// -----------------------------------------------------------------------------
//
// -----------------------------------------------------------------------------
void SurfaceMeshToNonconformalVtk::execute()
{
int err = 0;
setErrorCondition(err);
dataCheck();
if(getErrorCondition() < 0) { return; }
DataContainer::Pointer m = getDataContainerArray()->getDataContainer(m_SurfaceMeshFaceLabelsArrayPath.getDataContainerName());
TriangleGeom::Pointer triangleGeom = getDataContainerArray()->getDataContainer(getSurfaceMeshFaceLabelsArrayPath().getDataContainerName())->getGeometryAs<TriangleGeom>();
float* nodes = triangleGeom->getVertexPointer(0);
int64_t* triangles = triangleGeom->getTriPointer(0);
qint64 numNodes = triangleGeom->getNumberOfVertices();
int64_t numTriangles = triangleGeom->getNumberOfTris();
// Make sure any directory path is also available as the user may have just typed
// in a path without actually creating the full path
QFileInfo fi(getOutputVtkFile());
QDir parentPath = fi.path();
if(!parentPath.mkpath("."))
{
QString ss = QObject::tr("Error creating parent path '%1'").arg(parentPath.absolutePath());
setErrorCondition(-1);
notifyErrorMessage(getHumanLabel(), ss, getErrorCondition());
return;
}
// Open the output VTK File for writing
FILE* vtkFile = NULL;
vtkFile = fopen(getOutputVtkFile().toLatin1().data(), "wb");
if (NULL == vtkFile)
{
QString ss = QObject::tr("Error creating file '%1'").arg(getOutputVtkFile());
setErrorCondition(-18542);
notifyErrorMessage(getHumanLabel(), ss, getErrorCondition());
return;
}
ScopedFileMonitor vtkFileMonitor(vtkFile);
notifyStatusMessage(getHumanLabel(), "Writing Vertex Data ....");
fprintf(vtkFile, "# vtk DataFile Version 2.0\n");
fprintf(vtkFile, "Data set from DREAM.3D Surface Meshing Module\n");
if (m_WriteBinaryFile)
{
fprintf(vtkFile, "BINARY\n");
}
else
{
fprintf(vtkFile, "ASCII\n");
}
fprintf(vtkFile, "DATASET POLYDATA\n");
int numberWrittenNodes = 0;
for (int i = 0; i < numNodes; i++)
{
// Node& n = nodes[i]; // Get the current Node
if (m_SurfaceMeshNodeType[i] > 0) { ++numberWrittenNodes; }
else { qDebug() << "Node Type Invalid: " << i << "::" << (int)(m_SurfaceMeshNodeType[i]) ;}
}
fprintf(vtkFile, "POINTS %d float\n", numberWrittenNodes);
float pos[3] = {0.0f, 0.0f, 0.0f};
size_t totalWritten = 0;
// Write the POINTS data (Vertex)
for (int i = 0; i < numNodes; i++)
{
if (m_SurfaceMeshNodeType[i] > 0)
{
pos[0] = static_cast<float>(nodes[i * 3]);
pos[1] = static_cast<float>(nodes[i * 3 + 1]);
pos[2] = static_cast<float>(nodes[i * 3 + 2]);
if (m_WriteBinaryFile == true)
{
SIMPLib::Endian::FromSystemToBig::convert(pos[0]);
SIMPLib::Endian::FromSystemToBig::convert(pos[1]);
SIMPLib::Endian::FromSystemToBig::convert(pos[2]);
totalWritten = fwrite(pos, sizeof(float), 3, vtkFile);
if(totalWritten != 3) {}
}
else
{
fprintf(vtkFile, "%f %f %f\n", pos[0], pos[1], pos[2]); // Write the positions to the output file
}
}
}
// Write the triangle indices into the vtk File
notifyStatusMessage(getHumanLabel(), "Writing Faces ....");
int tData[4];
// Store all the unique Spins
QMap<int32_t, int32_t> featureTriangleCount;
for (int i = 0; i < numTriangles; i++)
{
if (featureTriangleCount.find(m_SurfaceMeshFaceLabels[i * 2]) == featureTriangleCount.end())
{
featureTriangleCount[m_SurfaceMeshFaceLabels[i * 2]] = 1;
}
else
{
featureTriangleCount[m_SurfaceMeshFaceLabels[i * 2]]++;
}
if (featureTriangleCount.find(m_SurfaceMeshFaceLabels[i * 2 + 1]) == featureTriangleCount.end())
{
featureTriangleCount[m_SurfaceMeshFaceLabels[i * 2 + 1]] = 1;
}
else
{
featureTriangleCount[m_SurfaceMeshFaceLabels[i * 2 + 1]]++;
}
}
// Write the POLYGONS
fprintf(vtkFile, "\nPOLYGONS %lld %lld\n", (long long int)(numTriangles * 2), (long long int)(numTriangles * 2 * 4));
size_t totalCells = 0;
// Loop over all the features
for(QMap<int32_t, int32_t>::iterator featureIter = featureTriangleCount.begin(); featureIter != featureTriangleCount.end(); ++featureIter)
{
totalCells += featureIter.value();
}
Q_ASSERT(totalCells == (size_t)(numTriangles * 2) );
// Loop over all the features
for(QMap<int32_t, int32_t>::iterator featureIter = featureTriangleCount.begin(); featureIter != featureTriangleCount.end(); ++featureIter)
{
int32_t gid = featureIter.key(); // The current Feature Id
int32_t numTriToWrite = featureIter.value(); // The number of triangles for this feature
uint8_t doWrite = 0;
// Loop over all the triangles looking for the current feature id
// this is probably sub-optimal as if we have 1000 features we are going to loop 1000 times but this will use the
// least amount of memory. We could run a filter to group the triangles by feature but then we would need an
// additional amount of memory equal to 3X the memory used for the triangle list because every triangle will be listed
// twice. We could get some slightly better performance if we buffered 4K worth of data then wrote out that data
// in one chunk versus what we are doing here.
for (int j = 0; j < numTriangles; j++)
{
doWrite = 0;
if (m_SurfaceMeshFaceLabels[j * 2] == gid ) { doWrite = 1; }
else if (m_SurfaceMeshFaceLabels[j * 2 + 1] == gid) { doWrite = 2; } // We need to flip the winding of the triangle
if (doWrite == 0) { continue; } // Labels in the triangle did match the current feature id.
if (doWrite == 1)
{
tData[0] = 3; // Push on the total number of entries for this entry
tData[1] = triangles[j * 3];
tData[2] = triangles[j * 3 + 1];
tData[3] = triangles[j * 3 + 2];
}
else
{
tData[0] = 3; // Push on the total number of entries for this entry
tData[1] = triangles[j * 3 + 2];
tData[2] = triangles[j * 3 + 1];
tData[3] = triangles[j * 3];
}
if (m_WriteBinaryFile == true)
{
SIMPLib::Endian::FromSystemToBig::convert(tData[0]);
SIMPLib::Endian::FromSystemToBig::convert(tData[1]); // Index of Vertex 0
SIMPLib::Endian::FromSystemToBig::convert(tData[2]); // Index of Vertex 1
SIMPLib::Endian::FromSystemToBig::convert(tData[3]); // Index of Vertex 2
fwrite(tData, sizeof(int), 4, vtkFile);
}
else
{
fprintf(vtkFile, "3 %d %d %d\n", tData[1], tData[2], tData[3]);
}
numTriToWrite--;
}
if (numTriToWrite != 0)
{
qDebug() << "Not enough triangles written: " << gid << "::" << numTriToWrite << " Total Triangles to Write " << featureIter.value();
}
}
// Write the POINT_DATA section
err = writePointData(vtkFile);
// Write the CELL_DATA section
err = writeCellData(vtkFile, featureTriangleCount);
fprintf(vtkFile, "\n");
setErrorCondition(0);
notifyStatusMessage(getHumanLabel(), "Complete");
}
// -----------------------------------------------------------------------------
//
// -----------------------------------------------------------------------------
void SurfaceMeshToVtk::execute()
{
int err = 0;
setErrorCondition(err);
dataCheck();
if(getErrorCondition() < 0) { return; }
setErrorCondition(0);
DataContainer::Pointer sm = getDataContainerArray()->getDataContainer(m_SurfaceMeshFaceLabelsArrayPath.getDataContainerName()); /* Place all your code to execute your filter here. */
TriangleGeom::Pointer triangleGeom = getDataContainerArray()->getDataContainer(getSurfaceMeshFaceLabelsArrayPath().getDataContainerName())->getGeometryAs<TriangleGeom>();
float* nodes = triangleGeom->getVertexPointer(0);
int64_t* triangles = triangleGeom->getTriPointer(0);
qint64 numNodes = triangleGeom->getNumberOfVertices();
int64_t numTriangles = triangleGeom->getNumberOfTris();
// Make sure any directory path is also available as the user may have just typed
// in a path without actually creating the full path
QFileInfo fi(getOutputVtkFile());
QDir parentPath = fi.path();
if(!parentPath.mkpath("."))
{
QString ss = QObject::tr("Error creating parent path '%1'").arg(parentPath.absolutePath());
notifyErrorMessage(getHumanLabel(), ss, -1);
setErrorCondition(-1);
return;
}
// Open the output VTK File for writing
FILE* vtkFile = NULL;
vtkFile = fopen(getOutputVtkFile().toLatin1().data(), "wb");
if (NULL == vtkFile)
{
QString ss = QObject::tr("Error creating file '%1'").arg(getOutputVtkFile());
notifyErrorMessage(getHumanLabel(), ss, -18542);
setErrorCondition(-18542);
return;
}
ScopedFileMonitor vtkFileMonitor(vtkFile);
fprintf(vtkFile, "# vtk DataFile Version 2.0\n");
fprintf(vtkFile, "Data set from DREAM.3D Surface Meshing Module\n");
if (m_WriteBinaryFile)
{
fprintf(vtkFile, "BINARY\n");
}
else
{
fprintf(vtkFile, "ASCII\n");
}
fprintf(vtkFile, "DATASET POLYDATA\n");
int numberWrittenumNodes = 0;
for (int i = 0; i < numNodes; i++)
{
// Node& n = nodes[i]; // Get the current Node
if (m_SurfaceMeshNodeType[i] > 0) { ++numberWrittenumNodes; }
}
fprintf(vtkFile, "POINTS %d float\n", numberWrittenumNodes);
float pos[3] = {0.0f, 0.0f, 0.0f};
size_t totalWritten = 0;
// Write the POINTS data (Vertex)
for (int i = 0; i < numNodes; i++)
{
if (m_SurfaceMeshNodeType[i] > 0)
{
pos[0] = static_cast<float>(nodes[i * 3]);
pos[1] = static_cast<float>(nodes[i * 3 + 1]);
pos[2] = static_cast<float>(nodes[i * 3 + 2]);
if (m_WriteBinaryFile == true)
{
SIMPLib::Endian::FromSystemToBig::convert(pos[0]);
SIMPLib::Endian::FromSystemToBig::convert(pos[1]);
SIMPLib::Endian::FromSystemToBig::convert(pos[2]);
totalWritten = fwrite(pos, sizeof(float), 3, vtkFile);
if (totalWritten != sizeof(float) * 3)
{
}
}
else
{
fprintf(vtkFile, "%f %f %f\n", pos[0], pos[1], pos[2]); // Write the positions to the output file
}
}
}
int tData[4];
int triangleCount = numTriangles;
// int tn1, tn2, tn3;
if (false == m_WriteConformalMesh)
{
triangleCount = numTriangles * 2;
}
// Write the POLYGONS
fprintf(vtkFile, "\nPOLYGONS %d %d\n", triangleCount, (triangleCount * 4));
for (int j = 0; j < numTriangles; j++)
{
// Triangle& t = triangles[j];
tData[1] = triangles[j * 3];
tData[2] = triangles[j * 3 + 1];
tData[3] = triangles[j * 3 + 2];
if (m_WriteBinaryFile == true)
{
tData[0] = 3; // Push on the total number of entries for this entry
SIMPLib::Endian::FromSystemToBig::convert(tData[0]);
SIMPLib::Endian::FromSystemToBig::convert(tData[1]); // Index of Vertex 0
SIMPLib::Endian::FromSystemToBig::convert(tData[2]); // Index of Vertex 1
SIMPLib::Endian::FromSystemToBig::convert(tData[3]); // Index of Vertex 2
fwrite(tData, sizeof(int), 4, vtkFile);
if (false == m_WriteConformalMesh)
{
tData[0] = tData[1];
tData[1] = tData[3];
tData[3] = tData[0];
tData[0] = 3;
SIMPLib::Endian::FromSystemToBig::convert(tData[0]);
fwrite(tData, sizeof(int), 4, vtkFile);
}
}
else
{
fprintf(vtkFile, "3 %d %d %d\n", tData[1], tData[2], tData[3]);
if (false == m_WriteConformalMesh)
{
fprintf(vtkFile, "3 %d %d %d\n", tData[3], tData[2], tData[1]);
}
}
}
// Write the POINT_DATA section
err = writePointData(vtkFile);
// Write the CELL_DATA section
err = writeCellData(vtkFile);
fprintf(vtkFile, "\n");
setErrorCondition(0);
notifyStatusMessage(getHumanLabel(), "Complete");
}
void KoSimpleOdsCell::writeCellData(KoXmlWriter* writer)
{
writeCellData(writer, text());
}
// -----------------------------------------------------------------------------
//
// -----------------------------------------------------------------------------
void VoxelDataContainerWriter::execute()
{
int err = 0;
std::stringstream ss;
setErrorCondition(err);
VoxelDataContainer* m = getVoxelDataContainer();
if(NULL == m)
{
setErrorCondition(-999);
notifyErrorMessage("The Voxel DataContainer Object was NULL", -999);
return;
}
setErrorCondition(0);
dataCheck(false, 1, 1, 1);
hid_t dcGid = -1;
// Create the HDF5 Group for the Data Container
err = H5Utilities::createGroupsFromPath(DREAM3D::HDF5::VoxelDataContainerName.c_str(), m_HdfFileId);
if (err < 0)
{
ss.str("");
ss << "Error creating HDF Group " << DREAM3D::HDF5::VoxelDataContainerName << std::endl;
setErrorCondition(-60);
notifyErrorMessage( ss.str(), err);
return;
}
dcGid = H5Gopen(m_HdfFileId, DREAM3D::HDF5::VoxelDataContainerName.c_str(), H5P_DEFAULT );
if (dcGid < 0)
{
ss.str("");
ss << "Error opening Group " << DREAM3D::HDF5::VoxelDataContainerName << std::endl;
setErrorCondition(-61);
notifyErrorMessage( ss.str(), err);
return;
}
// This just writes the header information
int64_t volDims[3] =
{ m->getXPoints(), m->getYPoints(), m->getZPoints() };
float spacing[3] =
{ m->getXRes(), m->getYRes(), m->getZRes() };
float origin[3] =
{ 0.0f, 0.0f, 0.0f };
m->getOrigin(origin);
err = writeMetaInfo(DREAM3D::HDF5::VoxelDataContainerName, volDims, spacing, origin);
if (err < 0)
{
ss.str("");
ss << ":Error Writing header information to output file" << std::endl;
setErrorCondition(-62);
notifyErrorMessage( ss.str(), err);
H5Gclose(dcGid); // Close the Data Container Group
return;
}
err = writeVertexData(dcGid);
if (err < 0)
{
H5Gclose(dcGid); // Close the Data Container Group
return;
}
err = writeEdgeData(dcGid);
if (err < 0)
{
H5Gclose(dcGid); // Close the Data Container Group
return;
}
err = writeFaceData(dcGid);
if (err < 0)
{
H5Gclose(dcGid); // Close the Data Container Group
return;
}
err = writeCellData(dcGid);
if (err < 0)
{
H5Gclose(dcGid); // Close the Data Container Group
return;
}
err = writeFieldData(dcGid);
if (err < 0)
{
H5Gclose(dcGid); // Close the Data Container Group
return;
}
err = writeEnsembleData(dcGid);
if (err < 0)
{
H5Gclose(dcGid); // Close the Data Container Group
return;
}
// Now finally close the group and the HDf5 File
H5Gclose(dcGid); // Close the Data Container Group
notifyStatusMessage("Complete");
}
