void PolyMolecule::computeNormals()
{
m_FaceNormals.fill(vec3_t(0,0,0), m_Faces.size());
m_NodeNormals.fill(vec3_t(0,0,0), m_Nodes.size());
for (int i = 0; i < m_Faces.size(); ++i) {
QVector<vec3_t> x(m_Faces[i].size() + 1);
vec3_t x_face(0,0,0);
for (int j = 0; j < m_Faces[i].size(); ++j) {
x[j] = getXNode(m_Faces[i][j]);
x_face += x[j];
}
x.last() = x.first();
x_face *= 1.0/m_Faces[i].size();
m_FaceNormals[i] = vec3_t(0,0,0);
for (int j = 0; j < m_Faces[i].size(); ++j) {
m_FaceNormals[i] += triNormal(x_face, x[j], x[j+1]);
}
for (int j = 0; j < m_Faces[i].size(); ++j) {
vec3_t n = m_FaceNormals[i];
//n.normalise();
m_NodeNormals[m_Faces[i][j]] += n;
}
}
for (int i = 0; i < m_Nodes.size(); ++i) {
m_NodeNormals[i].normalise();
}
}
void PolyMolecule::createPolyData(vtkPolyData *poly_data)
{
int N = m_Nodes.size();
EG_VTKSP(vtkPoints, points);
points->SetNumberOfPoints(N);
for (int i = 0; i < N; ++i) {
vec3_t x = getXNode(i);
points->SetPoint(i, x.data());
}
poly_data->Allocate(m_Faces.size());
poly_data->SetPoints(points);
for (int i = 0; i < m_Faces.size(); ++i) {
QVector<vtkIdType> pts(m_Faces[i].size());
for (int j = 0; j < m_Faces[i].size(); ++j) {
pts[j] = m_Faces[i][j];
}
if (pts.size() == 3) {
poly_data->InsertNextCell(VTK_TRIANGLE, pts.size(), pts.data());
} else if (pts.size() == 4) {
poly_data->InsertNextCell(VTK_QUAD, pts.size(), pts.data());
} else {
poly_data->InsertNextCell(VTK_POLYGON, pts.size(), pts.data());
}
}
}
void PolyMolecule::computeCentreOfGravity()
{
m_AllPositive = true;
// first guess of centre of gravity
vec3_t x_centre(0,0,0);
for (int i = 0; i < m_Faces.size(); ++i) {
x_centre += getXFace(i);
}
m_N2BadFaces.resize(m_Nodes.size());
for (int i = 0; i < m_Nodes.size(); ++i) {
m_N2BadFaces[i].clear();
}
x_centre *= 1.0/m_Faces.size();
for (int iter = 0; iter < 2; ++iter) {
double V_total = 0;
m_CentreOfGravity = vec3_t(0,0,0);
m_MaxPyramidVolume = -1e99;
m_MinPyramidVolume = 1e99;
for (int i = 0; i < m_Faces.size(); ++i) {
double V_pyramid = 0;
vec3_t x_face = getXFace(i);
QVector<vec3_t> x(m_Faces[i].size() + 1);
for (int j = 0; j < m_Faces[i].size(); ++j) {
x[j] = getXNode(m_Faces[i][j]);
}
x.last() = x.first();
for (int j = 0; j < m_Faces[i].size(); ++j) {
double V = GeometryTools::tetraVol(x_face, x[j+1], x[j], x_centre, true);
if (V <= 0) {
m_AllPositive = false;
}
V_total += V;
V_pyramid += V;
m_CentreOfGravity += 0.25*V*(x_face + x[j+1] + x[j] + x_centre);
}
if (V_pyramid <= 0) {
for (int j = 0; j < m_Faces[i].size(); ++j) {
m_N2BadFaces[m_Faces[i][j]].insert(i);
}
}
m_MaxPyramidVolume = max(V_pyramid, m_MaxPyramidVolume);
m_MinPyramidVolume = min(V_pyramid, m_MinPyramidVolume);
}
m_CentreOfGravity *= 1.0/V_total;
x_centre = m_CentreOfGravity;
}
}
void PolyMolecule::writeVtkFile(QString file_name)
{
EG_VTKSP(vtkUnstructuredGrid, grid);
allocateGrid(grid, m_Faces.size(), m_Nodes.size());
EG_VTKSP(vtkDoubleArray, normals);
normals->SetNumberOfComponents(3);
normals->SetNumberOfTuples(m_Nodes.size());
normals->SetName("N");
EG_VTKSP(vtkDoubleArray, badness);
badness->SetNumberOfComponents(1);
badness->SetNumberOfTuples(m_Nodes.size());
badness->SetName("badness");
for (int i = 0; i < m_Nodes.size(); ++i) {
vec3_t x = getXNode(i);
grid->GetPoints()->SetPoint(i, x.data());
normals->SetTuple(i, m_NodeNormals[i].data());
badness->SetValue(i, double(m_N2BadFaces[i].size()));
}
grid->GetPointData()->AddArray(normals);
grid->GetPointData()->AddArray(badness);
for (int i = 0; i < m_Faces.size(); ++i) {
QVector<vtkIdType> pts(m_Faces[i].size());
for (int j = 0; j < m_Faces[i].size(); ++j) {
pts[j] = m_Faces[i][j];
}
grid->InsertNextCell(VTK_POLYGON, m_Faces[i].size(), pts.data());
}
EG_VTKSP(vtkXMLUnstructuredGridWriter, vtu);
file_name = GuiMainWindow::pointer()->getCwd() + "/" + file_name + ".vtu";
vtu->SetFileName(qPrintable(file_name));
vtu->SetDataModeToBinary();
vtu->SetInputData(grid);
vtu->Write();
}
gboolean loadConfig(const gchar *filename, CfgFile *lcfg) {
/* Parse hosts.xml document. */
xmlDocPtr xcfg = xmlParseFile(filename);
if(xcfg == NULL)
return(FALSE);
/* Handle Xincludes. */
xmlSetGenericErrorFunc(NULL, xmlErrIgnoreHandler);
xmlXIncludeProcess(xcfg);
handleXMLError( xmlGetLastError() );
xmlSetGenericErrorFunc(NULL, NULL);
/* Validate against DTD. */
xmlValidCtxtPtr xval = xmlNewValidCtxt();
if(xmlValidateDocument(xval, xcfg) == 0) {
xmlFreeValidCtxt(xval);
return(FALSE);
}
xmlFreeValidCtxt(xval);
/* Allocate XPath context. */
xmlXPathContextPtr xctx = xmlXPathNewContext(xcfg);
if(!xctx) {
g_error("%s: xmlXPathNewContext failed!\n", filename);
return(FALSE);
}
xmlNodePtr s_ssh[2] = {getXNode(xctx, "/apt-dater/ssh"), NULL};
xmlNodePtr s_path[2] = {getXNode(xctx, "/apt-dater/paths"), NULL};
#ifdef FEAT_TMUX
xmlNodePtr s_tmux[2] = {getXNode(xctx, "/apt-dater/tmux"), NULL};
#else
xmlNodePtr s_screen[2] = {getXNode(xctx, "/apt-dater/screen"), NULL};
#endif
xmlNodePtr s_appearance[2] = {getXNode(xctx, "/apt-dater/appearance"), NULL};
xmlNodePtr s_notify[2] = {getXNode(xctx, "/apt-dater/notify"), NULL};
xmlNodePtr s_hooks[2] = {getXNode(xctx, "/apt-dater/hooks"), NULL};
#ifdef FEAT_AUTOREF
xmlNodePtr s_autoref[2] = {getXNode(xctx, "/apt-dater/auto-ref"), NULL};
#endif
#ifdef FEAT_HISTORY
xmlNodePtr s_history[2] = {getXNode(xctx, "/apt-dater/history"), NULL};
#endif
#ifdef FEAT_TCLFILTER
xmlNodePtr s_tclfilter[2] = {getXNode(xctx, "/apt-dater/tcl-filter"), NULL};
#endif
lcfg->ssh_optflags = getXPropStr(s_ssh, "opt-cmd-flags", "-t");
lcfg->ssh_cmd = getXPropStr(s_ssh, "cmd", "/usr/bin/ssh");
lcfg->sftp_cmd = getXPropStr(s_ssh, "sftp-cmd", "/usr/bin/sftp");
lcfg->umask = getXPropInt(s_path, "umask", S_IRWXG | S_IRWXO);
umask(lcfg->umask);
lcfg->hostsfile = getXPropStr(s_path, "hosts-file", g_strdup_printf("%s/%s/%s", g_get_user_config_dir(), PROG_NAME, "hosts.xml"));
lcfg->statsdir = getXPropStr(s_path, "stats-dir", g_strdup_printf("%s/%s/%s", g_get_user_cache_dir(), PROG_NAME, "stats"));
if(g_mkdir_with_parents(lcfg->statsdir, S_IRWXU | S_IRWXG) == -1) {
g_warning("Failed to create %s: %s", lcfg->statsdir, g_strerror(errno));
exit(1);
}
#ifdef FEAT_TMUX
lcfg->tmuxconffile = getXPropStr(s_tmux, "conf-file", g_strdup_printf("%s/%s/%s", g_get_user_config_dir(), PROG_NAME, "tmux.conf"));
lcfg->tmuxsockpath = getXPropStr(s_tmux, "socket-path", g_strdup_printf("%s/%s/%s", g_get_user_cache_dir(), PROG_NAME, "tmux"));
if(g_mkdir_with_parents(lcfg->tmuxsockpath, S_IRWXU | S_IRWXG) == -1) {
g_warning("Failed to create %s: %s", lcfg->tmuxsockpath, g_strerror(errno));
exit(1);
}
#else
lcfg->screenrcfile = getXPropStr(s_screen, "rc-file", g_strdup_printf("%s/%s/%s", g_get_user_config_dir(), PROG_NAME, "screenrc"));
lcfg->screentitle = getXPropStr(s_screen, "title", g_strdup("%m # %U%H"));
#endif
lcfg->ssh_agent = getXPropBool(s_ssh, "spawn-agent", FALSE);
xmlNodeSetPtr s_addkeys = getXNodes(xctx, "/apt-dater/ssh/add-key");
if(!xmlXPathNodeSetIsEmpty(s_addkeys)) {
lcfg->ssh_add = g_new0(char*, s_addkeys->nodeNr + 1);
int i;
for(i = 0; i < s_addkeys->nodeNr; i++) {
lcfg->ssh_add[i] = g_strdup((gchar *)xmlGetProp(s_addkeys->nodeTab[i], BAD_CAST("name")));
xmlChar *c = xmlGetProp(s_addkeys->nodeTab[i], BAD_CAST("fn"));
if(!c) {
g_printerr(_("Empty SSH key filename (%s/@fn) in configuration."), xmlGetNodePath(s_addkeys->nodeTab[i]));
exit(1);
}
lcfg->ssh_add[i] = g_strdup((gchar *)c);
}
lcfg->ssh_numadd = s_addkeys->nodeNr;
}
vec3_t PolyMolecule::getXFace(int face)
{
vec3_t x(0,0,0);
foreach (int i, m_Faces[face]) {
x += getXNode(i);
}
