// -----------------------------------------------------------------------------
//
// -----------------------------------------------------------------------------
void AdjustVolumeOrigin::updateSurfaceMesh()
{
int err = 0;
std::stringstream ss;
setErrorCondition(err);
SurfaceMeshDataContainer* m = getSurfaceMeshDataContainer();
if(NULL == m)
{
setErrorCondition(-999);
notifyErrorMessage("The SurfaceMeshing DataContainer Object was NULL", -999);
return;
}
setErrorCondition(0);
notifyStatusMessage("Starting");
#ifdef DREAM3D_USE_PARALLEL_ALGORITHMS
tbb::task_scheduler_init init;
bool doParallel = true;
#endif
DREAM3D::SurfaceMesh::VertListPointer_t nodesPtr = getSurfaceMeshDataContainer()->getVertices();
DREAM3D::SurfaceMesh::Vert_t* nodes = nodesPtr->GetPointer(0);
// First get the min/max coords.
float min[3] = { std::numeric_limits<float>::max(), std::numeric_limits<float>::max(), std::numeric_limits<float>::max() };
// float max[3] = { std::numeric_limits<float>::min(), std::numeric_limits<float>::min(), std::numeric_limits<float>::min() };
size_t count = nodesPtr->GetNumberOfTuples();
for (size_t i = 0; i < count; i++)
{
// if (nodes[i].pos[0] > max[0]) { max[0] = nodes[i].pos[0]; }
// if (nodes[i].pos[1] > max[1]) { max[1] = nodes[i].pos[1]; }
// if (nodes[i].pos[2] > max[2]) { max[2] = nodes[i].pos[2]; }
if (nodes[i].pos[0] < min[0]) { min[0] = nodes[i].pos[0]; }
if (nodes[i].pos[1] < min[1]) { min[1] = nodes[i].pos[1]; }
if (nodes[i].pos[2] < min[2]) { min[2] = nodes[i].pos[2]; }
}
float delta[3] = {min[0] - m_Origin.x, min[1] - m_Origin.y, min[2] - m_Origin.z };
#ifdef DREAM3D_USE_PARALLEL_ALGORITHMS
if (doParallel == true)
{
tbb::parallel_for(tbb::blocked_range<size_t>(0, count),
Detail::UpdateVerticesImpl(nodesPtr, delta), tbb::auto_partitioner());
}
else
#endif
{
Detail::UpdateVerticesImpl serial(nodesPtr, delta);
serial.generate(0, count);
}
}
// -----------------------------------------------------------------------------
//
// -----------------------------------------------------------------------------
void AbaqusSurfaceMeshWriter::execute()
{
int err = 0;
std::stringstream ss;
SurfaceMeshDataContainer* sm = getSurfaceMeshDataContainer();
dataCheck(false, 1, 1, 1);
if(getErrorCondition() < 0)
{
return;
}
// Make sure any directory path is also available as the user may have just typed
// in a path without actually creating the full path
std::string parentPath = MXAFileInfo::parentPath(getOutputFile());
if(!MXADir::mkdir(parentPath, true))
{
std::stringstream ss;
ss << "Error creating parent path '" << parentPath << "'";
notifyErrorMessage(ss.str(), -1);
setErrorCondition(-1);
return;
}
DREAM3D::SurfaceMesh::VertListPointer_t nodesPtr = sm->getVertices();
DREAM3D::SurfaceMesh::FaceListPointer_t trianglePtr = sm->getFaces();
// Get the Labels(GrainIds or Region Ids) for the triangles
Int32ArrayType::Pointer faceLabelsPtr = boost::dynamic_pointer_cast<Int32ArrayType>(sm->getFaceData(DREAM3D::FaceData::SurfaceMeshFaceLabels));
int32_t* faceLabels = faceLabelsPtr->GetPointer(0);
// Store all the unique Spins
std::set<int> uniqueSpins;
for (int i = 0; i < trianglePtr->GetNumberOfTuples(); i++)
{
uniqueSpins.insert(faceLabels[i*2]);
uniqueSpins.insert(faceLabels[i*2+1]);
}
FILE* f = fopen(m_OutputFile.c_str(), "wb");
ScopedFileMonitor fileMonitor(f);
err = writeHeader(f, nodesPtr->GetNumberOfTuples(), trianglePtr->GetNumberOfTuples(), uniqueSpins.size()-1);
err = writeNodes(f);
err = writeTriangles(f);
err = writeGrains(f);
setErrorCondition(0);
notifyStatusMessage("Complete");
return;
}
// -----------------------------------------------------------------------------
//
// -----------------------------------------------------------------------------
int AbaqusSurfaceMeshWriter::writeNodes(FILE* f)
{
DREAM3D::SurfaceMesh::VertListPointer_t nodesPtr = getSurfaceMeshDataContainer()->getVertices();
DREAM3D::SurfaceMesh::Vert_t* nodes = nodesPtr->GetPointer(0);
size_t numNodes = nodesPtr->GetNumberOfTuples();
int err = 0;
fprintf(f, "*Node,NSET=NALL\n");
//1, 72.520433763730, 70.306420652241, 100.000000000000
for(size_t i = 1; i <= numNodes; ++i)
{
DREAM3D::SurfaceMesh::Vert_t& n = nodes[i-1];
fprintf(f, "%lu, %0.6f, %0.6f, %0.6f\n", i, n.pos[0], n.pos[1], n.pos[2]);
}
return err;
}
void generate(size_t start, size_t end) const
{
DREAM3D::SurfaceMesh::Vert_t* nodes = m_Nodes->GetPointer(0);
for (size_t i = start; i < end; i++)
{
nodes[i].pos[0] = nodes[i].pos[0] - m_Delta[0];
nodes[i].pos[1] = nodes[i].pos[1] - m_Delta[1];
nodes[i].pos[2] = nodes[i].pos[2] - m_Delta[2];
}
}
/**
* @brief generate Generates the Normals for the triangles
* @param start The starting DREAM3D::SurfaceMesh::Face_t Index
* @param end The ending DREAM3D::SurfaceMesh::Face_t Index
*/
void generate(size_t start, size_t end) const
{
DREAM3D::SurfaceMesh::Vert_t* nodes = m_Nodes->GetPointer(0);
DREAM3D::SurfaceMesh::Face_t* triangles = m_Triangles->GetPointer(0);
for (size_t i = start; i < end; i++)
{
// Get the true indices of the 3 nodes
VectorType normal = TriangleOps::computeNormal(nodes[triangles[i].verts[0]], nodes[triangles[i].verts[1]], nodes[triangles[i].verts[2]]);
m_Normals[i*3+0] = normal.x;
m_Normals[i*3+1] = normal.y;
m_Normals[i*3+2] = normal.z;
}
}
// -----------------------------------------------------------------------------
//
// -----------------------------------------------------------------------------
void SurfaceMeshDataContainerWriter::writeXdmfGridHeader()
{
if (m_WriteXdmfFile == false || m_XdmfPtr == NULL)
{
return;
}
DREAM3D::SurfaceMesh::FaceListPointer_t faces = getSurfaceMeshDataContainer()->getFaces();
if (NULL == faces.get())
{
return;
}
DREAM3D::SurfaceMesh::VertListPointer_t verts = getSurfaceMeshDataContainer()->getVertices();
if(NULL == verts.get())
{
return;
}
std::ostream& out = *m_XdmfPtr;
out << " <Grid Name=\"SurfaceMesh DataContainer\">" << std::endl;
out << " <Topology TopologyType=\"Triangle\" NumberOfElements=\"" << faces->GetNumberOfTuples() << "\">" << std::endl;
out << " <DataItem Format=\"HDF\" NumberType=\"Int\" Dimensions=\"" << faces->GetNumberOfTuples() << " 3\">" << std::endl;
ssize_t nameSize = H5Fget_name(m_HdfFileId, NULL, 0) + 1;
std::vector<char> nameBuffer(nameSize, 0);
nameSize = H5Fget_name(m_HdfFileId, &(nameBuffer.front()), nameSize);
std::string hdfFileName(&(nameBuffer.front()), nameSize);
hdfFileName = MXAFileInfo::filename(hdfFileName);
out << " " << hdfFileName << ":/SurfaceMeshDataContainer/Faces" << std::endl;
out << " </DataItem>" << std::endl;
out << " </Topology>" << std::endl;
out << " <Geometry Type=\"XYZ\">" << std::endl;
out << " <DataItem Format=\"HDF\" Dimensions=\"" << verts->GetNumberOfTuples() << " 3\" NumberType=\"Float\" Precision=\"4\">" << std::endl;
out << " " << hdfFileName << ":/SurfaceMeshDataContainer/Vertices" << std::endl;
out << " </DataItem>" << std::endl;
out << " </Geometry>" << std::endl;
out << "" << std::endl;
}
// -----------------------------------------------------------------------------
//
// -----------------------------------------------------------------------------
void GoldfeatherReader::execute()
{
int err = 0;
std::stringstream ss;
setErrorCondition(err);
SurfaceMeshDataContainer* m = getSurfaceMeshDataContainer();
if(NULL == m)
{
setErrorCondition(-999);
notifyErrorMessage("The Voxel DataContainer Object was NULL", -999);
return;
}
setErrorCondition(0);
FILE* f = fopen(m_InputFile.c_str(), "r");
if (NULL == f)
{
setErrorCondition(-999);
notifyErrorMessage("Error opening Input file", getErrorCondition());
return;
}
ScopedFileMonitor fileMonitor(f);
int nNodes = 0;
fscanf(f, "%d\n", &nNodes);
dataCheck(false, nNodes, 1, 1);
// Allocate the Nodes, Normals, curvatures and principal direction vectors
DREAM3D::SurfaceMesh::VertListPointer_t nodesPtr = DREAM3D::SurfaceMesh::VertList_t::CreateArray(nNodes, DREAM3D::VertexData::SurfaceMeshNodes);
nodesPtr->initializeWithZeros();
DREAM3D::SurfaceMesh::Vert_t* nodes = nodesPtr->GetPointer(0);
DoubleArrayType::Pointer normalsPtr = DoubleArrayType::CreateArray(nNodes, 3, DREAM3D::VertexData::SurfaceMeshNodeNormals);
double* normals = normalsPtr->GetPointer(0);
DoubleArrayType::Pointer pcurv1Ptr = DoubleArrayType::CreateArray(nNodes, 1, "Principal_Curvature_1");
double* pcurv1 = pcurv1Ptr->GetPointer(0);
DoubleArrayType::Pointer pcurv2Ptr = DoubleArrayType::CreateArray(nNodes, 1, "Principal_Curvature_2");
double* pcurv2 = pcurv2Ptr->GetPointer(0);
DoubleArrayType::Pointer pDirection1Ptr = DoubleArrayType::CreateArray(nNodes, 3, "Principal_Direction_1");
double* pDirection1 = pDirection1Ptr->GetPointer(0);
DoubleArrayType::Pointer pDirection2Ptr = DoubleArrayType::CreateArray(nNodes, 3, "Principal_Direction_2");
double* pDirection2 = pDirection2Ptr->GetPointer(0);
float x, y, z, n0, n1, n2, p1, p2;
for(int n = 0; n < nNodes; ++n)
{
fscanf(f, "%f %f %f %f %f %f %f %f\n", &x, &y, &z, &n0, &n1, &n2, &p1, &p2);
nodes[n].pos[0] = x;
nodes[n].pos[1] = y;
nodes[n].pos[2] = z;
normals[n*3+0] = n0;
normals[n*3+1] = n1;
normals[n*3+2] = n2;
pcurv1[n] = p1;
pcurv2[n] = p2;
// Read the next line of the data which is the principal direction vectors
fscanf(f, "%f %f %f %f %f %f\n", &x, &y, &z, &n0, &n1, &n2);
pDirection1[n*3+0] = x;
pDirection1[n*3+1] = y;
pDirection1[n*3+2] = z;
pDirection2[n*3+0] = n0;
pDirection2[n*3+1] = n1;
pDirection2[n*3+2] = n2;
}
m->setVertices(nodesPtr);
m->addVertexData(normalsPtr->GetName(), normalsPtr);
m->addVertexData(pcurv1Ptr->GetName(), pcurv1Ptr);
m->addVertexData(pcurv2Ptr->GetName(), pcurv2Ptr);
m->addVertexData(pDirection1Ptr->GetName(), pDirection1Ptr);
m->addVertexData(pDirection2Ptr->GetName(), pDirection2Ptr);
int nTriangles = 0;
err = fscanf(f, "%d\n", &nTriangles);
if (err < 0)
{
off_t fpos;
fpos = ftell(f);
setErrorCondition(-876);
notifyErrorMessage("Error Reading the number of Triangles from the file", getErrorCondition());
return;
}
DREAM3D::SurfaceMesh::FaceListPointer_t trianglesPtr = DREAM3D::SurfaceMesh::FaceList_t::CreateArray(nTriangles, DREAM3D::FaceData::SurfaceMeshFaces);
trianglesPtr->initializeWithZeros();
DREAM3D::SurfaceMesh::Face_t* triangles = trianglesPtr->GetPointer(0);
DataArray<int32_t>::Pointer faceLabelPtr = DataArray<int32_t>::CreateArray(nTriangles, 2, DREAM3D::FaceData::SurfaceMeshFaceLabels);
faceLabelPtr->initializeWithZeros();
int32_t* faceLabels = faceLabelPtr->GetPointer(0);
DoubleArrayType::Pointer triNormalsPtr = DoubleArrayType::CreateArray(nTriangles, 3, DREAM3D::FaceData::SurfaceMeshFaceNormals);
double* triNormals = triNormalsPtr->GetPointer(0);
for(int t = 0; t < nTriangles; ++t)
{
fscanf(f, "%f %f %f %f %f %f", &x, &y, &z, &n0, &n1, &n2);
triangles[t].verts[0] = x;
triangles[t].verts[1] = y;
triangles[t].verts[2] = z;
// triangles[t].tIndex = t;
faceLabels[t*2] = 0;
faceLabels[t*2+1] = 1;
triNormals[t*3+0] = n0;
triNormals[t*3+1] = n1;
triNormals[t*3+2] = n2;
}
m->setFaces(trianglesPtr);
m->addFaceData(faceLabelPtr->GetName(), faceLabelPtr);
m->addFaceData(triNormalsPtr->GetName(), triNormalsPtr);
/* Let the GUI know we are done with this filter */
notifyStatusMessage("Complete");
}