// [[Rcpp::export]]
arma::mat BeQTL2(const arma::mat & A, const arma::mat & B, const arma::umat & Bootmat){
int bsi= Bootmat.n_rows;
arma::mat C(A.n_cols*B.n_cols,Bootmat.n_rows);
arma::mat tC(A.n_rows,B.n_rows);
for(int i=0; i<bsi; i++){
tC = cor(A.rows(Bootmat.row(i)),B.rows(Bootmat.row(i)));
C.col(i) = vectorise(tC,0);
}
C.elem(find_nonfinite(C)).zeros();
return reshape(median(C,1),A.n_cols,B.n_cols);
}
//Script that takes two matrices, performs bootstrapped correlation, and returns the median
// [[Rcpp::export]]
arma::mat BeQTL(const arma::mat & A, const arma::mat & B, const arma::umat & Bootmat){
int bsi= Bootmat.n_rows;
Rcpp::Rcout<<"Starting Bootstrap!"<<std::endl;
arma::mat C(A.n_cols*B.n_cols,Bootmat.n_rows);
arma::mat tA(A.n_rows,A.n_cols);
arma::mat tB(B.n_rows,B.n_cols);
arma::mat tC(A.n_rows,B.n_rows);
for(int i=0; i<bsi; i++){
tA = A.rows(Bootmat.row(i));
tB = B.rows(Bootmat.row(i));
tC = cor(tA,tB);
C.col(i) = vectorise(tC,0);
}
C.elem(find_nonfinite(C)).zeros();
return reshape(median(C,1),A.n_cols,B.n_cols);
}
int main()
{
EconomicEngine eE1;
EconomicEngine eE2;
EconomicEngine eE3;
XtremeEngine xE1;
EconomicCar eC(eE1);
MediumCar mC(eE2);
TopCar tC(eE3, xE1);
eC.drive();
eC.stop();
mC.changeEngine(eE3);
tC.drive();
tC.stop();
}
void Scene::AddTexturedObject(const std::string fname, Material* material, Shapes &objects, const std::string textName, const Point &ofs) const
{
size_t index = Shape::GetUniqueID();
// —читывание меша из файла
L3DS *l3ds = new L3DS(fname.c_str());
if(!l3ds || !l3ds->GetMeshCount())
throw Error("Error in loading extern files");
for(int i = 0; i<l3ds->GetMeshCount(); i++) {
LMesh *mesh = l3ds->GetMesh(i);
Texture *texture = new Texture(textName.c_str());
for(int j = 0; j<mesh->GetTriangleCount(); j++) {
LTriangle tr = mesh->GetTriangle(j);
Point a(mesh->GetVertex(tr.a).x, mesh->GetVertex(tr.a).y, mesh->GetVertex(tr.a).z);
Point b(mesh->GetVertex(tr.b).x, mesh->GetVertex(tr.b).y, mesh->GetVertex(tr.b).z);
Point c(mesh->GetVertex(tr.c).x, mesh->GetVertex(tr.c).y, mesh->GetVertex(tr.c).z);
TextureCoords tA(mesh->GetUV(tr.a).u, mesh->GetUV(tr.a).v);
TextureCoords tB(mesh->GetUV(tr.b).u, mesh->GetUV(tr.b).v);
TextureCoords tC(mesh->GetUV(tr.c).u, mesh->GetUV(tr.c).v);
tA.InvertU();
tB.InvertU();
tC.InvertU();
tA*=8;
tB*=8;
tC*=8;
if (Triangle::IsValidTrangle(a,b,c))
objects.push_back(new Triangle(a-ofs, b-ofs, c-ofs, material, index, texture, tA, tB, tC));
}
}
}
// identifierar alla mesharna i scenen och extraherar data fr�n dem
bool Exporter::IdentifyAndExtractMeshes()
{
UINT index = 0;
scene_.meshes.clear();
//itererar �ver DG:n och lagrar rgba-v�rden och texturnamn i ett tempor�rt material
material tempmaterial;
MItDependencyNodes matIt(MFn::kLambert);
MString aC("ambientColor"), dC("color"), sC("specularColor"), gC("incandescence"), tC("transparency");
while (!matIt.isDone()){
if (matIt.item().hasFn(MFn::kPhong))
{
MFnPhongShader tempphong(matIt.item());
tempmaterial.type = PHONG;
extractColor(tempmaterial.ambient, tempphong, aC);
extractColor(tempmaterial.diffuse, tempphong, dC);
extractColor(tempmaterial.specular, tempphong, sC);
extractColor(tempmaterial.glow, tempphong, gC);
extractColor(tempmaterial.transparency, tempphong, tC);
}
else if (matIt.thisNode().hasFn(MFn::kBlinn))
{
MFnBlinnShader tempblinn(matIt.item());
tempmaterial.type = BLINN;
extractColor(tempmaterial.ambient, tempblinn, aC);
extractColor(tempmaterial.diffuse, tempblinn, dC);
extractColor(tempmaterial.specular, tempblinn, sC);
extractColor(tempmaterial.glow, tempblinn, gC);
extractColor(tempmaterial.transparency, tempblinn, tC);
}
else if (matIt.item().hasFn(MFn::kLambert))
{
MFnLambertShader templamb(matIt.item());
tempmaterial.type = LAMBERT;
extractColor(tempmaterial.ambient, templamb, aC);
extractColor(tempmaterial.diffuse, templamb, dC);
extractColor(tempmaterial.specular, templamb, sC);
extractColor(tempmaterial.glow, templamb, gC);
extractColor(tempmaterial.transparency, templamb, tC);
}
else
printf("No material found\n");
scene_.materials.push_back(tempmaterial);
matIt.next();
}
//Turn off or on Blendshapes
matIt.reset(MFn::kBlendShape);
while (!matIt.isDone())
{
MFnBlendShapeDeformer bs(matIt.item());
//Get the envelope attribute plug
MPlug pl = bs.findPlug("en");
//Set the 0 to disable FFD effect, enable by setting it to 1:
pl.setValue(1.0f);
matIt.next();
}
//Get Actual Blendshapes
matIt.reset(MFn::kBlendShape);
while (!matIt.isDone())
{
MFnBlendShapeDeformer bs(matIt.item());
MObjectArray base_objects;
//print blend shape name
cout << "Blendshape " << bs.name().asChar() << endl;
//Get a list of objects that this blend shape deforms
bs.getBaseObjects(base_objects);
cout << "NumBaseOBjects " << base_objects.length() << endl;
//loop through each blendshaped object
for (int i = 0; i < base_objects.length(); ++i)
{
//Get the base shape
MObject Base = base_objects[i];
//Output all of the target shapes and weights
OutputBlendShapes(bs, Base);
}
//Get next blend shapes
matIt.next();
}
MDagPath dag_path;
MItDag dag_iter(MItDag::kBreadthFirst, MFn::kMesh);
while (!dag_iter.isDone())
{
if (dag_iter.getPath(dag_path))
{
MFnDagNode dag_node = dag_path.node();
// vill endast ha "icke-history"-f�rem�l
if (!dag_node.isIntermediateObject())
{
// triangulera meshen innan man h�mtar punkterna
MFnMesh mesh(dag_path);
ExtractMeshData(mesh, index);
index++;
}
}
dag_iter.next();
}
MItDependencyNodes it(MFn::kSkinClusterFilter);
for (; !it.isDone(); it.next()) {
MObject object = it.item();
OutputSkinCluster(object);
}
//Hitta kamera data
dag_iter.reset(dag_iter.root(), MItDag::kBreadthFirst, MFn::kCamera);
while (!dag_iter.isDone())
{
extractCamera(dag_iter.item());
dag_iter.next();
}
//itererar dag och s�ker data f�r tillg�ngliga ljus
//om ej ljus finns i scenen ignoreras denna iteration f�r sagda scen.
dag_iter.reset(dag_iter.root(), MItDag::kBreadthFirst, MFn::kLight);
while (!dag_iter.isDone())
{
//funktion till v�r iterator
MFnLight func(dag_iter.item());
//namn:
export_stream_ << "Light: " << func.name().asChar() << std::endl;
//kalla p�EextractLight function
extractLight(dag_iter.item());
//vidare till n�sta ljus i dag'en
dag_iter.next();
/*
if (dag_iter.getPath(dag_path))
{
auto test = dag_path.fullPathName();
export_stream_ << "light: " << test << std::endl;
}
dag_iter.next();
*/
}
dag_iter.reset(dag_iter.root(), MItDag::kBreadthFirst, MFn::kJoint);
while (!dag_iter.isDone())
{
if (dag_iter.getPath(dag_path))
{
MFnDagNode dag_node = dag_path.node();
if (!dag_node.isIntermediateObject())
{
extractJointData(dag_path);
}
}
dag_iter.next();
}
int breadth=0;
dag_iter.reset(dag_iter.root(), MItDag::kBreadthFirst, MFn::kTransform);
while (!dag_iter.isDone())
{
int depth = dag_iter.depth();
if (depth > 1)
break;
if (dag_iter.getPath(dag_path))
{
createSceneGraph(MFnDagNode(dag_path),-1);
}
breadth++;
dag_iter.next();
}
/*
//general purpose iterator, sista argument �r filtret
dag_iter.reset(dag_iter.root(), MItDag::kBreadthFirst, MFn::kLight);
while (!dag_iter.isDone())
{
if (dag_iter.getPath(dag_path))
{
}
dag_iter.next();
}
*/
return true;
}
void SimultaneousImpulseBasedConstraintSolverStrategy::computeConstraintsANDJacobian(std::vector<std::unique_ptr<IConstraint> >& c, const Mat<float>& q, const Mat<float>& qdot)
{
//MAJ qdot :
int b1 = 0;
int b2 = 0;
/*
for( auto& o : sim->simulatedObjects )
{
//((RigidBody*)(o.get()))->setPosition( extract(q, b1+1,1, b1+3,1) );
//((RigidBody*)(o.get()))->setMatOrientation( extract(q, b1+4,1, b1+7,1) );
((RigidBody*)(o.get()))->setLinearVelocity( extract( qdot, b2+1,1, b2+3,1) );
((RigidBody*)(o.get()))->setAngularVelocity( extract( qdot, b2+4,1, b2+6,1) );
b1+=7;
b2+=6;
}
*/
//-------------------------------------
//-------------------------------------
//-------------------------------------
size_t size = c.size();
int n = sim->simulatedObjects.size();
c[0]->computeJacobians();
int idA = 6 * ( c[0]->rbA.getID() );
int idB = 6 * ( c[0]->rbB.getID() );
Mat<float> tJA(c[0]->getJacobianA());
Mat<float> tJB(c[0]->getJacobianB());
//Constraint :
Mat<float> tC(c[0]->getConstraint());
int sl = tJA.getLine();
Mat<float> temp((float)0,sl, 6*n );
for(int i=1;i<=sl;i++)
{
for(int j=1;j<=6;j++)
{
temp.set( tJA.get(i,j) , i, idA+j);
temp.set( tJB.get(i,j), i, idB+j );
}
}
constraintsJacobian = temp;
//Constraint :
float baumgarteBAS = 1e-1f;
float baumgarteC = 1e-1f;
C = tC;
//----------------------------------------
//BAUMGARTE STABILIZATION
//----------------------------------------
//Contact offset :
if( c[0]->getType() == CTContactConstraint)
{
//Baumgarte stabilization :
//temp *= 0.1f/this->dt;
//float slop = -5e-1f;
//float pdepth = ((ContactConstraint*)(c[0].get()))->penetrationDepth;
//tC *= baumgarteC/this->dt*(pdepth-slop);
tC *= baumgarteC/this->dt;
}
//BAS JOINT :
if( c[0]->getType() == CTBallAndSocketJoint)
{
tC*= baumgarteBAS/this->dt;
}
//----------------------------------------
//----------------------------------------
offset = tC;
#ifdef debuglvl1
std::cout << "CONSTRAINTS : nbr = " << size << std::endl;
std::cout << "CONSTRAINTS : 0 : type = " << c[0]->getType() << " ; ids are : " << c[0]->rbA.getID() << " : " << c[0]->rbB.getID() << std::endl;
offset.afficher();
/*std::cout << "local Anchor A : " << std::endl;
c[0]->AnchorAL.afficher();
std::cout << "global Anchor A : " << std::endl;
c[0]->rbA.getPointInWorld(c[0]->AnchorAL).afficher();
std::cout << "local Anchor B : " << std::endl;
c[0]->AnchorBL.afficher();
std::cout << "global Anchor B : " << std::endl;
c[0]->rbB.getPointInWorld(c[0]->AnchorBL).afficher();*/
#endif
for(int i=1;i<size;i++)
{
c[i]->computeJacobians();
tJA = c[i]->getJacobianA();
tJB = c[i]->getJacobianB();
//Constraint :
tC = c[i]->getConstraint();
size_t sl = tJA.getLine();
int idA = 6 * ( c[i]->rbA.getID() );
int idB = 6 * ( c[i]->rbB.getID() );
temp = Mat<float>((float)0,sl, 6*n );
//Constraints :
C = operatorC(C, tC);
//----------------------------------------
//BAUMGARTE STABILIZATION
//----------------------------------------
//Contact offset :
if( c[i]->getType() == CTContactConstraint)
{
//Baumgarte stabilization :
//temp *= 0.1f/this->dt;
tC *= baumgarteC/this->dt;
}
//BAS JOINT :
if( c[i]->getType() == CTBallAndSocketJoint)
{
tC*= baumgarteBAS/this->dt;
}
//----------------------------------------
//----------------------------------------
for(int i=1;i<=sl;i++)
{
for(int j=1;j<=6;j++)
{
temp.set( tJA.get(i,j) , i, idA+j);
temp.set( tJB.get(i,j), i, idB+j );
}
}
constraintsJacobian = operatorC(constraintsJacobian, temp );
//Constraint :
offset = operatorC( offset, tC);
#ifdef debuglvl1
std::cout << "CONSTRAINTS : " << i << " type = " << c[i]->getType() << " ; ids are : " << c[i]->rbA.getID() << " : " << c[i]->rbB.getID() << std::endl;
offset.afficher();
#endif
}
//Let us delete the contact constraints that are ephemerous by essence :
std::vector<std::unique_ptr<IConstraint> >::iterator itC = c.begin();
bool erased = false;
while(itC != c.end())
{
if( (itC->get())->getType() == CTContactConstraint )
{
erased = true;
c.erase(itC);
}
if(!erased)
itC++;
erased = false;
}
}
void IterativeImpulseBasedConstraintSolverStrategy::computeConstraintsANDJacobian(std::vector<std::unique_ptr<IConstraint> >& c, const Mat<float>& q, const Mat<float>& qdot, const SparseMat<float>& invM)
{
//-------------------------------------
//-------------------------------------
//-------------------------------------
size_t size = c.size();
int n = sim->simulatedObjects.size();
float baumgarteBAS = 0.0f;//1e-1f;
float baumgarteC = -2e0f;
float baumgarteH = 0.0f;//1e-1f;
//---------------
// RESETTING :
constraintsC.clear();
constraintsJacobians.clear();
constraintsOffsets.clear();
constraintsIndexes.clear();
constraintsInvM.clear();
constraintsV.clear();
//----------------------
if( size > 0)
{
for(int k=0;k<size;k++)
{
int idA = ( c[k]->rbA.getID() );
int idB = ( c[k]->rbB.getID() );
std::vector<int> indexes(2);
//indexes are set during the creation of the simulation and they begin at 0.
indexes[0] = idA;
indexes[1] = idB;
constraintsIndexes.push_back( indexes );
//---------------------------
//Constraint :
c[k]->computeJacobians();
Mat<float> tJA(c[k]->getJacobianA());
Mat<float> tJB(c[k]->getJacobianB());
Mat<float> tC(c[k]->getConstraint());
constraintsC.push_back( tC );
int nbrlineJ = tJA.getLine();
Mat<float> JacobianAB( operatorL(tJA, tJB) );
constraintsJacobians.push_back( JacobianAB );
//----------------------------------------
//BAUMGARTE STABILIZATION
//----------------------------------------
//Contact offset :
if( c[k]->getType() == CTContactConstraint)
{
//----------------------------------------
//SLOP METHOD :
/*
float slop = 1e0f;
float pdepth = ((ContactConstraint*)(c[k].get()))->penetrationDepth;
std::cout << " ITERATIVE SOLVER :: CONTACT : pDepth = " << pdepth << std::endl;
tC *= baumgarteC/this->dt * fabs_(fabs_(pdepth)-slop);
*/
//----------------------------------------
//----------------------------------------
//DEFAULT METHOD :
tC *= baumgarteC/this->dt;
//----------------------------------------
//----------------------------------------
//METHOD 2 :
/*
float restitFactor = ( (ContactConstraint*) (c[k].get()) )->getRestitutionFactor();
std::cout << " ITERATIVE SOLVER :: CONTACT : restitFactor = " << restitFactor << std::endl;
Mat<float> Vrel( ( (ContactConstraint*) (c[k].get()) )->getRelativeVelocity() );
Mat<float> normal( ( (ContactConstraint*) (c[k].get()) )->getNormalVector() );
std::cout << " ITERATIVE SOLVER :: CONTACT : Normal vector : " << std::endl;
transpose(normal).afficher();
tC += restitFactor * transpose(Vrel)*normal;
*/
//----------------------------------------
std::cout << " ITERATIVE SOLVER :: CONTACT : Contact Constraint : " << std::endl;
transpose(tC).afficher();
std::cout << " ITERATIVE SOLVER :: CONTACT : Relative Velocity vector : " << std::endl;
transpose(( (ContactConstraint*) (c[k].get()) )->getRelativeVelocity()).afficher();
//std::cout << " ITERATIVE SOLVER :: CONTACT : First derivative of Contact Constraint : " << std::endl;
//(transpose(tJA)*).afficher();
}
//BAS JOINT :
if( c[k]->getType() == CTBallAndSocketJoint)
{
tC *= baumgarteBAS/this->dt;
}
//HINGE JOINT :
if( c[k]->getType() == CTHingeJoint)
{
tC *= baumgarteH/this->dt;
}
//BAUMGARTE OFFSET for the moments...
constraintsOffsets.push_back( tC );
//----------------------------------------
//----------------------------------------
//-------------------
// invM matrixes :
Mat<float> invmij(0.0f,12,12);
for(int k=0;k<=1;k++)
{
for(int i=1;i<=6;i++)
{
for(int j=1;j<=6;j++)
{
invmij.set( invM.get( indexes[k]*6+i, indexes[k]*6+j), k*6+i,k*6+j);
}
}
}
constraintsInvM.push_back( invmij);
//-------------------
// Vdot matrixes :
Mat<float> vij(0.0f,12,1);
for(int k=0;k<=1;k++)
{
for(int i=1;i<=6;i++)
{
vij.set( qdot.get( indexes[k]*6+i, 1), k*6+i,1);
}
}
constraintsV.push_back( vij);
}
}
}
