// -----------------------------------------------------------------------------
//
// -----------------------------------------------------------------------------
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;
}
// -----------------------------------------------------------------------------
//
// -----------------------------------------------------------------------------
void SurfaceMeshDataContainerWriter::writeXdmfGridFooter()
{
if (m_WriteXdmfFile == false || m_XdmfPtr == NULL)
{
return;
}
DREAM3D::SurfaceMesh::FaceListPointer_t faces = getSurfaceMeshDataContainer()->getFaces();
if (NULL == faces.get())
{
return;
}
std::ostream& out = *m_XdmfPtr;
out << " </Grid>" << std::endl;
out << " <!-- *************** END OF SurfaceMesh DataContainer *************** -->" << std::endl;
out << std::endl;
}
// -----------------------------------------------------------------------------
//
// -----------------------------------------------------------------------------
void TriangleNormalFilter::execute()
{
int err = 0;
std::stringstream ss;
setErrorCondition(err);
SurfaceMeshDataContainer* m = getSurfaceMeshDataContainer();
if(NULL == m)
{
setErrorCondition(-999);
notifyErrorMessage("The SurfaceMesh DataContainer Object was NULL", -999);
return;
}
setErrorCondition(0);
notifyStatusMessage("Starting");
#ifdef DREAM3D_USE_PARALLEL_ALGORITHMS
bool doParallel = true;
#endif
DREAM3D::SurfaceMesh::VertListPointer_t nodesPtr = getSurfaceMeshDataContainer()->getVertices();
DREAM3D::SurfaceMesh::FaceListPointer_t trianglesPtr = getSurfaceMeshDataContainer()->getFaces();
size_t totalPoints = trianglesPtr->GetNumberOfTuples();
// Run the data check to allocate the memory for the centroid array
dataCheck(false, trianglesPtr->GetNumberOfTuples(), 0, 0);
#ifdef DREAM3D_USE_PARALLEL_ALGORITHMS
if (doParallel == true)
{
tbb::parallel_for(tbb::blocked_range<size_t>(0, totalPoints),
CalculateNormalsImpl(nodesPtr, trianglesPtr, m_SurfaceMeshTriangleNormals), tbb::auto_partitioner());
}
else
#endif
{
CalculateNormalsImpl serial(nodesPtr, trianglesPtr, m_SurfaceMeshTriangleNormals);
serial.generate(0, totalPoints);
}
/* Let the GUI know we are done with this filter */
notifyStatusMessage("Complete");
}
// -----------------------------------------------------------------------------
//
// -----------------------------------------------------------------------------
int AbaqusSurfaceMeshWriter::writeTriangles(FILE* f)
{
int err = 0;
DREAM3D::SurfaceMesh::FaceListPointer_t trianglePtr = getSurfaceMeshDataContainer()->getFaces();
DREAM3D::SurfaceMesh::Face_t* triangles = trianglePtr->GetPointer(0);
size_t numTri = trianglePtr->GetNumberOfTuples();
fprintf(f, "*ELEMENT, TYPE=%s\n", TRI_ELEMENT_TYPE);
for(size_t i = 1; i <= numTri; ++i)
{
// When we get the node index, add 1 to it because Abaqus number is 1 based.
int nId0 = triangles[i-1].verts[0] + 1;
int nId1 = triangles[i-1].verts[1] + 1;
int nId2 = triangles[i-1].verts[2] + 1;
fprintf(f, "%lu, %d, %d, %d\n", i, nId0, nId1, nId2);
}
return err;
}
/**
* @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 generateNeighborLists(DREAM3D::SurfaceMesh::VertListPointer_t nodes,
DREAM3D::SurfaceMesh::FaceListPointer_t faces,
MeshVertLinks::Pointer cellLinks)
{
size_t nFaces = faces->GetNumberOfTuples();
allocate(faces->GetNumberOfTuples());
// Allocate an array of bools that we use each iteration of triangle so that we don't put duplicates into the array
boost::shared_array<bool> visitedPtr(new bool[nFaces]);
bool* visited = visitedPtr.get();
::memset(visitedPtr.get(), 0, nFaces);
// Reuse this vector for each loop. Avoids re-allocating the memory each time through the loop
std::vector<int> loop_neighbors(32, 0);
// Build up the Face Adjacency list now that we have the cell links
for(size_t t = 0; t < nFaces; ++t)
{
// std::cout << "Analyzing Face " << t << std::endl;
DREAM3D::SurfaceMesh::Face_t& seedFace = *(faces->GetPointer(t));
for(size_t v = 0; v < 3; ++v)
{
// std::cout << " vert " << v << std::endl;
int nTris = cellLinks->getNumberOfFaces(seedFace.verts[v]);
int* vertIdxs = cellLinks->getFaceListPointer(seedFace.verts[v]);
for(int vt = 0; vt < nTris; ++vt)
{
if (vertIdxs[vt] == static_cast<int>(t) ) { continue; } // This is the same triangle as our "source" triangle
if (visited[vertIdxs[vt]] == true) { continue; } // We already added this triangle so loop again
// std::cout << " Comparing Face " << vertIdxs[vt] << std::endl;
DREAM3D::SurfaceMesh::Face_t& vertTri = *(faces->GetPointer(vertIdxs[vt]));
int vCount = 0;
// Loop over all the vertex indices of this triangle and try to match 2 of them to the current loop triangle
// If there are 2 matches then that triangle is a neighbor of this triangle. if there are more than 2 matches
// then there is a real problem with the mesh and the program is going to assert.
// Unrolled the loop to shave about 25% of time off the outer loop.
int seedTriVert0 = seedFace.verts[0];
int seedTriVert1 = seedFace.verts[1];
int seedTriVert2 = seedFace.verts[2];
int trgtTriVert0 = vertTri.verts[0];
int trgtTriVert1 = vertTri.verts[1];
int trgtTriVert2 = vertTri.verts[2];
if (seedTriVert0 == trgtTriVert0 || seedTriVert0 == trgtTriVert1 || seedTriVert0 == trgtTriVert2 )
{
vCount++;
}
if (seedTriVert1 == trgtTriVert0 || seedTriVert1 == trgtTriVert1 || seedTriVert1 == trgtTriVert2 )
{
vCount++;
}
if (seedTriVert2 == trgtTriVert0 || seedTriVert2 == trgtTriVert1 || seedTriVert2 == trgtTriVert2 )
{
vCount++;
}
BOOST_ASSERT(vCount < 3); // No way 2 faces can share all 3 vertices. Something is VERY wrong at this point
// So if our vertex match count is 2 and we have not visited the triangle in question then add this triangle index
// into the list of Face Indices as neighbors for the source triangle.
if (vCount == 2)
{
//std::cout << " Neighbor: " << vertIdxs[vt] << std::endl;
// Use the current count of neighbors as the index
// into the loop_neighbors vector and place the value of the vertex triangle at that index
loop_neighbors[this->Array[t].ncells] = vertIdxs[vt];
this->Array[t].ncells++;// Increment the count for the next time through
if (this->Array[t].ncells >= loop_neighbors.size())
{
loop_neighbors.resize(loop_neighbors.size() + 10);
}
visited[vertIdxs[vt]] = true; // Set this triangle as visited so we do NOT add it again
}
}
}
BOOST_ASSERT(this->Array[t].ncells > 2);
// Reset all the visited triangle indexs back to false (zero)
for(size_t k = 0;k < this->Array[t].ncells; ++k)
{
visited[loop_neighbors[k]] = false;
}
// Allocate the array storage for the current triangle to hold its Face list
this->Array[t].cells = new int[this->Array[t].ncells];
// Only copy the first "N" values from the loop_neighbors vector into the storage array
::memcpy(this->Array[t].cells, &(loop_neighbors[0]), sizeof(int) * this->Array[t].ncells);
}
}
// -----------------------------------------------------------------------------
//
// -----------------------------------------------------------------------------
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");
}
// -----------------------------------------------------------------------------
//
// -----------------------------------------------------------------------------
int AbaqusSurfaceMeshWriter::writeGrains(FILE* f)
{
//*Elset, elset=Grain1
//1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16
int err = 0;
std::stringstream ss;
SurfaceMeshDataContainer* sm = getSurfaceMeshDataContainer();
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);
int nTriangles = trianglePtr->GetNumberOfTuples();
// Store all the unique Spins
std::set<int> uniqueSpins;
for (int i = 0; i < nTriangles; i++)
{
uniqueSpins.insert(faceLabels[i*2]);
uniqueSpins.insert(faceLabels[i*2+1]);
}
int spin = 0;
//Loop over the unique Spins
for (std::set<int>::iterator spinIter = uniqueSpins.begin(); spinIter != uniqueSpins.end(); ++spinIter )
{
spin = *spinIter;
if(spin < 0) { continue; }
fprintf(f, "*ELSET, ELSET=Grain%d\n", spin);
ss.str("");
ss << "Writing ELSET for Grain Id " << spin;
notifyStatusMessage(ss.str());
// Loop over all the triangles for this spin
int lineCount = 0;
for(int t = 0; t < nTriangles; ++t)
{
if (faceLabels[t*2] != spin && faceLabels[t*2+1] != spin)
{
continue; // We do not match either spin so move to the next triangle
}
// Only print 15 Triangles per line
if (lineCount == 15)
{
fprintf(f, ", %d\n", t);
lineCount = 0;
}
else if(lineCount == 0) // First value on the line
{
fprintf(f,"%d", t);
lineCount++;
}
else
{
fprintf(f,", %d", t);
lineCount++;
}
}
// Make sure we have a new line at the end of the section
if (lineCount != 0)
{
fprintf(f, "\n");
}
}
return err;
}