void
MeshEdgeElementTable::calcNormalVector(int index)
{
if (normals == NULL)
return;
// Create normal
const int* nodeIds = getNodeIds(index);
Point3& normal = normals[index];
Point3& p1 = meshNodes[nodeIds[0]];
Point3& p2 = meshNodes[nodeIds[1]];
Point3 a;
diff3(p2, p1, a);
normal[0] = -a[1];
normal[1] = a[0];
normal[2] = 0.0;
normalize(normal);
for (int i = 0; i < 3; i++) {
if ( isZero(normal[i]) ) {
normal[i] = 0.0;
}
}
}
void
MeshEdgeElementTable::draw(Renderer* renderer, bool el_selected)
{
meshElementCode elem_code;
int elem_type;
for (int i = 0; i < nofElements; i++) {
elem_code = getElementCode(i);
elem_type = MeshElementDesc[elem_code][DESC_ELEM_TYPE];
renderer->drawMeshElement(elem_type, getNodeIds(i), NULL, meshNodes,
1, el_selected);
}
}
std::string EpidemicDataSet::getVariableSummaryNodeVsTime(const std::string &varName)
{
if(variables_.count(varName) == 0)
{
put_flog(LOG_ERROR, "no such variable %s", varName.c_str());
return std::string();
}
// nodeIds
std::vector<int> nodeIds = getNodeIds();
// generate the CSV
std::stringstream out;
// set maximum decimal precision for stringstream
out.precision(16);
// header
out << "t";
// header: for each node
for(unsigned int i=0; i<nodeIds.size(); i++)
{
out << "," << nodeIds[i];
}
out << std::endl;
// row for each time
for(unsigned t=0; t<getNumTimes(); t++)
{
out << t;
for(unsigned int n=0; n<nodeIds.size(); n++)
{
out << "," << getValue(varName, t, nodeIds[n]);
}
out << std::endl;
}
return out.str();
}
// Method finds subelement ("face") index in the parent by
// comparing subelement's node-ids to that of the potential
// parent.
// Returns NO_INDEX if subelement doesn't belong to the parent
int
MeshElementTable::findSubElementIndex(int elem_index,
int& direction, int& start_position,
int nof_sub_nodes, const int* sub_node_ids)
{
static int my_sub_node_ids[64];
meshElementCode elem_code = getElementCode(elem_index);
int my_nof_sub_elems = MeshElementDesc[elem_code][DESC_NOF_BNDR_ELEMS];
int nof_nodes_to_check = nof_sub_nodes;
int i, my_pos, my_pos2;
const int* my_node_ids = getNodeIds(elem_index);
//---Loop all faces in the element and compare node ids
for (int my_sub_index = 0; my_sub_index < my_nof_sub_elems; my_sub_index++) {
// Collect face node ids and check if this COULD be the face
for (i = 0; i < nof_sub_nodes; i++) {
int local_id = MeshElementBndrNodes[elem_code][my_sub_index][i];
my_sub_node_ids[i] = my_node_ids[local_id];
}
int start2;
if ( !idLoopsAreMatching(nof_sub_nodes, nof_nodes_to_check,
my_sub_node_ids, sub_node_ids,
direction, start_position, start2) ) {
continue;
// Match found
} else {
return my_sub_index;
}
}
// No match
return (int) NO_INDEX;
}
Math::RigidTransform3d Fem2DLocalization::getElementPose()
{
auto femRepresentation = std::static_pointer_cast<Fem2DRepresentation>(getRepresentation());
auto position = getLocalPosition();
auto femElement = femRepresentation->getFemElement(getLocalPosition().index);
const auto& nodeIds = femElement->getNodeIds();
std::array<Math::Vector3d, 3> nodePositions =
{femRepresentation->getCurrentState()->getPosition(nodeIds[0]),
femRepresentation->getCurrentState()->getPosition(nodeIds[1]),
femRepresentation->getCurrentState()->getPosition(nodeIds[2])};
Math::Vector3d edge, normal, binormal;
edge = (nodePositions[1] - nodePositions[0]).normalized();
normal = (nodePositions[2] - nodePositions[0]).cross(edge).normalized();
binormal = edge.cross(normal);
Math::Matrix33d rotation;
rotation << edge, normal, binormal;
return Math::makeRigidTransform(rotation, (nodePositions[0] + nodePositions[1] + nodePositions[2]) / 3.0);
}
void
MeshElementTable::calcCenter(int index)
{
if (centers == NULL)
return;
const int* nodeIds = getNodeIds(index);
// Create center point
Point3& center = centers[index];
centerPoint(index, center);
// Calculate square of the distance of the first node
// from the center
Point3 r;
diff3(meshNodes[nodeIds[0]], center, r);
double rsquared = dot3(r, r);
rSquares[index] = rsquared;
}
void
MeshElementTable::centerPoint(int index, Point3& center)
{
const int* nodeIds = getNodeIds(index);
center[0] = 0;
center[1] = 0;
center[2] = 0;
meshElementCode elem_code = getElementCode(index);
short nof_nodes = MeshElementDesc[elem_code][DESC_NOF_NODES];
for (short i = 0; i < nof_nodes; i++) {
Point3& p = meshNodes[nodeIds[i]];
center[0] += p[0];
center[1] += p[1];
center[2] += p[2];
}
center[0] /= nof_nodes;
center[1] /= nof_nodes;
center[2] /= nof_nodes;
}
std::string EpidemicDataSet::getVariableStratified2NodeVsTime(const std::string &varName)
{
if(variables_.count(varName) == 0)
{
put_flog(LOG_ERROR, "no such variable %s", varName.c_str());
return std::string();
}
// make sure we have at least two stratifications
std::vector<std::vector<std::string> > stratifications = getStratifications();
if(stratifications.size() < 2)
{
put_flog(LOG_ERROR, "need at least 2 stratifications");
return std::string();
}
// nodeIds
std::vector<int> nodeIds = getNodeIds();
// generate the CSV
std::stringstream out;
// set maximum decimal precision for stringstream
out.precision(16);
// header
out << "t,group";
// header: for each node
for(unsigned int i=0; i<nodeIds.size(); i++)
{
out << "," << nodeIds[i];
}
out << std::endl;
// row for each time and stratification value combination
std::vector<int> stratificationValues(2, 0);
for(unsigned t=0; t<getNumTimes(); t++)
{
for(unsigned int s1=0; s1<stratifications[0].size(); s1++)
{
stratificationValues[0] = s1;
for(unsigned int s2=0; s2<stratifications[1].size(); s2++)
{
stratificationValues[1] = s2;
// group name
std::string groupName = stratifications[0][s1] + " " + stratifications[1][s2];
out << t << "," << groupName;
for(unsigned int n=0; n<nodeIds.size(); n++)
{
out << "," << getValue(varName, t, nodeIds[n], stratificationValues);
}
out << std::endl;
}
}
}
return out.str();
}
bool
MeshElementTable::isSameElement(int index,
short& direction, short& start_position,
int other_elem_code, int other_nof_nodes, int* other_node_ids)
{
meshElementCode elem_code = getElementCode(index);
if (elem_code != other_elem_code)
return false;
int nof_nodes = other_nof_nodes;
const int* my_node_ids = getNodeIds(index);
int i;
// First trivial sum check
int my_sum = 0;
int other_sum = 0;
for (i = 0; i < nof_nodes; i++) {
my_sum += my_node_ids[i];
other_sum += other_node_ids[i];
}
if (my_sum != other_sum)
return false;
// Now simply compare in order if node ids matches
start_position = -1;
int other_start_position;
for (i = 0; i < nof_nodes; i++) {
for (int j = i; j < nof_nodes; j++) {
if (my_node_ids[i] == other_node_ids[j]) {
start_position = i;
other_start_position = j;
break;
}
}
// If common node was found
if (start_position != -1)
break;
}
if (start_position == -1)
return false;
int my_pos, other_pos;
// Find direction for my nodes
my_pos = start_position + 1;
if (my_pos == nof_nodes)
my_pos = 0;
other_pos = other_start_position + 1;
if (other_pos == nof_nodes)
other_pos = 0;
// Try first the positive direction
if ( my_node_ids[my_pos] == other_node_ids[other_pos]) {
direction = 1;
// Try next the negative direction
} else {
my_pos = start_position - 1;
if (my_pos < 0)
my_pos = nof_nodes - 1;
if ( my_node_ids[my_pos] == other_node_ids[other_pos]) {
direction = -1;
// Ok, no match in either direction
} else {
return false;
}
}
// Continue checking the match
my_pos += direction;
other_pos +=1;
// Loop enough nodes the match
for (i = 2; i < nof_nodes; i++) {
//-check first array edges
// "dropping" from left
if (my_pos < 0)
my_pos = nof_nodes - 1;
// "dropping" from right
else if (my_pos == nof_nodes)
my_pos = 0;
if (other_pos == nof_nodes)
other_pos = 0;
//-if nodes are different, we can stop
if (my_node_ids[my_pos] != other_node_ids[other_pos]) {
return false;
}
//-next check positions
my_pos += direction;
other_pos += 1;
}
return true;
}
int
MeshEdgeElementTable::calcLineIntersections(int elem_index, short elem_dir,
Point3& lstart, Point3& ldir, Point3* isec_points)
{
meshElementCode elem_code = getElementCode(elem_index);
if (elem_code < MEC_202 || elem_code >= 303)
return 0;
const int* nodeIds = getNodeIds(elem_index, elem_dir);
Point3& p0 = meshNodes[nodeIds[0]];
Point3& p1 = meshNodes[nodeIds[1]];
Point3& normal = normals[elem_index];
if (elem_dir == -1)
scalarmult(-1, normal, normal);
// Check end-point cases
if ( samepoint(p0, lstart) ){
copy3(p0, *isec_points);
return 1;
}
if ( samepoint(p1, lstart) ){
copy3(p1, *isec_points);
return 1;
}
Point3 edge_dir, l_delta0, tmp;
// Edge direction vector (normalized)
edge_dir[0] = normal[1];
edge_dir[1] = -1 * normal[0];
edge_dir[2] = 0.0;
// Edge length
diff3(p1, p0, tmp);
double edge_len = dot3(edge_dir, tmp);
// Vector l_delta0 = lstart - p0
diff3(lstart, p0, l_delta0);
// Check that intersection is "within" the edge
// project the intersection point to the edge
double t = dot3(edge_dir, l_delta0);
if ( isLess(t, 0.0) ||
isGreater(t, edge_len)
)
return 0;
// Check that intersection distance from the edge is ok
// project intersection point to the edge normal
double d = dot3(normal, l_delta0);
if (d < 0)
d *= -1;
if ( isGreater(d, MeshEdgeElementTable::pickingTolerance) )
return 0;
// Intersection point is: p0 + t * (p1 - p0)
scalarmult(t, edge_dir, tmp);
add3(p0, tmp, *isec_points);
return 1;
}