool::run() {
//Set the max number of points a ligament or muscle path can contain
_max_path_points = 100;
//Make results directory
int makeDir_out = IO::makeDir(get_results_directory());
if (errno == ENOENT && makeDir_out == -1) {
OPENSIM_THROW(Exception, "Could not create " +
get_results_directory() +
"Possible reason: This tool cannot make new folder with subfolder.");
}
if (_model == NULL) {
OPENSIM_THROW(Exception, "No model was set in JointMechanicsTool");
}
SimTK::State state = _model->initSystem();
readStatesFromFile();
initialize(state);
//loop over each frame
for (int i = 0; i < _n_frames; ++i) {
//Set Time
state.setTime(_time[i]);
std::cout << "Time: " << _time[i] << std::endl;
//Set Qs and Us
int nCoord = 0;
for (const Coordinate& coord : _model->getComponentList<Coordinate>()) {
coord.setValue(state, _q_matrix(i, nCoord));
coord.setSpeedValue(state, _u_matrix(i, nCoord));
nCoord++;
}
//Set Muscle States
if(!_muscle_paths.empty()){
int nMsl = 0;
for (const Muscle& msl : _model->updComponentList<Muscle>()) {
for (int j = 0; j < _muscle_state_names[nMsl].size(); ++j) {
msl.setStateVariableValue(state, _muscle_state_names[nMsl][j], _muscle_state_data[nMsl][j][i]);
}
nMsl++;
}
}
//Record Values
record(state,i);
//Perform analyses
if (i == 0) {
_model->updAnalysisSet().begin(state);
}
else {
_model->updAnalysisSet().step(state, i);
}
}
printResults(get_results_file_basename(), get_results_directory());
}
void JointMechanicsTool::readStatesFromFile() {
std::string saveWorkingDirectory = IO::getCwd();
IO::chDir(_directoryOfSetupFile);
Storage store = Storage(get_states_file());
IO::chDir(saveWorkingDirectory);
//Set Start and Stop Times
store.getTimeColumn(_time);
if (get_start_time() == -1) {
set_start_time(_time.get(0));
}
if (get_stop_time() == -1) {
set_stop_time(_time.getLast());
}
const CoordinateSet& coordinateSet = _model->getCoordinateSet();
if (store.isInDegrees()) {
_model->getSimbodyEngine().convertDegreesToRadians(store);
}
else if (get_lowpass_filter_frequency() != -1) {
store.pad(store.getSize() / 2);
store.lowpassIIR(get_lowpass_filter_frequency());
}
//Cut to start and stop times
store.crop(get_start_time(), get_stop_time());
if (get_normalize_to_cycle() == true) {
double norm_dt = (get_stop_time() - get_start_time()) / 100;
store.resampleLinear(norm_dt);
}
else if (get_resample_step_size() != -1 && get_normalize_to_cycle() == false) {
store.resampleLinear(get_resample_step_size());
}
if (get_print_processed_kinematics()) {
store.print(get_results_directory() + "/" + get_results_file_basename() + "_processed_kinematics.sto");
}
//Update the time
store.getTimeColumn(_time);
//Set number of Frames
_n_frames = _time.size();
//Gather Q and U values
Array<std::string> col_labels = store.getColumnLabels();
Array<int> q_col_map(-1, _model->getNumCoordinates());
for (int i = 0; i < col_labels.size(); ++i) {
std::vector<std::string> split_label = split_string(col_labels[i], "/");
int j = 0;
for (const Coordinate& coord : _model->getComponentList<Coordinate>()) {
if (contains_string(split_label, coord.getName())) {
if (split_label.back() == "value" || split_label.back() == coord.getName()) {
q_col_map[j] = i;
}
}
j++;
}
}
_q_matrix.resize(_n_frames, _model->getNumCoordinates());
_u_matrix.resize(_n_frames, _model->getNumCoordinates());
_q_matrix = 0;
_u_matrix = 0;
int j = 0;
for (const Coordinate& coord : _model->getComponentList<Coordinate>()) {
if (q_col_map[j] != -1) {
double* data = NULL;
store.getDataColumn(col_labels[q_col_map[j]], data);
for (int i = 0; i < _n_frames; ++i) {
_q_matrix(i, j) = data[i];
}
}
else {
std::cout << "Coordinate Value: " << coord.getName() << " not found in coordinates_file, assuming 0." << std::endl;
}
GCVSpline q_spline;
q_spline.setDegree(5);
for (int i = 0; i < _n_frames; ++i) {
q_spline.addPoint(_time[i], _q_matrix(i,j));
}
for (int i = 0; i < _n_frames; ++i) {
SimTK::Vector x(1);
x(0) = _time[i];
std::vector<int> u_order = { 0 };
_u_matrix(i, j) = q_spline.calcDerivative(u_order, x);
}
j++;
}
//Gather Muscle States
//if(!_muscle_paths.empty()){
for (const Muscle& msl : _model->updComponentList<Muscle>()) {
std::vector<std::string> state_names;
std::vector<SimTK::Vector> state_values;
Array<std::string> stateVariableNames = msl.getStateVariableNames();
for (int i = 0; i < stateVariableNames.getSize(); ++i) {
state_names.push_back(stateVariableNames[i]);
}
_muscle_state_names.push_back(state_names);
for (std::string msl_state : state_names) {
int col_ind = -1;
for (int j = 0; j < col_labels.size(); ++j) {
if (col_labels[j] == msl_state) {
col_ind = j;
break;
}
}
SimTK::Vector state_data(_n_frames, 0.0);
if (col_ind == -1) {
// std::cout << "WARNING:: Muscle state (" + msl_state + ") NOT found in coordinates file. Assumed 0.0" << std::endl;
}
else {
Array<double> data;
store.getDataColumn(col_labels[col_ind], data);
for (int j = 0; j < data.getSize(); ++j) {
state_data.set(j, data[j]);
}
}
state_values.push_back(state_data);
}
_muscle_state_data.push_back(state_values);
}
//}
}
void JointMechanicsTool::initialize(SimTK::State& state) {
//States
if (get_h5_states_data()) {
StatesReporter* states_rep = new StatesReporter();
states_rep->setName("states_analysis");
states_rep->setStepInterval(1);
states_rep->setPrintResultFiles(false);
_model->addAnalysis(states_rep);
}
//Add Analysis set
AnalysisSet aSet = get_AnalysisSet();
int size = aSet.getSize();
for(int i=0;i<size;i++) {
Analysis *analysis = aSet.get(i).clone();
_model->addAnalysis(analysis);
}
AnalysisSet& analysisSet = _model->updAnalysisSet();
state = _model->initSystem();
setupContactStorage(state);
setupLigamentStorage();
setupMuscleStorage();
setupAttachedGeometriesStorage();
if (get_h5_kinematics_data()) {
setupCoordinateStorage();
}
}
void JointMechanicsTool::setupContactStorage(SimTK::State& state) {
if (_model->countNumComponents<Smith2018ArticularContactForce>() == 0) return;
//Contact Names
if (getProperty_contacts().size() == 0 || get_contacts(0) == "none") {
return;
}
else if (get_contacts(0) == "all") {
for (const Smith2018ArticularContactForce& contactForce : _model->getComponentList<Smith2018ArticularContactForce>()) {
_contact_force_names.push_back(contactForce.getName());
_contact_force_paths.push_back(contactForce.getAbsolutePathString());
std::string casting_mesh_name = contactForce.getConnectee<Smith2018ContactMesh>("casting_mesh").getName();
std::string target_mesh_name = contactForce.getConnectee<Smith2018ContactMesh>("target_mesh").getName();
std::string casting_mesh_path = contactForce.getConnectee<Smith2018ContactMesh>("casting_mesh").getAbsolutePathString();
std::string target_mesh_path = contactForce.getConnectee<Smith2018ContactMesh>("target_mesh").getAbsolutePathString();
if (!contains_string(_contact_mesh_names, casting_mesh_name)) {
_contact_mesh_names.push_back(casting_mesh_name);
_contact_mesh_paths.push_back(casting_mesh_path);
}
if (!contains_string(_contact_mesh_names, target_mesh_name)) {
_contact_mesh_names.push_back(target_mesh_name);
_contact_mesh_paths.push_back(target_mesh_path);
}
}
}
else {
for (int i = 0; i < getProperty_contacts().size(); ++i) {
try {
const Smith2018ArticularContactForce& contactForce = _model->getComponent<Smith2018ArticularContactForce>(get_contacts(i));
_contact_force_names.push_back(contactForce.getName());
_contact_force_paths.push_back(contactForce.getAbsolutePathString());
std::string casting_mesh_name = contactForce.getConnectee<Smith2018ContactMesh>("casting_mesh").getName();
std::string target_mesh_name = contactForce.getConnectee<Smith2018ContactMesh>("target_mesh").getName();
std::string casting_mesh_path = contactForce.getConnectee<Smith2018ContactMesh>("casting_mesh").getAbsolutePathString();
std::string target_mesh_path = contactForce.getConnectee<Smith2018ContactMesh>("target_mesh").getAbsolutePathString();
if (!contains_string(_contact_mesh_names, casting_mesh_name)) {
_contact_mesh_names.push_back(casting_mesh_name);
_contact_mesh_paths.push_back(casting_mesh_path);
}
if (!contains_string(_contact_mesh_names, target_mesh_name)) {
_contact_mesh_names.push_back(target_mesh_name);
_contact_mesh_paths.push_back(target_mesh_path);
}
}
catch (ComponentNotFoundOnSpecifiedPath){
OPENSIM_THROW(Exception, "contact_name: " + get_contacts(i)
+ " was not found as a Smith2018ArticularContactForce path"
" in the model. Did you use absolute path?");
}
}
}
//Turn on mesh flipping so metrics are computed for casting and target
for (int i = 0; i < _contact_force_paths.size(); ++i) {
Smith2018ArticularContactForce& contactForce = _model->updComponent
<Smith2018ArticularContactForce>(_contact_force_paths[i]);
contactForce.setModelingOption(state, "flip_meshes", 1);
}
//Realize Report so the sizes of output vectors are known
_model->realizeReport(state);
//Contact Outputs
const Smith2018ArticularContactForce& frc0 = _model->getComponent
<Smith2018ArticularContactForce>(_contact_force_paths[0]);
if (get_contact_outputs(0) == "all") {
for (const auto& entry : frc0.getOutputs()) {
const std::string& output_name = entry.first;
const AbstractOutput* output = entry.second.get();
if(output->isListOutput()){continue;}
if (output->getTypeName() == "double") {
_contact_output_double_names.push_back(output->getName());
}
if (output->getTypeName() == "Vec3") {
_contact_output_vec3_names.push_back(output->getName());
}
if (output->getTypeName() == "Vector") {
_contact_output_vector_double_names.push_back(
output->getName());
}
}
}
else if (getProperty_contact_outputs().size() != 0 &&
get_contact_outputs(0) != "none") {
for (int i = 0; i < getProperty_contact_outputs().size(); ++i) {
try {
std::string output_name = get_contact_outputs(i);
const AbstractOutput& output = frc0.getOutput(output_name);
if (output.getTypeName() == "double") {
_contact_output_double_names.push_back(output_name);
}
if (output.getTypeName() == "Vec3") {
_contact_output_vec3_names.push_back(output_name);
}
if (output.getTypeName() == "Vector") {
_contact_output_vector_double_names.push_back(output_name);
}
}
catch (Exception){
OPENSIM_THROW(Exception, "contact_output: " +
get_contact_outputs(i) + " is not a valid "
"Smith2018ArticularContactForce output name")
}
}
}
// Output Storage
int nOutputDouble = _contact_output_double_names.size();
int nOutputVec3 = _contact_output_vec3_names.size();
int nOutputVector = _contact_output_vector_double_names.size();
SimTK::Matrix double_data(_n_frames, nOutputDouble,-1);
SimTK::Matrix_<SimTK::Vec3> vec3_data(_n_frames, nOutputVec3,SimTK::Vec3(-1));
for (std::string frc_path : _contact_force_paths) {
const Smith2018ArticularContactForce& frc = _model->updComponent<Smith2018ArticularContactForce>(frc_path);
_contact_output_double_values.push_back(double_data);
_contact_output_vec3_values.push_back(vec3_data);
std::vector<SimTK::Matrix> def_output_vector;
for (int i = 0; i < nOutputVector; ++i) {
const AbstractOutput& abs_output = frc.getOutput(_contact_output_vector_double_names[i]);
const Output<SimTK::Vector>& vector_output = dynamic_cast<const Output<SimTK::Vector>&>(abs_output);
int output_vector_size = vector_output.getValue(state).size();
def_output_vector.push_back(SimTK::Matrix(_n_frames, output_vector_size,-1));
}
_contact_output_vector_double_values.push_back(def_output_vector);
}
//Vertex location storage
_mesh_vertex_locations.resize(_contact_mesh_paths.size());
for (int i = 0; i < _contact_mesh_paths.size(); ++i) {
int mesh_nVer = _model->getComponent<Smith2018ContactMesh>
(_contact_mesh_paths[i]).getPolygonalMesh().getNumVertices();
_mesh_vertex_locations[i].resize(_n_frames, mesh_nVer);
}
}
void JointMechanicsTool::setupAttachedGeometriesStorage() {
std::vector<std::string> body_path_list;
if (get_attached_geometry_bodies(0) == "none" ||
getProperty_attached_geometry_bodies().empty()) {
return;
}
else if (get_attached_geometry_bodies(0) == "all") {
for (const Frame& frame : _model->updComponentList<Frame>()) {
body_path_list.push_back(frame.getAbsolutePathString());
}
}
else {
int nAttachedGeoBodies = getProperty_attached_geometry_bodies().size();
for (int i = 0; i < nAttachedGeoBodies; ++i) {
try {
const Frame& frame = _model->updComponent<Frame>
(get_attached_geometry_bodies(i));
body_path_list.push_back(frame.getAbsolutePathString());
}
catch (Exception) {
OPENSIM_THROW(Exception, "attached_geometry_bodies: " +
get_attached_geometry_bodies(i) + "does not exist as a "
"Frame component in model. Did you use Absolute Path?");
}
}
}
for (std::string body_path : body_path_list){
const Frame& frame = _model->updComponent<Frame>(body_path);
int nAttachedGeos = frame.getProperty_attached_geometry().size();
for (int i = 0; i < nAttachedGeos; ++i) {
const Geometry& geo = frame.get_attached_geometry(i);
if (geo.getConcreteClassName() != "Mesh") {
continue;
}
if (contains_string(_attach_geo_names, geo.getName())) {
continue;
}
Mesh* mesh = (Mesh*)&geo;
std::string filename = findMeshFile(mesh->get_mesh_file());
SimTK::PolygonalMesh ply_mesh;
ply_mesh.loadFile(filename);
//Apply Scale Factors
SimTK::Vec3 scale = mesh->get_scale_factors();
if (scale != SimTK::Vec3(1)) {
SimTK::PolygonalMesh scaled_mesh;
for (int v = 0; v < ply_mesh.getNumVertices(); ++v) {
scaled_mesh.addVertex(ply_mesh.
getVertexPosition(v).elementwiseMultiply(scale));
}
for (int f = 0; f < ply_mesh.getNumFaces(); ++f) {
SimTK::Array_<int> facevertex;
int numVertex = ply_mesh.getNumVerticesForFace(f);
for (int k = 0; k < numVertex; ++k) {
facevertex.push_back(ply_mesh.getFaceVertex(f, k));
}
scaled_mesh.addFace(facevertex);
}
ply_mesh.copyAssign(scaled_mesh);
}
_attach_geo_names.push_back(geo.getName());
_attach_geo_frames.push_back(frame.getAbsolutePathString());
_attach_geo_meshes.push_back(ply_mesh);
_attach_geo_vertex_locations.push_back(SimTK::Matrix_<SimTK::Vec3>(_n_frames, ply_mesh.getNumVertices()));
}
}
}
std::string JointMechanicsTool::findMeshFile(const std::string& mesh_file) {
std::string model_file =
SimTK::Pathname::getAbsolutePathname(_model->getDocumentFileName());
std::string model_dir, dummy1, dummy2;
bool dummyBool;
SimTK::Pathname::deconstructPathname(model_file,
dummyBool, model_dir, dummy1, dummy2);
std::string mesh_full_path;
std::ifstream file(mesh_file);
if (!file) {
mesh_full_path = model_dir + mesh_file;
file.open(mesh_full_path);
}
if (!file) {
mesh_full_path = model_dir + "Geometry/" + mesh_file;
file.open(mesh_full_path);
}
if (!file) {
OPENSIM_THROW(Exception, "Attached Geometry file doesn't exist:\n"
+ model_dir + "[Geometry/]" + mesh_file);
}
return mesh_full_path;
}
void JointMechanicsTool::setupLigamentStorage() {
if (_model->countNumComponents<Blankevoort1991Ligament>() == 0) return;
//Ligament Names
if (getProperty_ligaments().size() == 0 || get_ligaments(0) == "none") {
return;
}
else if (get_ligaments(0) == "all") {
for (const Blankevoort1991Ligament& lig :
_model->updComponentList<Blankevoort1991Ligament>()) {
_ligament_names.push_back(lig.getName());
_ligament_paths.push_back(lig.getAbsolutePathString());
}
}
else
{
for (int i = 0; i < getProperty_ligaments().size(); ++i)
{
try {
const Blankevoort1991Ligament& lig = _model->updComponent
<Blankevoort1991Ligament>(get_ligaments(i));
_ligament_names.push_back(lig.getName());
_ligament_paths.push_back(lig.getAbsolutePathString());
}
catch (ComponentNotFoundOnSpecifiedPath) {
OPENSIM_THROW(Exception, "ligament: " + get_ligaments(i) +
" was not found in the model. "
"Are you using the absolute path?");
}
}
}
//Ligament Outputs
const Blankevoort1991Ligament& lig0 = _model->
updComponentList<Blankevoort1991Ligament>().begin().deref();
if (get_ligament_outputs(0) == "all") {
for (const auto& entry : lig0.getOutputs()) {
const AbstractOutput* output = entry.second.get();
if(output->isListOutput()){continue;}
if (output->getTypeName() == "double") {
_ligament_output_double_names.push_back(output->getName());
}
}
}
else if (getProperty_ligament_outputs().size() != 0 &&
get_ligament_outputs(0) != "none") {
for (int i = 0; i < getProperty_ligament_outputs().size(); ++i) {
try {
std::string output_name = get_ligament_outputs(i);
lig0.getOutput(output_name);
_ligament_output_double_names.push_back(output_name);
}
catch (Exception){
OPENSIM_THROW(Exception, "ligament_output: " +
get_ligament_outputs(i) + " is not a valid "
"Blankevoort1991Ligament output name")
}
}
}
int nLigamentOutputs = _ligament_output_double_names.size();
SimTK::Matrix lig_output_data(_n_frames, nLigamentOutputs,-1);
//Ligament Storage
for (std::string lig_path : _ligament_paths) {
Blankevoort1991Ligament lig =
_model->updComponent<Blankevoort1991Ligament>(lig_path);
//Path Point Storage
SimTK::Matrix_<SimTK::Vec3> lig_matrix(_n_frames,
_max_path_points, SimTK::Vec3(-1));
SimTK::Vector lig_vector(_n_frames, -1);
_ligament_path_points.push_back(lig_matrix);
_ligament_path_nPoints.push_back(lig_vector);
//Output Data Storage
_ligament_output_double_values.push_back(lig_output_data);
}
}
void JointMechanicsTool::setupMuscleStorage() {
if (_model->countNumComponents<Muscle>() == 0) return;
//Muscle Names
if (getProperty_muscles().size() == 0 || get_muscles(0) == "none") {
return;
}
else if (get_muscles(0) == "all") {
for (const Muscle& msl :
_model->updComponentList<Muscle>()) {
_muscle_names.push_back(msl.getName());
_muscle_paths.push_back(msl.getAbsolutePathString());
}
}
else
{
for (int i = 0; i < getProperty_muscles().size(); ++i)
{
try {
const Muscle& msl = _model->updComponent
<Muscle>(get_muscles(i));
_muscle_names.push_back(msl.getName());
_muscle_paths.push_back(msl.getAbsolutePathString());
}
catch (ComponentNotFoundOnSpecifiedPath) {
OPENSIM_THROW(Exception, "Muscle: " + get_muscles(i) +
" was not found in the model. "
"Are you using the absolute path?");
}
}
}
//Muscle Outputs
const Muscle& msl0 = _model->getMuscles().get(0);
if (get_muscle_outputs(0) == "all") {
for (const auto& entry : msl0.getOutputs()) {
const AbstractOutput* output = entry.second.get();
if(output->isListOutput()){continue;}
if (output->getTypeName() == "double") {
_muscle_output_double_names.push_back(output->getName());
}
}
}
else if (getProperty_muscle_outputs().size() != 0 &&
get_muscle_outputs(0) != "none") {
for (int i = 0; i < getProperty_muscle_outputs().size(); ++i) {
try {
std::string output_name = get_muscle_outputs(i);
msl0.getOutput(output_name);
_muscle_output_double_names.push_back(output_name);
}
catch (Exception){
OPENSIM_THROW(Exception, "muscle_output: " +
get_muscle_outputs(i) + " is not a valid "
"Muscle output name")
}
}
}
int nMuscleOutputs = _muscle_output_double_names.size();
SimTK::Matrix msl_output_data(_n_frames, nMuscleOutputs,-1);
//Muscle Storage
for (std::string msl_path : _muscle_paths) {
const Muscle& msl =
_model->updComponent<Muscle>(msl_path);
//Path Point Storage
SimTK::Matrix_<SimTK::Vec3> msl_matrix(_n_frames,
_max_path_points, SimTK::Vec3(-1));
SimTK::Vector msl_vector(_n_frames, -1);
_muscle_path_points.push_back(msl_matrix);
_muscle_path_nPoints.push_back(msl_vector);
//Output Data Storage
_muscle_output_double_values.push_back(msl_output_data);
}
}
void JointMechanicsTool::setupCoordinateStorage() {
_coordinate_output_double_names.push_back("value");
_coordinate_output_double_names.push_back("speed");
for (const Coordinate& coord : _model->updComponentList<Coordinate>()) {
_coordinate_names.push_back(coord.getName());
SimTK::Matrix coord_data(_n_frames, 2, -1.0);
_coordinate_output_double_values.push_back(coord_data);
}
}
int JointMechanicsTool::record(const SimTK::State& s, const int frame_num)
{
_model->realizeReport(s);
//Store mesh vertex locations
std::string frame_name = get_output_frame();
const Frame& frame = _model->updComponent<Frame>(frame_name);
std::string origin_name = get_output_origin();
const Frame& origin = _model->updComponent<Frame>(origin_name);
SimTK::Vec3 origin_pos = origin.findStationLocationInAnotherFrame(s, SimTK::Vec3(0), frame);
for (int i = 0; i < _contact_mesh_paths.size(); ++i) {
int nVertex = _mesh_vertex_locations[i].ncol();
SimTK::Vector_<SimTK::Vec3> ver = _model->getComponent<Smith2018ContactMesh>
(_contact_mesh_paths[i]).getVertexLocations();
const SimTK::Transform& T = _model->getComponent<Smith2018ContactMesh>
(_contact_mesh_paths[i]).getMeshFrame().findTransformBetween(s,frame);
for (int j = 0; j < nVertex; ++j) {
_mesh_vertex_locations[i](frame_num, j) = T.shiftFrameStationToBase(ver(j)) - origin_pos;
}
}
// Store Attached Geometries
if (!_attach_geo_names.empty()) {
for (int i = 0; i < _attach_geo_names.size(); ++i) {
const SimTK::PolygonalMesh& mesh = _attach_geo_meshes[i];
SimTK::Transform trans = _model->updComponent<PhysicalFrame>(_attach_geo_frames[i]).findTransformBetween(s, frame);
for (int j = 0; j < mesh.getNumVertices(); ++j) {
_attach_geo_vertex_locations[i](frame_num, j) = trans.shiftFrameStationToBase(mesh.getVertexPosition(j)) - origin_pos;
}
}
}
//Store Contact data
if (!_contact_force_paths.empty()) {
int nFrc = 0;
for (std::string frc_path : _contact_force_paths) {
const Smith2018ArticularContactForce& frc = _model->updComponent<Smith2018ArticularContactForce>(frc_path);
int nDouble = 0;
for (std::string output_name : _contact_output_double_names) {
_contact_output_double_values[nFrc].set(frame_num, nDouble, frc.getOutputValue<double>(s, output_name));
nDouble++;
}
int nVec3 = 0;
for (std::string output_name : _contact_output_vec3_names) {
_contact_output_vec3_values[nFrc].set(frame_num, nVec3, frc.getOutputValue<SimTK::Vec3>(s, output_name));
nVec3++;
}
int nVector = 0;
for (std::string output_name : _contact_output_vector_double_names) {
_contact_output_vector_double_values[nFrc][nVector].updRow(frame_num) = ~frc.getOutputValue<SimTK::Vector>(s, output_name);
nVector++;
}
nFrc++;
}
}
//Store ligament data
if (!_ligament_paths.empty()) {
int nLig = 0;
for (const std::string& lig_path : _ligament_paths) {
Blankevoort1991Ligament& lig = _model->updComponent<Blankevoort1991Ligament>(lig_path);
//Path Points
const GeometryPath& geoPath = lig.upd_GeometryPath();
int nPoints = 0;
SimTK::Vector_<SimTK::Vec3> path_points(_max_path_points, SimTK::Vec3(-1));
getGeometryPathPoints(s, geoPath, path_points, nPoints);
for (int i = 0; i < nPoints; ++i) {
_ligament_path_points[nLig].set(frame_num,i,path_points(i));
}
_ligament_path_nPoints[nLig][frame_num] = nPoints;
//Output Data
int j = 0;
for (std::string output_name : _ligament_output_double_names) {
_ligament_output_double_values[nLig].set(frame_num,j, lig.getOutputValue<double>(s, output_name));
j++;
}
nLig++;
}
}
//Store muscle data
if (!_muscle_paths.empty()) {
int nMsl = 0;
for (const std::string& msl_path : _muscle_paths) {
Muscle& msl = _model->updComponent<Muscle>(msl_path);
//Path Points
const GeometryPath& geoPath = msl.upd_GeometryPath();
int nPoints = 0;
SimTK::Vector_<SimTK::Vec3> path_points(_max_path_points,SimTK::Vec3(-1));
getGeometryPathPoints(s, geoPath, path_points, nPoints);
for (int i = 0; i < nPoints; ++i) {
_muscle_path_points[nMsl].set(frame_num,i,path_points(i));
}
_muscle_path_nPoints[nMsl][frame_num] = nPoints;
//Output Data
int j = 0;
for (std::string output_name : _muscle_output_double_names) {
_muscle_output_double_values[nMsl].set(frame_num,j, msl.getOutputValue<double>(s, output_name));
j++;
}
nMsl++;
}
}
//Store Coordinate Data
if (get_h5_kinematics_data()) {
int nCoord = 0;
for (const Coordinate& coord : _model->updComponentList<Coordinate>()) {
_coordinate_output_double_values[nCoord](frame_num,0) = coord.getValue(s);
_coordinate_output_double_values[nCoord](frame_num,1) = coord.getSpeedValue(s);
nCoord++;
}
}
return(0);
}
void JointMechanicsTool::getGeometryPathPoints(const SimTK::State& s, const GeometryPath& geoPath, SimTK::Vector_<SimTK::Vec3>& path_points, int& nPoints) {
const Frame& out_frame = _model->getComponent<Frame>(get_output_frame());
const Frame& origin = _model->getComponent<Frame>(get_output_origin());
SimTK::Vec3 origin_pos = origin.findStationLocationInAnotherFrame(s, SimTK::Vec3(0), out_frame);
const Array<AbstractPathPoint*>& pathPoints = geoPath.getCurrentPath(s);
nPoints = 0;
for (int i = 0; i < pathPoints.getSize(); ++i) {
AbstractPathPoint* point = pathPoints[i];
PathWrapPoint* pwp = dynamic_cast<PathWrapPoint*>(point);
SimTK::Vec3 pos;
//If wrapping point, need to collect all points on wrap object surface
if (pwp) {
Array<SimTK::Vec3>& surfacePoints = pwp->getWrapPath();
const SimTK::Transform& X_BG = pwp->getParentFrame().findTransformBetween(s, out_frame);
// Cycle through each surface point and tranform to output frame
for (int j = 0; j < surfacePoints.getSize(); ++j) {
pos = X_BG * surfacePoints[j]-origin_pos;
path_points.set(nPoints, pos);
nPoints++;
}
}
else { // otherwise a regular PathPoint so just draw its location
const SimTK::Transform& X_BG = point->getParentFrame().findTransformBetween(s, out_frame);
pos = X_BG * point->getLocation(s)-origin_pos;
path_points.set(nPoints, pos);
nPoints++;
}
}
}
//=============================================================================
// IO
//=============================================================================
//_____________________________________________________________________________
/**
* Print results.
*
* The file names are constructed as
* aDir + "/" + aBaseName + "_" + ComponentName + aExtension
*
* @param aDir Directory in which the results reside.
* @param aBaseName Base file name.
* @param aDT Desired time interval between adjacent storage vectors. Linear
* interpolation is used to print the data out at the desired interval.
* @param aExtension File extension.
*
* @return 0 on success, -1 on error.
*/
int JointMechanicsTool::printResults(const std::string &aBaseName,const std::string &aDir)