void XMLDocument::addPhysicalOffsetFrame(SimTK::Xml::Element& element,
const std::string& frameName,
const std::string& parentFrameName,
const SimTK::Vec3& location, const SimTK::Vec3& orientation)
{
SimTK::Xml::element_iterator frames_node = element.element_begin("frames");
//SimTK::String debug; //Only used for debugging
if (frames_node == element.element_end()) {
SimTK::Xml::Element framesElement("frames");
element.insertNodeBefore(element.element_begin(), framesElement);
frames_node = element.element_begin("frames");
}
// Here we're guaranteed frames node exists, add individual frame
SimTK::Xml::Element newFrameElement("PhysicalOffsetFrame");
newFrameElement.setAttributeValue("name", frameName);
//newFrameElement.writeToString(debug);
XMLDocument::addConnector(newFrameElement, "Connector_PhysicalFrame_", "parent", parentFrameName);
std::ostringstream transValue;
transValue << location[0] << " " << location[1] << " " << location[2];
SimTK::Xml::Element translationElement("translation", transValue.str());
newFrameElement.insertNodeAfter(newFrameElement.element_end(), translationElement);
std::ostringstream orientValue;
orientValue << orientation[0] << " " << orientation[1] << " " << orientation[2];
SimTK::Xml::Element orientationElement("orientation", orientValue.str());
newFrameElement.insertNodeAfter(newFrameElement.element_end(), orientationElement);
frames_node->insertNodeAfter(frames_node->element_end(), newFrameElement);
//frames_node->writeToString(debug);
}
void Body::updateFromXMLNode(SimTK::Xml::Element& aNode, int versionNumber)
{
if (versionNumber < XMLDocument::getLatestVersion()) {
if (versionNumber < 30500) {
SimTK::Vec6 newInertia(1.0, 1.0, 1.0, 0., 0., 0.);
std::string inertiaComponents[] = { "inertia_xx", "inertia_yy", "inertia_zz", "inertia_xy", "inertia_xz", "inertia_yz" };
for (int i = 0; i < 6; ++i) {
SimTK::Xml::element_iterator iIter = aNode.element_begin(inertiaComponents[i]);
if (iIter != aNode.element_end()) {
newInertia[i] = iIter->getValueAs<double>();
aNode.removeNode(iIter);
}
}
std::ostringstream strs;
for (int i = 0; i < 6; ++i) {
strs << newInertia[i];
if (i < 5) strs << " ";
}
std::string strInertia = strs.str();
SimTK::Xml::Element inertiaNode("inertia", strInertia);
aNode.insertNodeAfter(aNode.element_end(), inertiaNode);
}
}
Super::updateFromXMLNode(aNode, versionNumber);
}
/*static*/
void XMLDocument::renameChildNode(SimTK::Xml::Element& aNode, std::string oldElementName, std::string newElementName)
{
Xml::element_iterator elmtIter(aNode.element_begin(oldElementName));
if (elmtIter!=aNode.element_end()){
elmtIter->setElementTag(newElementName);
}
}
/*virtual*/
void Marker::updateFromXMLNode(SimTK::Xml::Element& aNode, int versionNumber)
{
if (versionNumber < XMLDocument::getLatestVersion()){
if (versionNumber < 30501) {
// Parse name of Body under <body>node
SimTK::Xml::element_iterator bIter = aNode.element_begin("body");
SimTK::String bName = bIter->getValue();
// Create nodes for new layout
SimTK::Xml::Element connectorsElement("connectors");
SimTK::Xml::Element frameElement("Connector_PhysicalFrame_");
connectorsElement.insertNodeAfter(connectorsElement.node_end(), frameElement);
frameElement.setAttributeValue("name", "parent_frame");
SimTK::Xml::Element connecteeElement("connectee_name");
// Markers in pre-4.0 models are necessarily 1 level deep
// (model, markers), and Bodies were necessarily 1 level deep;
// here we create the correct relative path (accounting for sets
// being components).
bName = XMLDocument::updateConnecteePath30517("bodyset", bName);
connecteeElement.setValue(bName);
frameElement.insertNodeAfter(frameElement.node_end(), connecteeElement);
aNode.insertNodeAfter(bIter, connectorsElement);
aNode.eraseNode(bIter);
}
}
// Call base class now assuming _node has been corrected for current version
Super::updateFromXMLNode(aNode, versionNumber);
}
void PointToPointSpring::updateFromXMLNode(SimTK::Xml::Element& aNode, int versionNumber)
{
int documentVersion = versionNumber;
if (documentVersion < XMLDocument::getLatestVersion()) {
if (documentVersion<30500) {
// replace old properties with latest use of Connectors
SimTK::Xml::element_iterator body1Element = aNode.element_begin("body1");
SimTK::Xml::element_iterator body2Element = aNode.element_begin("body2");
std::string body1_name(""), body2_name("");
// If default constructed then elements not serialized since they
// are default values. Check that we have associated elements, then
// extract their values.
// Forces in pre-4.0 models are necessarily 1 level deep
// Bodies are also necessarily 1 level deep.
// Here we create the correct relative path (accounting for sets
// being components).
if (body1Element != aNode.element_end()) {
body1Element->getValueAs<std::string>(body1_name);
body1_name = XMLDocument::updateConnecteePath30517("bodyset",
body1_name);
}
if (body2Element != aNode.element_end()) {
body2Element->getValueAs<std::string>(body2_name);
body2_name = XMLDocument::updateConnecteePath30517("bodyset",
body2_name);
}
XMLDocument::addConnector(aNode, "Connector_PhysicalFrame_",
"body1", body1_name);
XMLDocument::addConnector(aNode, "Connector_PhysicalFrame_",
"body2", body2_name);
}
}
Super::updateFromXMLNode(aNode, versionNumber);
}
// Handle conversion from older format
void VisibleObject::updateFromXMLNode(SimTK::Xml::Element& aNode, int versionNumber)
{
SimTK::Array_<SimTK::String> oldGeometryFiles;
if ( versionNumber < XMLDocument::getLatestVersion()){
if (versionNumber<20101){
SimTK::Xml::element_iterator visPropIter = aNode.element_begin("VisibleProperties");
// Get geometry files and Preferences if any and set them into
if (visPropIter!=aNode.element_end()){
// Move display_prference, and show_axes nodes up to VisibleObject
SimTK::Xml::element_iterator prefIter = visPropIter->element_begin("display_preference");
if (prefIter!= visPropIter->element_end()){
SimTK::Xml::Node moveNode = visPropIter->removeNode(prefIter);
aNode.insertNodeAfter(aNode.element_end(), moveNode);
}
SimTK::Xml::element_iterator showAxesIter = visPropIter->element_begin("show_axes");
if (showAxesIter!=aNode.element_end()){
SimTK::Xml::Node moveNode = visPropIter->removeNode(showAxesIter);
aNode.insertNodeAfter(aNode.element_end(), moveNode);
}
}
SimTK::Xml::element_iterator geometryIter = aNode.element_begin("geometry_files");
string propValue="";
bool hasPieces=false;
if (geometryIter!= aNode.element_end()){
geometryIter->getValueAs(oldGeometryFiles);
}
}
}
Object::updateFromXMLNode(aNode, versionNumber);
if (oldGeometryFiles.size()>0){
for(unsigned i=0; i< oldGeometryFiles.size(); i++)
setGeometryFileName(i, oldGeometryFiles[i]);
}
}
void ModelComponent::updateFromXMLNode(SimTK::Xml::Element& aNode,
int versionNumber) {
if (versionNumber < XMLDocument::getLatestVersion()) {
if (versionNumber < 30506) {
// geometry list property removed. Everything that was in this list
// should be moved to the components list property.
SimTK::Xml::element_iterator geometry = aNode.element_begin("geometry");
if (geometry != aNode.element_end()) {
// We found a list property of geometry.
SimTK::Xml::Element componentsNode;
SimTK::Xml::element_iterator componentsIt = aNode.element_begin("components");
if (componentsIt == aNode.element_end()) {
// This component does not yet have a list property of
// components, so we'll create one.
componentsNode = SimTK::Xml::Element("components");
aNode.insertNodeBefore(aNode.element_begin(), componentsNode);
} else {
componentsNode = *componentsIt;
}
// Copy each node under <geometry> into <components>.
for (auto geomIt = geometry->element_begin();
geomIt != geometry->element_end(); ++geomIt) {
componentsNode.appendNode(geomIt->clone());
}
// Now that we moved over the geometry, we can delete the
// <geometry> element.
aNode.eraseNode(geometry);
}
}
}
Super::updateFromXMLNode(aNode, versionNumber);
}
void XMLDocument::writeDefaultObjects(SimTK::Xml::Element& elmt)
{
if (_defaultObjects.getSize()==0) return;
// Make node for "defaults"
SimTK::Xml::Element defaultsElement("defaults");
elmt.insertNodeAfter(elmt.node_end(), defaultsElement);
for(int i=0; i < _defaultObjects.getSize(); i++){
_defaultObjects.get(i)->updateXMLNode(defaultsElement);
}
}
void ContactGeometry::updateFromXMLNode(SimTK::Xml::Element& node,
int versionNumber) {
if (versionNumber < XMLDocument::getLatestVersion()) {
if (versionNumber < 30505) {
SimTK::Xml::element_iterator bodyElement =
node.element_begin("body_name");
std::string body_name("");
// Element may not exist if body_name property had default value.
if (bodyElement != node.element_end()) {
bodyElement->getValueAs<std::string>(body_name);
}
XMLDocument::addConnector(node, "Connector_PhysicalFrame_",
"frame", body_name);
}
}
Super::updateFromXMLNode(node, versionNumber);
}
void PathPoint::updateFromXMLNode(SimTK::Xml::Element& aNode, int versionNumber)
{
int documentVersion = versionNumber;
if (documentVersion < XMLDocument::getLatestVersion()) {
if (documentVersion < 30505) {
// replace old properties with latest use of Connectors
SimTK::Xml::element_iterator bodyElement = aNode.element_begin("body");
std::string bodyName("");
if (bodyElement != aNode.element_end()) {
bodyElement->getValueAs<std::string>(bodyName);
XMLDocument::addConnector(aNode, "Connector_PhysicalFrame_",
"parent_frame", bodyName);
}
}
}
Super::updateFromXMLNode(aNode, versionNumber);
}
/**
* Override default implementation by object to intercept and fix the XML node
* underneath the tool to match current version
*/
/*virtual*/ void ForwardTool::updateFromXMLNode(SimTK::Xml::Element& aNode, int versionNumber)
{
int documentVersion = versionNumber;
bool neededSprings=false;
std::string savedCwd;
if(getDocument()) {
savedCwd = IO::getCwd();
IO::chDir(IO::getParentDirectory(getDocument()->getFileName()));
}
if ( documentVersion < XMLDocument::getLatestVersion()){
// Now check if we need to create a correction controller to replace springs
if (documentVersion<10904){
std::string propNames[]={
"body1_linear_corrective_spring_active",
"body1_torsional_corrective_spring_active",
"body2_linear_corrective_spring_active",
"body2_torsional_corrective_spring_active"
};
int i=0;
while (!neededSprings && i<4){
neededSprings = (aNode.element_begin(propNames[i++])!=aNode.element_end());
}
AbstractTool::updateFromXMLNode(aNode, versionNumber);
if (neededSprings){
CorrectionController* cc = new CorrectionController();
cc->setKp(16.0);
cc->setKv(8.0);
_controllerSet.adoptAndAppend(cc);
_parsingLog+= "This setup file contains corrective springs.\n";
_parsingLog+= "Corrective springs are deprecated in OpenSim 2.0\n";
_parsingLog+= "Instead, a Corrective Controller has been created.\n";
}
}
else
AbstractTool::updateFromXMLNode(aNode, versionNumber);
}
else
AbstractTool::updateFromXMLNode(aNode, versionNumber);
if(getDocument()) IO::chDir(savedCwd);
//Object::updateFromXMLNode(aNode, versionNumber);
}
/*
* Helper function to add connector to the xmlElement passed in
*/
void XMLDocument::addConnector(SimTK::Xml::Element& element, const std::string& connectorTag, const std::string& connectorName, const std::string& connectorValue)
{
SimTK::Xml::element_iterator connectors_node = element.element_begin("connectors");
SimTK::String debug;
if (connectors_node == element.element_end()){
SimTK::Xml::Element connectorsElement("connectors");
element.insertNodeBefore(element.element_begin(), connectorsElement);
connectors_node = element.element_begin("connectors");
}
// Here we're guaranteed connectors node exist, add individual connector
SimTK::Xml::Element newConnectorElement(connectorTag);
newConnectorElement.setAttributeValue("name", connectorName);
newConnectorElement.writeToString(debug);
SimTK::Xml::Element connecteeElement("connectee_name");
connecteeElement.insertNodeAfter(connecteeElement.element_end(), SimTK::Xml::Text(connectorValue));
// Insert text under newConnectorElement
newConnectorElement.insertNodeAfter(newConnectorElement.element_end(), connecteeElement);
connectors_node->insertNodeAfter(connectors_node->element_end(), newConnectorElement);
connectors_node->writeToString(debug);
}
void ConstantDistanceConstraint::updateFromXMLNode(SimTK::Xml::Element& aNode, int versionNumber)
{
int documentVersion = versionNumber;
if (documentVersion < XMLDocument::getLatestVersion()){
if (documentVersion<30500){
// replace old properties with latest use of Connectors
SimTK::Xml::element_iterator body1Element = aNode.element_begin("body_1");
SimTK::Xml::element_iterator body2Element = aNode.element_begin("body_2");
std::string body1_name(""), body2_name("");
// If default constructed then elements not serialized since they are default
// values. Check that we have associated elements, then extract their values.
if (body1Element != aNode.element_end())
body1Element->getValueAs<std::string>(body1_name);
if (body2Element != aNode.element_end())
body2Element->getValueAs<std::string>(body2_name);
XMLDocument::addConnector(aNode, "Connector_PhysicalFrame_", "body_1", body1_name);
XMLDocument::addConnector(aNode, "Connector_PhysicalFrame_", "body_2", body2_name);
}
}
Super::updateFromXMLNode(aNode, versionNumber);
}// Visual support ConstantDistanceConstraint drawing in SimTK visualizer.
void Controller::updateFromXMLNode(SimTK::Xml::Element& node,
int versionNumber) {
if(versionNumber < XMLDocument::getLatestVersion()) {
if(versionNumber < 30509) {
// Rename property 'isDisabled' to 'enabled' and
// negate the contained value.
std::string oldName{"isDisabled"};
std::string newName{"enabled"};
if(node.hasElement(oldName)) {
auto elem = node.getRequiredElement(oldName);
bool isDisabled = false;
elem.getValue().tryConvertToBool(isDisabled);
// now update tag name to 'enabled'
elem.setElementTag(newName);
// update its value to be the opposite of 'isDisabled'
elem.setValue(SimTK::String(!isDisabled));
}
}
}
Super::updateFromXMLNode(node, versionNumber);
}
/*virtual*/
void Marker::updateFromXMLNode(SimTK::Xml::Element& aNode, int versionNumber)
{
if (versionNumber < XMLDocument::getLatestVersion()){
if (versionNumber < 30501) {
// Parse name of Body under <body>node
SimTK::Xml::element_iterator bIter = aNode.element_begin("body");
SimTK::String bName = bIter->getValue();
// Create nodes for new layout
SimTK::Xml::Element connectorsElement("connectors");
SimTK::Xml::Element frameElement("Connector_PhysicalFrame_");
connectorsElement.insertNodeAfter(connectorsElement.node_end(), frameElement);
frameElement.setAttributeValue("name", "reference_frame");
SimTK::Xml::Element connecteeElement("connectee_name");
connecteeElement.setValue(bName);
frameElement.insertNodeAfter(frameElement.node_end(), connecteeElement);
aNode.insertNodeAfter(bIter, connectorsElement);
aNode.eraseNode(bIter);
}
}
// Call base class now assuming _node has been corrected for current version
Object::updateFromXMLNode(aNode, versionNumber);
}
/**
* Update this object based on its XML node.
*/
void PrescribedForce::updateFromXMLNode(SimTK::Xml::Element& aNode, int versionNumber)
{
// Base class
// This test for veversion number needs to change when we have a new version number otherwise
// subsequent versions will continue to trigger the conversion below. -Ayman 4/16
if (versionNumber != 30505) {
// Convert body property into a connector to PhysicalFrame with name "frame"
SimTK::Xml::element_iterator bodyElement = aNode.element_begin("body");
std::string frame_name("");
if (bodyElement != aNode.element_end()) {
bodyElement->getValueAs<std::string>(frame_name);
XMLDocument::addConnector(aNode, "Connector_PhysicalFrame_", "frame", frame_name);
}
}
Super::updateFromXMLNode(aNode, versionNumber);
const FunctionSet& forceFunctions = getForceFunctions();
const FunctionSet& pointFunctions = getPointFunctions();
const FunctionSet& torqueFunctions = getTorqueFunctions();
//Specify all or none of the components
if(forceFunctions.getSize() != 3 && forceFunctions.getSize() != 0)
{
throw Exception("PrescribedForce:: three components of the force must be specified.");
}
if(pointFunctions.getSize() != 3 && pointFunctions.getSize() != 0)
{
throw Exception("PrescribedForce:: three components of the point must be specified.");
}
if(torqueFunctions.getSize() != 3 && torqueFunctions.getSize() != 0)
{
throw Exception("PrescribedForce:: three components of the torque must be specified.");
}
}
/** Override of the default implementation to account for versioning. */
void CustomJoint::
updateFromXMLNode(SimTK::Xml::Element& aNode, int versionNumber)
{
int documentVersion = versionNumber;
if ( documentVersion < XMLDocument::getLatestVersion()){
if (Object::getDebugLevel()>=1)
cout << "Updating CustomJoint to latest format..." << endl;
// Version before refactoring spatialTransform
if (documentVersion<10901){
// replace TransformAxisSet with SpatialTransform
/////renameChildNode("TransformAxisSet", "SpatialTransform");
// Check how many TransformAxes are defined
SimTK::Xml::element_iterator spatialTransformNode =
aNode.element_begin("TransformAxisSet");
if (spatialTransformNode == aNode.element_end()) return;
SimTK::Xml::element_iterator axesSetNode =
spatialTransformNode->element_begin("objects");
/////if (axesSetNode != NULL)
///// spatialTransformNode->removeChild(axesSetNode);
/////DOMElement*grpNode = XMLNode::GetFirstChildElementByTagName(spatialTransformNode,"groups");
/////if (grpNode != NULL)
///// spatialTransformNode->removeChild(grpNode);
// (0, 1, 2 rotations & 3, 4, 5 translations then remove the is_rotation node)
SimTK::Array_<SimTK::Xml::Element> list =
axesSetNode->getAllElements();
unsigned int listLength = list.size();
int objectsFound = 0;
Array<int> translationIndices(-1, 0);
Array<int> rotationIndices(-1, 0);
int nextAxis = 0;
std::vector<TransformAxis *> axes;
// Add children for all six axes here
//////_node->removeChild(SpatialTransformNode);
// Create a blank Spatial Transform and use it to populate the
// XML structure
for(int i=0; i<6; i++)
updSpatialTransform()[i].setFunction(new OpenSim::Constant(0));
Array<OpenSim::TransformAxis*> oldAxes;
for(unsigned int j=0;j<listLength;j++) {
// getChildNodes() returns all types of DOMNodes including
// comments, text, etc., but we only want
// to process element nodes
SimTK::Xml::Element objElmt = list[j];
string objectType = objElmt.getElementTag();
// (sherm) this is cleaning up old TransformAxis here but
// that should really be done in TransformAxis instead.
if (objectType == "TransformAxis"){
OpenSim::TransformAxis* readAxis =
new OpenSim::TransformAxis(objElmt);
assert(nextAxis <=5);
bool isRotation = false;
SimTK::Xml::element_iterator rotationNode =
objElmt.element_begin("is_rotation");
if (rotationNode != objElmt.element_end()){
SimTK::String sValue =
rotationNode->getValueAs<SimTK::String>();
bool value = (sValue.toLower() == "true");
isRotation = value;
objElmt.eraseNode(rotationNode);
}
SimTK::Xml::element_iterator coordinateNode =
objElmt.element_begin("coordinate");
SimTK::String coordinateName =
coordinateNode->getValueAs<SimTK::String>();
Array<std::string> names("");
names.append(coordinateName);
readAxis->setCoordinateNames(names);
SimTK::Xml::element_iterator axisNode =
objElmt.element_begin("axis");
SimTK::Vec3 axisVec= axisNode->getValueAs<SimTK::Vec3>();
readAxis->setAxis(axisVec);
if (isRotation){
rotationIndices.append(nextAxis);
}
else {
translationIndices.append(nextAxis);
}
axes.push_back(readAxis);
nextAxis++;
}
}
assert(rotationIndices.getSize() <=3);
assert(translationIndices.getSize() <=3);
//XMLNode::RemoveChildren(SpatialTransformAxesNode);
int nRotations = rotationIndices.getSize();
int nTranslations = translationIndices.getSize();
// Now copy coordinateName, Axis, Function into proper slot
for (int i=0; i<nRotations; i++){
updSpatialTransform()[i] = *axes[rotationIndices[i]];
}
updSpatialTransform().constructIndependentAxes(nRotations, 0);
// Add Translations from old list then pad with default ones,
// make sure no singularity.
for (int i=0; i<nTranslations; i++){
updSpatialTransform()[i+3] = *axes[translationIndices[i]];
}
updSpatialTransform().constructIndependentAxes(nTranslations, 3);
}
}
// Delegate to superclass now.
Super::updateFromXMLNode(aNode, versionNumber);
const CoordinateSet& coordinateSet = get_CoordinateSet();
// Fix coordinate type post deserialization
// Fix coordinate type post deserialization
for (int i=0; i<coordinateSet.getSize(); i++){
OpenSim::Coordinate& nextCoord = coordinateSet.get(i);
// Find TransformAxis for the coordinate and use it to set Coordinate's motionType
for(int axisIndex=0; axisIndex<6; axisIndex++){
const TransformAxis& nextAxis = getSpatialTransform()[axisIndex];
const Property<std::string>& coordNames = nextAxis.getCoordinateNames();
if (coordNames.findIndex(nextCoord.getName())!=-1){
coordinateSet.get(i).setMotionType((axisIndex>2)?
Coordinate::Translational : Coordinate::Rotational);
break;
}
}
}
// Axes should be independent otherwise Simbody throws an exception in addToSystem
double tol = 1e-5;
// Verify that none of the rotation axes are colinear
const std::vector<SimTK::Vec3> axes=getSpatialTransform().getAxes();
for(int startIndex=0; startIndex<=3; startIndex+=3){
if(((axes[startIndex+0]%axes[startIndex+1]).norm() < tol)||
((axes[startIndex+0]%axes[startIndex+2]).norm() < tol)||
((axes[startIndex+1]%axes[startIndex+2]).norm() < tol)){
throw(Exception("CustomJoint " + getName() +
" has colinear axes and so is not well-defined."
" Please fix and retry loading.."));
}
}
updProperty_SpatialTransform().setValueIsDefault(false);
}
//-----------------------------------------------------------------------------
// UPDATE FROM OLDER VERSION
//-----------------------------------------------------------------------------
//_____________________________________________________________________________
void ExternalLoads::updateFromXMLNode(SimTK::Xml::Element& aNode, int versionNumber)
{
int documentVersion = versionNumber;
if ( documentVersion < 20301){
if (Object::getDebugLevel()>=1)
cout << "Updating ExternalLoad object to latest format..." << endl;
_dataFileName="";
SimTK::Xml::element_iterator dataFileElementIter =aNode.element_begin("datafile");
if(dataFileElementIter!=aNode.element_end()) {
// Could still be empty or whiteSpace
SimTK::String transcoded = dataFileElementIter->getValueAs<SimTK::String>();
if (transcoded.length()>0)
_dataFileName =transcoded;
}
SimTK::Xml::element_iterator kinFileNode = aNode.element_begin("external_loads_model_kinematics_file");
if (kinFileNode != aNode.element_end()){
SimTK::String transcoded = kinFileNode->getValueAs<SimTK::String>();
if (transcoded.length()>0)
_externalLoadsModelKinematicsFileName =transcoded;
}
SimTK::Xml::element_iterator kinFilterNode = aNode.element_begin("lowpass_cutoff_frequency_for_load_kinematics");
if (kinFilterNode != aNode.element_end()){
_lowpassCutoffFrequencyForLoadKinematics = kinFilterNode->getValueAs<double>();
}
bool changeWorkingDir = false;
std::string savedCwd;
// Change to directory of Document
if(!ifstream(_dataFileName.c_str(), ios_base::in).good()) {
string msg =
"Object: ERR- Could not open file " + _dataFileName+ "IO. It may not exist or you don't have permission to read it.";
cout << msg;
// Try switching to directory of setup file before aborting
if(getDocument()) {
savedCwd = IO::getCwd();
IO::chDir(IO::getParentDirectory(getDocument()->getFileName()));
changeWorkingDir=true;
}
if(!ifstream(_dataFileName.c_str(), ios_base::in).good()) {
if(changeWorkingDir) IO::chDir(savedCwd);
throw Exception(msg,__FILE__,__LINE__);
}
}
Storage* dataSource = new Storage(_dataFileName, true);
if (!dataSource->makeStorageLabelsUnique()){
cout << "Making labels unique in storage file "<< _dataFileName << endl;
dataSource = new Storage(_dataFileName);
dataSource->makeStorageLabelsUnique();
dataSource->print(_dataFileName);
}
if(changeWorkingDir) IO::chDir(savedCwd);
const Array<string> &labels = dataSource->getColumnLabels();
// Populate data file and other things that haven't changed
// Create a ForceSet out of this XML node, this will create a set of PrescribedForces then we can reassign at a higher level to ExternalForces
ModelComponentSet<PrescribedForce> oldForces(updModel(), getDocument()->getFileName(), true);
for(int i=0; i< oldForces.getSize(); i++){
PrescribedForce& oldPrescribedForce = oldForces.get(i);
ExternalForce* newExternalForce = new ExternalForce();
newExternalForce->setName(oldPrescribedForce.getName());
newExternalForce->setAppliedToBodyName(oldPrescribedForce.getBodyName());
newExternalForce->setPointExpressedInBodyName("ground");
newExternalForce->setForceExpressedInBodyName("ground");
// Reconstruct function names and use these to extract the identifier(s)
OpenSim::Array<std::string> aFunctionNames;
oldPrescribedForce.getForceFunctionNames(aFunctionNames);
// Get names from force functions
newExternalForce->setForceIdentifier(createIdentifier(aFunctionNames, labels));
aFunctionNames.setSize(0);
oldPrescribedForce.getPointFunctionNames(aFunctionNames);
newExternalForce->setPointIdentifier(createIdentifier(aFunctionNames, labels));
aFunctionNames.setSize(0);
// Now the torques
oldPrescribedForce.getTorqueFunctionNames(aFunctionNames);
newExternalForce->setTorqueIdentifier(createIdentifier(aFunctionNames, labels));
//newExternalForce->setDataSourceName("");
adoptAndAppend(newExternalForce);
}
delete dataSource;
}
else
// Call base class now assuming _node has been corrected for current version
ModelComponentSet<ExternalForce>::updateFromXMLNode(aNode, versionNumber);
}
bool XMLDocument::isElementEqual(SimTK::Xml::Element& elt1, SimTK::Xml::Element& elt2, double toleranceForDoubles)
{
SimTK::String s1,s2;
elt1.writeToString(s1);
elt2.writeToString(s2);
SimTK::Xml::attribute_iterator att1 = elt1.attribute_begin();
SimTK::Xml::attribute_iterator att2 = elt2.attribute_begin();
// Handle different # attributes
if ( (att1 == elt1.attribute_end() && att2 != elt2.attribute_end()) ||
(att1 != elt1.attribute_end() && att2 == elt2.attribute_end()) ){
cout << "Number of attributes is different, element " << elt1.getElementTag() << endl;
return false;
}
bool equal =true;
// Same size attributes including none
for(att1 = elt1.attribute_begin(); att1 != elt1.attribute_end() && equal; att1++, att2++){
equal = (att1->getName() == att2->getName());
equal = equal && (att1->getValue() == att2->getValue());
if (!equal) {
cout << "Attribute " << att1->getName() << " is different " << att1->getValue() <<
"vs." << att2->getValue() << endl;
}
}
if (!equal) return false;
// Attributes match now children
SimTK::Array_<SimTK::Xml::Element> elts1 = elt1.getAllElements();
SimTK::Array_<SimTK::Xml::Element> elts2 = elt2.getAllElements();
if (elts1.size() != elts2.size()){
cout << "Different number of children for Element " << elt1.getElementTag() << endl;
equal = false;
}
if (!equal) return false;
// Recursively compare Elements unless Value Elements in that case do direct compare
for(unsigned it = 0; it < elts1.size() && equal; it++){
SimTK::String elt1Tag = elts1[it].getElementTag();
cout << "Compare " << elt1Tag << endl;
SimTK::Xml::element_iterator elt2_iter = elt2.element_begin(elt1Tag);
if (elt2_iter==elt2.element_end()){
cout << "Element " << elt1Tag << " was not found in reference document" << endl;
equal = false;
break;
}
bool value1 = elts1[it].isValueElement();
bool value2 = elt2_iter->isValueElement();
equal = (value1 == value2);
if (!equal){
cout << elts1[it].getElementTag() << " is different. One is Value Element the other isn't" << endl;
return false;
}
if (value1){
// We should check if this's a double or array of doubles in that case we can getValueAs<double> anbd
try {
SimTK::Array_<double> v1, v2;
elts1[it].getValueAs(v1);
elt2_iter->getValueAs(v2);
for(unsigned ix=0; ix<v1.size() && equal; ix++)
equal = (std::fabs(v1[ix]-v2[ix]) < toleranceForDoubles);
}
catch(...){
equal = (elts1[it].getValue() == elt2_iter->getValue());
}
}
else // recur
equal = isElementEqual(elts1[it], elts2[it], toleranceForDoubles);
if (!equal){
cout << elts1[it].getElementTag() << " is different" << endl;
SimTK::String pad;
elts1[it].writeToString(pad);
cout << pad << endl;
cout << "------------------- vs. ------" << endl;
elts2[it].writeToString(pad);
cout << pad << endl;
return equal;
}
}
return equal;
}
void Joint::updateFromXMLNode(SimTK::Xml::Element& aNode, int versionNumber)
{
int documentVersion = versionNumber;
//bool converting = false;
if (documentVersion < XMLDocument::getLatestVersion()){
if (documentVersion<30500){
XMLDocument::renameChildNode(aNode, "location", "location_in_child");
XMLDocument::renameChildNode(aNode, "orientation", "orientation_in_child");
}
// Version 30501 converted Connector_Body_ to Connector_PhysicalFrame_
if (documentVersion < 30501) {
// Handle any models that have the Joint connecting to Bodies instead
// of PhyscialFrames
XMLDocument::renameChildNode(aNode, "Connector_Body_",
"Connector_PhysicalFrame_");
}
// Version 30505 changed "parent_body" connector name to "parent_frame"
// Convert location and orientation into PhysicalOffsetFrames owned by the Joint
if (documentVersion < 30505) {
// Elements for the parent and child names the joint connects
SimTK::Xml::element_iterator parentNameElt;
SimTK::Xml::element_iterator childNameElt;
// The names of the two PhysicalFrames this joint connects
std::string parentFrameName("");
std::string childFrameName("");
SimTK::Xml::element_iterator connectors_node = aNode.element_begin("connectors");
SimTK::Xml::element_iterator connectorElement =
connectors_node->element_begin("Connector_PhysicalFrame_");
while (connectorElement != aNode.element_end()) {
// If connector name is "parent_body" rename it to "parent_frame"
if (connectorElement->getRequiredAttributeValue("name") == "parent_body") {
connectorElement->setAttributeValue("name", "parent_frame");
}
// If connector name is "parent_frame" get the name of the connectee
if (connectorElement->getRequiredAttributeValue("name") == "parent_frame"){
parentNameElt = connectorElement->element_begin("connectee_name");
parentNameElt->getValueAs<std::string>(parentFrameName);
const auto slashLoc = parentFrameName.rfind('/');
if (slashLoc != std::string::npos)
parentFrameName = parentFrameName.substr(slashLoc + 1);
}
if (connectorElement->getRequiredAttributeValue("name") == "child_body") {
connectorElement->setAttributeValue("name", "child_frame");
}
if (connectorElement->getRequiredAttributeValue("name") == "child_frame") {
childNameElt = connectorElement->element_begin("connectee_name");
childNameElt->getValueAs<std::string>(childFrameName);
const auto slashLoc = childFrameName.rfind('/');
if (slashLoc != std::string::npos)
childFrameName = childFrameName.substr(slashLoc + 1);
}
++connectorElement;
}
SimTK::Xml::element_iterator locParentElt =
aNode.element_begin("location_in_parent");
SimTK::Xml::element_iterator orientParentElt =
aNode.element_begin("orientation_in_parent");
SimTK::Xml::element_iterator locChildElt =
aNode.element_begin("location_in_child");
SimTK::Xml::element_iterator orientChildElt =
aNode.element_begin("orientation_in_child");
Vec3 location_in_parent(0);
Vec3 orientation_in_parent(0);
Vec3 location_in_child(0);
Vec3 orientation_in_child(0);
if (locParentElt != aNode.element_end()){
locParentElt->getValueAs<Vec3>(location_in_parent);
}
if (orientParentElt != aNode.element_end()){
orientParentElt->getValueAs<Vec3>(orientation_in_parent);
}
if (locChildElt != aNode.element_end()){
locChildElt->getValueAs<Vec3>(location_in_child);
}
if (orientChildElt != aNode.element_end()){
orientChildElt->getValueAs<Vec3>(orientation_in_child);
}
// now append updated frames to the property list for
// both parent and child
XMLDocument::addPhysicalOffsetFrame30505_30517(aNode, parentFrameName+"_offset",
parentFrameName, location_in_parent, orientation_in_parent);
parentNameElt->setValue(parentFrameName + "_offset");
XMLDocument::addPhysicalOffsetFrame30505_30517(aNode, childFrameName + "_offset",
childFrameName, location_in_child, orientation_in_child);
childNameElt->setValue(childFrameName + "_offset");
}
// Version 30507 replaced Joint's CoordinateSet with a "coordinates"
// list property.
if (documentVersion < 30507) {
if (aNode.hasElement("CoordinateSet")) {
auto coordSetIter = aNode.element_begin("CoordinateSet");
if (coordSetIter->hasElement("objects")) {
auto coordIter = coordSetIter->getRequiredElement("objects")
.element_begin("Coordinate");
if (coordIter != aNode.element_end()) {
// A "CoordinateSet" element exists, it contains an
// "objects" element, and the "objects" element contains
// at least one "Coordinate" element.
// Create an element for the new layout.
Xml::Element coordinatesElement("coordinates");
// Copy all "Coordinate" elements from the old layout.
while (coordIter != aNode.element_end()) {
coordinatesElement.appendNode(coordIter->clone());
++coordIter;
}
// Insert new "coordinates" element.
aNode.insertNodeAfter(coordSetIter, coordinatesElement);
}
}
// Remove old "CoordinateSet" element.
aNode.eraseNode(coordSetIter);
}
}
// Version 30514 removed the user-facing "reverse" property from Joint.
// The parent and child frames are swapped if a "reverse" element is
// found and its value is "true".
if (documentVersion < 30514) {
auto reverseElt = aNode.element_begin("reverse");
if (reverseElt != aNode.element_end()) {
bool swapFrames = false;
reverseElt->getValue().tryConvertToBool(swapFrames);
if (swapFrames) {
std::string oldParentFrameName = "";
std::string oldChildFrameName = "";
// Find names of parent and child frames. If more than one
// "parent_frame" or "child_frame" element exists, keep the
// first one. The "parent_frame" and "child_frame" elements
// may be listed in either order.
SimTK::Xml::element_iterator connectorsNode =
aNode.element_begin("connectors");
SimTK::Xml::element_iterator connectorElt = connectorsNode->
element_begin("Connector_PhysicalFrame_");
SimTK::Xml::element_iterator connecteeNameElt;
while (connectorElt != connectorsNode->element_end())
{
if (connectorElt->getRequiredAttributeValue("name") ==
"parent_frame" && oldParentFrameName.empty())
{
connecteeNameElt = connectorElt->
element_begin("connectee_name");
connecteeNameElt->getValueAs<std::string>(
oldParentFrameName);
}
else if (connectorElt->getRequiredAttributeValue("name")
== "child_frame" && oldChildFrameName.empty())
{
connecteeNameElt = connectorElt->
element_begin("connectee_name");
connecteeNameElt->getValueAs<std::string>(
oldChildFrameName);
}
++connectorElt;
}
// Swap parent and child frame names. If more than one
// "parent_frame" or "child_frame" element exists, assign
// the same value to all such elements.
connectorsNode = aNode.element_begin("connectors");
connectorElt = connectorsNode->element_begin(
"Connector_PhysicalFrame_");
while (connectorElt != connectorsNode->element_end())
{
if (connectorElt->getRequiredAttributeValue("name") ==
"parent_frame")
{
connecteeNameElt = connectorElt->
element_begin("connectee_name");
connecteeNameElt->setValue(oldChildFrameName);
}
else if (connectorElt->getRequiredAttributeValue("name")
== "child_frame")
{
connecteeNameElt = connectorElt->
element_begin("connectee_name");
connecteeNameElt->setValue(oldParentFrameName);
}
++connectorElt;
}
}
// Remove "reverse" element regardless of its value (it is no
// longer a property of Joint).
aNode.eraseNode(reverseElt);
}
}
}
Super::updateFromXMLNode(aNode, versionNumber);
}
//_____________________________________________________________________________
// Override default implementation by object to intercept and fix the XML node
// underneath the model to match current version.
void Muscle::updateFromXMLNode(SimTK::Xml::Element& aNode, int versionNumber)
{
if ( versionNumber < XMLDocument::getLatestVersion()) {
if (Object::getDebugLevel()>=1)
cout << "Updating Muscle object to latest format..." << endl;
if (versionNumber <= 20301){
SimTK::Xml::element_iterator pathIter =
aNode.element_begin("GeometryPath");
if (pathIter != aNode.element_end()) {
XMLDocument::renameChildNode(*pathIter, "MusclePointSet", "PathPointSet");
XMLDocument::renameChildNode(*pathIter, "MuscleWrapSet", "PathWrapSet");
} else { // There was no GeometryPath, just MusclePointSet
SimTK::Xml::element_iterator musclePointSetIter = aNode.element_begin("MusclePointSet");
bool pathPointSetFound=false;
if (musclePointSetIter != aNode.element_end()){
XMLDocument::renameChildNode(aNode, "MusclePointSet", "PathPointSet");
pathPointSetFound=true;
}
bool pathWrapSetFound=false;
SimTK::Xml::element_iterator muscleWrapSetIter = aNode.element_begin("MuscleWrapSet");
if (muscleWrapSetIter != aNode.element_end()){
XMLDocument::renameChildNode(aNode, "MuscleWrapSet", "PathWrapSet");
pathWrapSetFound=true;
}
// Now create a "GeometryPath" node and move MusclePointSet & MuscleWrapSet under it
SimTK::Xml::Element myPathElement("GeometryPath");
SimTK::Xml::Node moveNode;
if (pathPointSetFound) {
SimTK::Xml::element_iterator pathPointSetIter = aNode.element_begin("PathPointSet");
moveNode = aNode.removeNode(pathPointSetIter);
myPathElement.insertNodeAfter(myPathElement.element_end(),moveNode);
}
if (pathWrapSetFound) {
SimTK::Xml::element_iterator pathWrapSetIter = aNode.element_begin("PathWrapSet");
moveNode = aNode.removeNode(pathWrapSetIter);
myPathElement.insertNodeAfter(myPathElement.element_end(),moveNode);
}
aNode.insertNodeAfter(aNode.element_end(), myPathElement);
}
XMLDocument::renameChildNode(aNode, "pennation_angle", "pennation_angle_at_optimal");
}
}
// Call base class now assuming aNode has been corrected for current version
Super::updateFromXMLNode(aNode, versionNumber);
}