PView *GMSH_EigenvectorsPlugin::execute(PView *v)
{
int scale = (int)EigenvectorsOptions_Number[0].def;
int iView = (int)EigenvectorsOptions_Number[1].def;
PView *v1 = getView(iView, v);
if(!v1) return v;
PViewData *data1 = getPossiblyAdaptiveData(v1);
if(data1->hasMultipleMeshes()){
Msg::Error("Eigenvectors plugin cannot be run on multi-mesh views");
return v;
}
PView *min = new PView();
PView *mid = new PView();
PView *max = new PView();
PViewDataList *dmin = getDataList(min);
PViewDataList *dmid = getDataList(mid);
PViewDataList *dmax = getDataList(max);
int nbcomplex = 0;
fullMatrix<double> mat(3, 3), vl(3, 3), vr(3, 3);
fullVector<double> dr(3), di(3);
for(int ent = 0; ent < data1->getNumEntities(0); ent++){
for(int ele = 0; ele < data1->getNumElements(0, ent); ele++){
if(data1->skipElement(0, ent, ele)) continue;
int numComp = data1->getNumComponents(0, ent, ele);
if(numComp != 9) continue;
int type = data1->getType(0, ent, ele);
int numNodes = data1->getNumNodes(0, ent, ele);
std::vector<double> *outmin = dmin->incrementList(3, type, numNodes);
std::vector<double> *outmid = dmid->incrementList(3, type, numNodes);
std::vector<double> *outmax = dmax->incrementList(3, type, numNodes);
if(!outmin || !outmid || !outmax) continue;
double xyz[3][8];
for(int nod = 0; nod < numNodes; nod++)
data1->getNode(0, ent, ele, nod, xyz[0][nod], xyz[1][nod], xyz[2][nod]);
for(int i = 0; i < 3; i++){
for(int nod = 0; nod < numNodes; nod++){
outmin->push_back(xyz[i][nod]);
outmid->push_back(xyz[i][nod]);
outmax->push_back(xyz[i][nod]);
}
}
for(int step = 0; step < data1->getNumTimeSteps(); step++){
for(int nod = 0; nod < numNodes; nod++){
for(int i = 0; i < 3; i++)
for(int j = 0; j < 3; j++)
data1->getValue(step, ent, ele, nod, 3 * i + j, mat(i, j));
if(mat.eig(dr, di, vl, vr, true)){
if(!scale) dr(0) = dr(1) = dr(2) = 1.;
for(int i = 0; i < 3; i++){
double res;
res = dr(0) * vr(i, 0); outmin->push_back(res);
res = dr(1) * vr(i, 1); outmid->push_back(res);
res = dr(2) * vr(i, 2); outmax->push_back(res);
}
if(di(0) || di(1) || di(2)) nbcomplex++;
}
else{
Msg::Error("Could not compute eigenvalues/vectors");
}
}
}
}
}
if(nbcomplex)
Msg::Error("%d tensors have complex eigenvalues", nbcomplex);
for(int i = 0; i < data1->getNumTimeSteps(); i++){
double time = data1->getTime(i);
dmin->Time.push_back(time);
dmid->Time.push_back(time);
dmax->Time.push_back(time);
}
dmin->setName(data1->getName() + "_MinEigenvectors");
dmin->setFileName(data1->getName() + "_MinEigenvectors.pos");
dmin->finalize();
dmid->setName(data1->getName() + "_MidEigenvectors");
dmid->setFileName(data1->getName() + "_MidEigenvectors.pos");
dmid->finalize();
dmax->setName(data1->getName() + "_MaxEigenvectors");
dmax->setFileName(data1->getName() + "_MaxEigenvectors.pos");
dmax->finalize();
return 0;
}
int GModel::readPLY(const std::string &name)
{
// this is crazy!?
replaceCommaByDot(name);
FILE *fp = Fopen(name.c_str(), "r");
if(!fp){
Msg::Error("Unable to open file '%s'", name.c_str());
return 0;
}
std::vector<MVertex*> vertexVector;
std::map<int, std::vector<MElement*> > elements[5];
std::map<int, std::vector<double> > properties;
char buffer[256], str[256], str2[256], str3[256];
std::string s1;
int elementary = getMaxElementaryNumber(-1) + 1;
int nbv = 0, nbf = 0;
int nbprop = 0;
int nbView = 0;
std::vector<std::string> propName;
while(!feof(fp)) {
if(!fgets(buffer, sizeof(buffer), fp)) break;
if(buffer[0] != '#'){ // skip comments
sscanf(buffer, "%s %s", str, str2);
if(!strcmp(str, "element") && !strcmp(str2, "vertex")){
sscanf(buffer, "%s %s %d", str, str2, &nbv);
}
if(!strcmp(str, "format") && strcmp(str2, "ascii")){
Msg::Error("Only reading of ascii PLY files implemented");
fclose(fp);
return 0;
}
if(!strcmp(str, "property") && strcmp(str2, "list")){
nbprop++;
sscanf(buffer, "%s %s %s", str, str2, str3);
if (nbprop > 3) propName.push_back(s1+str3);
}
if(!strcmp(str, "element") && !strcmp(str2, "face")){
sscanf(buffer, "%s %s %d", str, str2, &nbf);
}
if(!strcmp(str, "end_header")){
nbView = nbprop -3;
Msg::Info("%d elements", nbv);
Msg::Info("%d triangles", nbf);
Msg::Info("%d properties", nbView);
vertexVector.resize(nbv);
for(int i = 0; i < nbv; i++) {
double x,y,z;
char line[10000], *pEnd, *pEnd2, *pEnd3;
if(!fgets(line, sizeof(line), fp)){ fclose(fp); return 0; }
x = strtod(line, &pEnd);
y = strtod(pEnd, &pEnd2);
z = strtod(pEnd2, &pEnd3);
vertexVector[i] = new MVertex(x, y, z);
pEnd = pEnd3;
std::vector<double> prop(nbView);
for (int k = 0; k < nbView; k++){
prop[k]=strtod(pEnd, &pEnd2);
pEnd = pEnd2;
properties[k].push_back(prop[k]);
}
}
for(int i = 0; i < nbf; i++) {
if(!fgets(buffer, sizeof(buffer), fp)) break;
int n[3], nbe;
sscanf(buffer, "%d %d %d %d", &nbe, &n[0], &n[1], &n[2]);
std::vector<MVertex*> vertices;
if(!getVertices(3, n, vertexVector, vertices)){ fclose(fp); return 0; }
elements[0][elementary].push_back(new MTriangle(vertices));
}
}
}
}
for(int i = 0; i < (int)(sizeof(elements) / sizeof(elements[0])); i++)
_storeElementsInEntities(elements[i]);
_associateEntityWithMeshVertices();
_storeVerticesInEntities(vertexVector);
#if defined(HAVE_POST)
// create PViews here
std::vector<GEntity*> _entities;
getEntities(_entities);
for (int iV=0; iV< nbView; iV++){
PView *view = new PView();
PViewDataList *data = dynamic_cast<PViewDataList*>(view->getData());
for(unsigned int ii = 0; ii < _entities.size(); ii++){
for(unsigned int i = 0; i < _entities[ii]->getNumMeshElements(); i++){
MElement *e = _entities[ii]->getMeshElement(i);
int numNodes = e->getNumVertices();
std::vector<double> x(numNodes), y(numNodes), z(numNodes);
std::vector<double> *out = data->incrementList(1, e->getType());
for(int nod = 0; nod < numNodes; nod++) out->push_back((e->getVertex(nod))->x());
for(int nod = 0; nod < numNodes; nod++) out->push_back((e->getVertex(nod))->y());
for(int nod = 0; nod < numNodes; nod++) out->push_back((e->getVertex(nod))->z());
std::vector<double> props;
int n[3];
n[0] = e->getVertex(0)->getNum()-1;
n[1] = e->getVertex(1)->getNum()-1;
n[2] = e->getVertex(2)->getNum()-1;
if(!getProperties(3, n, properties[iV], props)){ fclose(fp); return 0; }
for(int nod = 0; nod < numNodes; nod++) out->push_back(props[nod]);
}
}
data->setName(propName[iV]);
data->Time.push_back(0);
data->setFileName("property.pos");
data->finalize();
}
#endif
fclose(fp);
return 1;
}
PView *GMSH_Scal2VecPlugin::execute(PView *v)
{
int iViewX = (int)Scal2VecOptions_Number[0].def;
int iViewY = (int)Scal2VecOptions_Number[1].def;
int iViewZ = (int)Scal2VecOptions_Number[2].def;
std::string nameNewView = Scal2VecOptions_String[0].def;
PView *vRef = 0, *vX = 0, *vY = 0, *vZ = 0;
PViewData *dataRef = 0, *dataX = 0, *dataY = 0, *dataZ = 0;
// Load data
if(iViewX >= 0){
vX = getView(iViewX, v);
if(!vX){
Msg::Error("Scal2Vec plugin could not find View X: %i", iViewX);
return v;
}
dataX = vX->getData();
if(!vRef){
vRef = vX;
dataRef = dataX;
}
}
if(iViewY >= 0){
vY = getView(iViewY, v);
if(!vY){
Msg::Error("Scal2Vec plugin could not find View Y: %i", iViewY);
return v;
}
dataY = vY->getData();
if(!vRef){
vRef = vY;
dataRef = dataY;
}
}
if(iViewZ >= 0){
vZ = getView(iViewZ, v);
if(!vZ){
Msg::Error("Scal2Vec plugin could not find View Z: %i", iViewZ);
return v;
}
dataZ = vZ->getData();
if(!vRef){
vRef = vZ;
dataRef = dataZ;
}
}
if(!vRef){
Msg::Error("Scal2Vec plugin could not find any view.", iViewZ);
return v;
}
// Initialize the new view
PView *vNew = new PView();
PViewDataList *dataNew = getDataList(vNew);
for(int ent = 0; ent < dataRef->getNumEntities(0); ent++){
for(int ele = 0; ele < dataRef->getNumElements(0, ent); ele++){
if(dataRef->skipElement(0, ent, ele)) continue;
int numComp = 3; // The 3 components of the new view: x,y,z
int type = dataRef->getType(0, ent, ele);
int numNodes = dataRef->getNumNodes(0, ent, ele);
std::vector<double> *out = dataNew->incrementList(numComp, type, numNodes); // Pointer in data of the new view
if(!out) continue;
double x[8], y[8], z[8], valX, valY, valZ;
for(int nod = 0; nod < numNodes; nod++)
dataRef->getNode(0, ent, ele, nod, x[nod], y[nod], z[nod]);
int dim = dataRef->getDimension(0, ent, ele);
elementFactory factory;
element *element = factory.create(numNodes, dim, x, y, z);
if(!element) continue;
for(int nod = 0; nod < numNodes; nod++) out->push_back(x[nod]); // Save coordinates (x,y,z)
for(int nod = 0; nod < numNodes; nod++) out->push_back(y[nod]);
for(int nod = 0; nod < numNodes; nod++) out->push_back(z[nod]);
for(int step = 0; step < dataRef->getNumTimeSteps(); step++){
for(int nod = 0; nod < numNodes; nod++){
if(vX) dataX->getValue(step, ent, ele, nod, 0, valX); else valX = 0;
if(vY) dataY->getValue(step, ent, ele, nod, 0, valY); else valY = 0;
if(vZ) dataZ->getValue(step, ent, ele, nod, 0, valZ); else valZ = 0;
out->push_back(valX); // Save values (fx,fy,fz)
out->push_back(valY);
out->push_back(valZ);
}
}
delete element;
}
}
for(int step = 0; step < dataRef->getNumTimeSteps(); step++){
if(dataRef->hasTimeStep(step)){
double time = dataRef->getTime(step);
dataNew->Time.push_back(time);
}
}
dataNew->setName(nameNewView);
dataNew->setFileName(nameNewView + ".pos");
dataNew->finalize();
return vNew;
}
PView *GMSH_MinMaxPlugin::execute(PView * v)
{
int iView = (int)MinMaxOptions_Number[0].def;
int overTime = (int)MinMaxOptions_Number[1].def;
int argument = (int)MinMaxOptions_Number[2].def;
PView *v1 = getView(iView, v);
if(!v1) return v;
PViewData *data1 = v1->getData(true);
PView *vMin = new PView();
PView *vMax = new PView();
PViewDataList *dataMin = getDataList(vMin);
PViewDataList *dataMax = getDataList(vMax);
if(!argument){
double x = data1->getBoundingBox().center().x();
double y = data1->getBoundingBox().center().y();
double z = data1->getBoundingBox().center().z();
dataMin->SP.push_back(x); dataMin->SP.push_back(y); dataMin->SP.push_back(z);
dataMax->SP.push_back(x); dataMax->SP.push_back(y); dataMax->SP.push_back(z);
dataMin->NbSP = 1;
dataMax->NbSP = 1;
}
double min=VAL_INF, max=-VAL_INF, timeMin=0, timeMax=0;
for(int step = 0; step < data1->getNumTimeSteps(); step++){
if(data1->hasTimeStep(step)){
double minView = VAL_INF, maxView = -VAL_INF;
double xmin = 0., ymin = 0., zmin = 0., xmax = 0., ymax = 0., zmax = 0.;
for(int ent = 0; ent < data1->getNumEntities(step); ent++){
for(int ele = 0; ele < data1->getNumElements(step, ent); ele++){
for(int nod = 0; nod < data1->getNumNodes(step, ent, ele); nod++){
double val;
data1->getScalarValue(step, ent, ele, nod, val);
if(val < minView){
data1->getNode(step, ent, ele, nod, xmin, ymin, zmin);
minView = val;
}
if(val > maxView){
data1->getNode(step, ent, ele, nod, xmax, ymax, zmax);
maxView = val;
}
}
}
}
if(!overTime){
if(argument){
dataMin->SP.push_back(xmin); dataMin->SP.push_back(ymin); dataMin->SP.push_back(zmin);
dataMax->SP.push_back(xmax); dataMax->SP.push_back(ymax); dataMax->SP.push_back(zmax);
(dataMin->NbSP)++;
(dataMax->NbSP)++;
}
else{
double time = data1->getTime(step);
dataMin->Time.push_back(time);
dataMax->Time.push_back(time);
}
dataMin->SP.push_back(minView);
dataMax->SP.push_back(maxView);
}
else{
if(minView < min){
min = minView;
timeMin = data1->getTime(step);
}
if(maxView > max){
max = maxView;
timeMax = data1->getTime(step);
}
}
}
}
if(overTime){
dataMin->SP.push_back(min);
dataMax->SP.push_back(max);
dataMin->Time.push_back(timeMin);
dataMax->Time.push_back(timeMax);
}
vMin->getOptions()->intervalsType = PViewOptions::Numeric;
vMax->getOptions()->intervalsType = PViewOptions::Numeric;
dataMin->setName(data1->getName() + "_Min");
dataMin->setFileName(data1->getName() + "_Min.pos");
dataMin->finalize();
dataMax->setName(data1->getName() + "_Max");
dataMax->setFileName(data1->getName() + "_Max.pos");
dataMax->finalize();
return 0;
}
PView *GMSH_Scal2VecPlugin::execute(PView *v)
{
// Load options
int iView[3];
for (int comp=0; comp<3; comp++)
iView[comp] = (int)Scal2VecOptions_Number[comp].def;
// Load data
PView *vRef=0, *vComp[3];
for (int comp=0; comp<3; comp++) {
if (iView[comp]<0) vComp[comp] = 0;
else {
vComp[comp] = getView(iView[comp], v);
if (!vComp[comp]) {
Msg::Error("Scal2Vec plugin could not find View '%i'", iView[comp]);
return v;
}
if (!vRef) vRef = vComp[comp];
}
}
if (!vRef) {
Msg::Error("Scal2Vec plugin could not find any view.");
return v;
}
PViewData *dataRef = vRef->getData();
// Initialize the new view
PView *vNew = new PView();
PViewDataList *dataNew = getDataList(vNew);
int step0 = dataRef->getFirstNonEmptyTimeStep();
for (int ent=0; ent < dataRef->getNumEntities(step0); ent++) {
for (int ele=0; ele < dataRef->getNumElements(step0, ent); ele++) {
if (dataRef->skipElement(step0, ent, ele)) continue;
int type = dataRef->getType(step0, ent, ele);
int numNodes = dataRef->getNumNodes(step0, ent, ele);
std::vector<double> *out = dataNew->incrementList(3, type, numNodes); // Pointer in data of the new view
if (!out) continue;
double x[8], y[8], z[8];
for (int nod=0; nod<numNodes; nod++)
dataRef->getNode(step0, ent, ele, nod, x[nod], y[nod], z[nod]);
int dim = dataRef->getDimension(step0, ent, ele);
elementFactory factory;
element *element = factory.create(numNodes, dim, x, y, z);
if (!element) continue;
for (int nod=0; nod<numNodes; nod++) out->push_back(x[nod]); // Save coordinates (x,y,z)
for (int nod=0; nod<numNodes; nod++) out->push_back(y[nod]);
for (int nod=0; nod<numNodes; nod++) out->push_back(z[nod]);
for (int step=step0; step < dataRef->getNumTimeSteps(); step++) {
if (!dataRef->hasTimeStep(step)) continue;
for (int nod=0; nod<numNodes; nod++) {
for (int comp=0; comp<3; comp++) {
double val=0.;
if(vComp[comp]) vComp[comp]->getData()->getValue(step, ent, ele, nod, 0, val);
out->push_back(val); // Save value
}
}
}
delete element;
}
}
for (int step=step0; step < dataRef->getNumTimeSteps(); step++) {
if (!dataRef->hasTimeStep(step)) continue;
dataNew->Time.push_back(dataRef->getTime(step));
}
std::string nameNewView = Scal2VecOptions_String[0].def;
dataNew->setName(nameNewView);
dataNew->setFileName(nameNewView + ".pos");
dataNew->finalize();
return vNew;
}
PView *GMSH_EigenvaluesPlugin::execute(PView *v)
{
int iView = (int)EigenvaluesOptions_Number[0].def;
PView *v1 = getView(iView, v);
if(!v1) return v;
PViewData *data1 = getPossiblyAdaptiveData(v1);
if(data1->hasMultipleMeshes()){
Msg::Error("Eigenvalues plugin cannot be run on multi-mesh views");
return v;
}
PView *min = new PView();
PView *mid = new PView();
PView *max = new PView();
PViewDataList *dmin = getDataList(min);
PViewDataList *dmid = getDataList(mid);
PViewDataList *dmax = getDataList(max);
for(int ent = 0; ent < data1->getNumEntities(0); ent++){
for(int ele = 0; ele < data1->getNumElements(0, ent); ele++){
if(data1->skipElement(0, ent, ele)) continue;
int numComp = data1->getNumComponents(0, ent, ele);
if(numComp != 9) continue;
int type = data1->getType(0, ent, ele);
int numNodes = data1->getNumNodes(0, ent, ele);
std::vector<double> *outmin = dmin->incrementList(1, type, numNodes);
std::vector<double> *outmid = dmid->incrementList(1, type, numNodes);
std::vector<double> *outmax = dmax->incrementList(1, type, numNodes);
if(!outmin || !outmid || !outmax) continue;
double xyz[3][8];
for(int nod = 0; nod < numNodes; nod++)
data1->getNode(0, ent, ele, nod, xyz[0][nod], xyz[1][nod], xyz[2][nod]);
for(int i = 0; i < 3; i++){
for(int nod = 0; nod < numNodes; nod++){
outmin->push_back(xyz[i][nod]);
outmid->push_back(xyz[i][nod]);
outmax->push_back(xyz[i][nod]);
}
}
for(int step = 0; step < data1->getNumTimeSteps(); step++){
for(int nod = 0; nod < numNodes; nod++){
double val[9], w[3];
for(int comp = 0; comp < numComp; comp++)
data1->getValue(step, ent, ele, nod, comp, val[comp]);
double A[3][3] = {{val[0], val[1], val[2]},
{val[3], val[4], val[5]},
{val[6], val[7], val[8]}};
eigenvalue(A, w);
outmin->push_back(w[2]);
outmid->push_back(w[1]);
outmax->push_back(w[0]);
}
}
}
}
for(int i = 0; i < data1->getNumTimeSteps(); i++){
double time = data1->getTime(i);
dmin->Time.push_back(time);
dmid->Time.push_back(time);
dmax->Time.push_back(time);
}
dmin->setName(data1->getName() + "_MinEigenvalues");
dmin->setFileName(data1->getName() + "_MinEigenvalues.pos");
dmin->finalize();
dmid->setName(data1->getName() + "_MidEigenvalues");
dmid->setFileName(data1->getName() + "_MidEigenvalues.pos");
dmid->finalize();
dmax->setName(data1->getName() + "_MaxEigenvalues");
dmax->setFileName(data1->getName() + "_MaxEigenvalues.pos");
dmax->finalize();
return 0;
}
PView *GMSH_LevelsetPlugin::execute(PView *v)
{
// for adapted views we can only run the plugin on one step at a time
if(v->getData()->getAdaptiveData()){
PViewOptions *opt = v->getOptions();
v->getData()->getAdaptiveData()->changeResolution
(opt->timeStep, _recurLevel, _targetError, this);
v->setChanged(true);
}
PViewData *vdata = getPossiblyAdaptiveData(v), *wdata;
if(_valueView < 0) {
wdata = vdata;
}
else if(_valueView > (int)PView::list.size() - 1){
Msg::Error("View[%d] does not exist: reverting to View[%d]",
_valueView, v->getIndex());
wdata = vdata;
}
else{
wdata = getPossiblyAdaptiveData(PView::list[_valueView]);
}
// sanity checks
if(vdata->getNumEntities() != wdata->getNumEntities() ||
vdata->getNumElements() != wdata->getNumElements()){
Msg::Error("Incompatible views");
return v;
}
if(_valueTimeStep >= wdata->getNumTimeSteps()) {
Msg::Error("Wrong time step %d in view", _valueTimeStep);
return v;
}
// Force creation of one view per time step if we have multi meshes
if(vdata->hasMultipleMeshes()) _valueIndependent = 0;
double x[8], y[8], z[8], levels[8];
double scalarValues[8] = {0., 0., 0., 0., 0., 0., 0., 0.};
if(_valueIndependent) {
// create a single output view containing the (possibly
// multi-step) levelset
int firstNonEmptyStep = vdata->getFirstNonEmptyTimeStep();
PViewDataList *out = getDataList(new PView());
for(int ent = 0; ent < vdata->getNumEntities(firstNonEmptyStep); ent++){
for(int ele = 0; ele < vdata->getNumElements(firstNonEmptyStep, ent); ele++){
if(vdata->skipElement(firstNonEmptyStep, ent, ele)) continue;
for(int nod = 0; nod < vdata->getNumNodes(firstNonEmptyStep, ent, ele); nod++){
vdata->getNode(firstNonEmptyStep, ent, ele, nod, x[nod], y[nod], z[nod]);
levels[nod] = levelset(x[nod], y[nod], z[nod], 0.);
}
_cutAndAddElements(vdata, wdata, ent, ele, -1, _valueTimeStep, x, y, z,
levels, scalarValues, out);
}
}
out->setName(vdata->getName() + "_Levelset");
out->setFileName(vdata->getFileName() + "_Levelset.pos");
out->finalize();
}
else{
// create one view per timestep
for(int step = 0; step < vdata->getNumTimeSteps(); step++){
if(!vdata->hasTimeStep(step)) continue;
PViewDataList *out = getDataList(new PView());
for(int ent = 0; ent < vdata->getNumEntities(step); ent++){
for(int ele = 0; ele < vdata->getNumElements(step, ent); ele++){
if(vdata->skipElement(step, ent, ele)) continue;
for(int nod = 0; nod < vdata->getNumNodes(step, ent, ele); nod++){
vdata->getNode(step, ent, ele, nod, x[nod], y[nod], z[nod]);
vdata->getScalarValue(step, ent, ele, nod, scalarValues[nod]);
levels[nod] = levelset(x[nod], y[nod], z[nod], scalarValues[nod]);
}
int wstep = (_valueTimeStep < 0) ? step : _valueTimeStep;
_cutAndAddElements(vdata, wdata, ent, ele, step, wstep, x, y, z,
levels, scalarValues, out);
}
}
char tmp[246];
sprintf(tmp, "_Levelset_%d", step);
out->setName(vdata->getName() + tmp);
out->setFileName(vdata->getFileName() + tmp + ".pos");
out->finalize();
}
}
return 0;
}