// -----------------------------------------------------------------------------
//
// -----------------------------------------------------------------------------
void FindTwinBoundarySchmidFactors::dataCheckSurfaceMesh()
{
setErrorCondition(0);
DataArrayPath tempPath;
QVector<DataArrayPath> dataArrayPaths;
getDataContainerArray()->getPrereqGeometryFromDataContainer<TriangleGeom, AbstractFilter>(this, getSurfaceMeshFaceLabelsArrayPath().getDataContainerName());
QVector<size_t> cDims(1, 2);
m_SurfaceMeshFaceLabelsPtr = getDataContainerArray()->getPrereqArrayFromPath<DataArray<int32_t>, AbstractFilter>(this, getSurfaceMeshFaceLabelsArrayPath(), cDims); /* Assigns the shared_ptr<> to an instance variable that is a weak_ptr<> */
if( NULL != m_SurfaceMeshFaceLabelsPtr.lock().get() ) /* Validate the Weak Pointer wraps a non-NULL pointer to a DataArray<T> object */
{ m_SurfaceMeshFaceLabels = m_SurfaceMeshFaceLabelsPtr.lock()->getPointer(0); } /* Now assign the raw pointer to data from the DataArray<T> object */
if(getErrorCondition() >= 0) { dataArrayPaths.push_back(getSurfaceMeshFaceLabelsArrayPath()); }
cDims[0] = 3;
m_SurfaceMeshFaceNormalsPtr = getDataContainerArray()->getPrereqArrayFromPath<DataArray<double>, AbstractFilter>(this, getSurfaceMeshFaceNormalsArrayPath(), cDims); /* Assigns the shared_ptr<> to an instance variable that is a weak_ptr<> */
if( NULL != m_SurfaceMeshFaceNormalsPtr.lock().get() ) /* Validate the Weak Pointer wraps a non-NULL pointer to a DataArray<T> object */
{ m_SurfaceMeshFaceNormals = m_SurfaceMeshFaceNormalsPtr.lock()->getPointer(0); } /* Now assign the raw pointer to data from the DataArray<T> object */
if(getErrorCondition() >= 0) { dataArrayPaths.push_back(getSurfaceMeshFaceNormalsArrayPath()); }
tempPath.update(getSurfaceMeshFaceLabelsArrayPath().getDataContainerName(), getSurfaceMeshFaceLabelsArrayPath().getAttributeMatrixName(), getSurfaceMeshTwinBoundarySchmidFactorsArrayName() );
m_SurfaceMeshTwinBoundarySchmidFactorsPtr = getDataContainerArray()->createNonPrereqArrayFromPath<DataArray<float>, AbstractFilter, float>(this, tempPath, 0, cDims); /* Assigns the shared_ptr<> to an instance variable that is a weak_ptr<> */
if( NULL != m_SurfaceMeshTwinBoundarySchmidFactorsPtr.lock().get() ) /* Validate the Weak Pointer wraps a non-NULL pointer to a DataArray<T> object */
{ m_SurfaceMeshTwinBoundarySchmidFactors = m_SurfaceMeshTwinBoundarySchmidFactorsPtr.lock()->getPointer(0); } /* Now assign the raw pointer to data from the DataArray<T> object */
cDims[0] = 1;
m_SurfaceMeshTwinBoundaryPtr = getDataContainerArray()->getPrereqArrayFromPath<DataArray<bool>, AbstractFilter>(this, getSurfaceMeshTwinBoundaryArrayPath(), cDims); /* Assigns the shared_ptr<> to an instance variable that is a weak_ptr<> */
if( NULL != m_SurfaceMeshTwinBoundaryPtr.lock().get() ) /* Validate the Weak Pointer wraps a non-NULL pointer to a DataArray<T> object */
{ m_SurfaceMeshTwinBoundary = m_SurfaceMeshTwinBoundaryPtr.lock()->getPointer(0); } /* Now assign the raw pointer to data from the DataArray<T> object */
if(getErrorCondition() >= 0) { dataArrayPaths.push_back(getSurfaceMeshTwinBoundaryArrayPath()); }
getDataContainerArray()->validateNumberOfTuples<AbstractFilter>(this, dataArrayPaths);
}
// -----------------------------------------------------------------------------
//
// -----------------------------------------------------------------------------
void LaplacianSmoothing::dataCheck()
{
TriangleGeom::Pointer triangles = getDataContainerArray()->getPrereqGeometryFromDataContainer<TriangleGeom, AbstractFilter>(this, getSurfaceMeshFaceLabelsArrayPath().getDataContainerName());
QVector<IDataArray::Pointer> faceDataArrays;
QVector<IDataArray::Pointer> nodeDataArrays;
if(getErrorCondition() >= 0) { faceDataArrays.push_back(triangles->getTriangles()); nodeDataArrays.push_back(triangles->getVertices()); }
QVector<size_t> cDims(1, 1);
m_SurfaceMeshNodeTypePtr = getDataContainerArray()->getPrereqArrayFromPath<DataArray<int8_t>, AbstractFilter>(this, getSurfaceMeshNodeTypeArrayPath(), cDims); /* Assigns the shared_ptr<> to an instance variable that is a weak_ptr<> */
if( NULL != m_SurfaceMeshNodeTypePtr.lock().get() ) /* Validate the Weak Pointer wraps a non-NULL pointer to a DataArray<T> object */
{ m_SurfaceMeshNodeType = m_SurfaceMeshNodeTypePtr.lock()->getPointer(0); } /* Now assign the raw pointer to data from the DataArray<T> object */
if(getErrorCondition() >= 0) { nodeDataArrays.push_back(m_SurfaceMeshNodeTypePtr.lock()); }
cDims[0] = 2;
m_SurfaceMeshFaceLabelsPtr = getDataContainerArray()->getPrereqArrayFromPath<DataArray<int32_t>, AbstractFilter>(this, getSurfaceMeshFaceLabelsArrayPath(), cDims); /* Assigns the shared_ptr<> to an instance variable that is a weak_ptr<> */
if( NULL != m_SurfaceMeshFaceLabelsPtr.lock().get() ) /* Validate the Weak Pointer wraps a non-NULL pointer to a DataArray<T> object */
{ m_SurfaceMeshFaceLabels = m_SurfaceMeshFaceLabelsPtr.lock()->getPointer(0); } /* Now assign the raw pointer to data from the DataArray<T> object */
if(getErrorCondition() >= 0) { faceDataArrays.push_back(m_SurfaceMeshFaceLabelsPtr.lock()); }
getDataContainerArray()->validateNumberOfTuples<AbstractFilter>(this, faceDataArrays);
getDataContainerArray()->validateNumberOfTuples<AbstractFilter>(this, nodeDataArrays);
setSurfaceDataContainerName(getSurfaceMeshFaceLabelsArrayPath().getDataContainerName());
}
// -----------------------------------------------------------------------------
//
// -----------------------------------------------------------------------------
int32_t AbaqusSurfaceMeshWriter::writeNodes(FILE* f)
{
TriangleGeom::Pointer triangleGeom = getDataContainerArray()->getDataContainer(getSurfaceMeshFaceLabelsArrayPath().getDataContainerName())->getGeometryAs<TriangleGeom>();
float* nodes = triangleGeom->getVertexPointer(0);
int64_t numNodes = triangleGeom->getNumberOfVertices();
int32_t err = 0;
fprintf(f, "*Node,NSET=NALL\n");
//1, 72.520433763730, 70.306420652241, 100.000000000000
// Abaqus Starts number at 1 NOT 0(Zero).
for (int64_t i = 1; i <= numNodes; ++i)
{
fprintf(f, "%lld, %0.6f, %0.6f, %0.6f\n", (long long int)i, nodes[(i - 1) * 3], nodes[(i - 1) * 3 + 1], nodes[(i - 1) * 3 + 2]);
}
return err;
}
// -----------------------------------------------------------------------------
//
// -----------------------------------------------------------------------------
int32_t AbaqusSurfaceMeshWriter::writeTriangles(FILE* f)
{
int32_t err = 0;
TriangleGeom::Pointer triangleGeom = getDataContainerArray()->getDataContainer(getSurfaceMeshFaceLabelsArrayPath().getDataContainerName())->getGeometryAs<TriangleGeom>();
int64_t numTri = triangleGeom->getNumberOfTris();
int64_t* triangles = triangleGeom->getTriPointer(0);
fprintf(f, "*ELEMENT, TYPE=%s\n", TRI_ELEMENT_TYPE);
for (int64_t i = 1; i <= numTri; ++i)
{
// When we get the node index, add 1 to it because Abaqus number is 1 based.
int64_t nId0 = triangles[(i - 1) * 3] + 1;
int64_t nId1 = triangles[(i - 1) * 3 + 1] + 1;
int64_t nId2 = triangles[(i - 1) * 3 + 2] + 1;
fprintf(f, "%lld, %lld, %lld, %lld\n", (long long int)i, (long long int)nId0, (long long int)nId1, (long long int)nId2);
}
return err;
}
// -----------------------------------------------------------------------------
//
// -----------------------------------------------------------------------------
void InsertAtoms::dataCheck()
{
setErrorCondition(0);
DataArrayPath tempPath;
TriangleGeom::Pointer triangles = getDataContainerArray()->getPrereqGeometryFromDataContainer<TriangleGeom, AbstractFilter>(this, getSurfaceMeshFaceLabelsArrayPath().getDataContainerName());
QVector<IDataArray::Pointer> dataArrays;
if(getErrorCondition() >= 0) { dataArrays.push_back(triangles->getTriangles()); }
DataContainer::Pointer v = getDataContainerArray()->createNonPrereqDataContainer<AbstractFilter>(this, getVertexDataContainerName());
if(getErrorCondition() < 0) { return; }
VertexGeom::Pointer vertices = VertexGeom::CreateGeometry(0, DREAM3D::Geometry::VertexGeometry);
v->setGeometry(vertices);
QVector<size_t> tDims(1, 0);
AttributeMatrix::Pointer vertexAttrMat = v->createNonPrereqAttributeMatrix<AbstractFilter>(this, getVertexAttributeMatrixName(), tDims, DREAM3D::AttributeMatrixType::Vertex);
if(getErrorCondition() < 0 || NULL == vertexAttrMat.get()) { return; }
QVector<size_t> cDims(1, 2);
m_SurfaceMeshFaceLabelsPtr = getDataContainerArray()->getPrereqArrayFromPath<DataArray<int32_t>, AbstractFilter>(this, getSurfaceMeshFaceLabelsArrayPath(), cDims); /* Assigns the shared_ptr<> to an instance variable that is a weak_ptr<> */
if( NULL != m_SurfaceMeshFaceLabelsPtr.lock().get() ) /* Validate the Weak Pointer wraps a non-NULL pointer to a DataArray<T> object */
{ m_SurfaceMeshFaceLabels = m_SurfaceMeshFaceLabelsPtr.lock()->getPointer(0); } /* Now assign the raw pointer to data from the DataArray<T> object */
if(getErrorCondition() >= 0) { dataArrays.push_back(m_SurfaceMeshFaceLabelsPtr.lock()); }
cDims[0] = 4;
m_AvgQuatsPtr = getDataContainerArray()->getPrereqArrayFromPath<DataArray<float>, AbstractFilter>(this, getAvgQuatsArrayPath(), cDims); /* Assigns the shared_ptr<> to an instance variable that is a weak_ptr<> */
if( NULL != m_AvgQuatsPtr.lock().get() ) /* Validate the Weak Pointer wraps a non-NULL pointer to a DataArray<T> object */
{ m_AvgQuats = m_AvgQuatsPtr.lock()->getPointer(0); } /* Now assign the raw pointer to data from the DataArray<T> object */
cDims[0] = 1;
tempPath.update(getVertexDataContainerName(), getVertexAttributeMatrixName(), getAtomFeatureLabelsArrayName() );
m_AtomFeatureLabelsPtr = getDataContainerArray()->createNonPrereqArrayFromPath<DataArray<int32_t>, AbstractFilter, int32_t>(this, tempPath, -301, cDims); /* Assigns the shared_ptr<>(this, tempPath, -301, dims); Assigns the shared_ptr<> to an instance variable that is a weak_ptr<> */
if( NULL != m_AtomFeatureLabelsPtr.lock().get() ) /* Validate the Weak Pointer wraps a non-NULL pointer to a DataArray<T> object */
{ m_AtomFeatureLabels = m_AtomFeatureLabelsPtr.lock()->getPointer(0); } /* Now assign the raw pointer to data from the DataArray<T> object */
getDataContainerArray()->validateNumberOfTuples<AbstractFilter>(this, dataArrays);
}
// -----------------------------------------------------------------------------
//
// -----------------------------------------------------------------------------
void InsertAtoms::setupFilterParameters()
{
FilterParameterVector parameters;
parameters.push_back(FloatVec3FilterParameter::New("Lattice Constants (Angstroms)", "LatticeConstants", getLatticeConstants(), FilterParameter::Parameter));
{
ChoiceFilterParameter::Pointer parameter = ChoiceFilterParameter::New();
parameter->setHumanLabel("Crystal Basis");
parameter->setPropertyName("Basis");
QVector<QString> choices;
choices.push_back("Simple Cubic");
choices.push_back("Body Centered Cubic");
choices.push_back("Face Centered Cubic");
parameter->setChoices(choices);
parameter->setCategory(FilterParameter::Parameter);
parameters.push_back(parameter);
}
parameters.push_back(SeparatorFilterParameter::New("Face Data", FilterParameter::RequiredArray));
{
DataArraySelectionFilterParameter::RequirementType req = DataArraySelectionFilterParameter::CreateRequirement(DREAM3D::TypeNames::Int32, 2, DREAM3D::AttributeMatrixType::Face, DREAM3D::GeometryType::TriangleGeometry);
parameters.push_back(DataArraySelectionFilterParameter::New("Face Labels", "SurfaceMeshFaceLabelsArrayPath", getSurfaceMeshFaceLabelsArrayPath(), FilterParameter::RequiredArray, req));
}
parameters.push_back(SeparatorFilterParameter::New("Cell Feature Data", FilterParameter::RequiredArray));
{
DataArraySelectionFilterParameter::RequirementType req = DataArraySelectionFilterParameter::CreateRequirement(DREAM3D::TypeNames::Float, 4, DREAM3D::AttributeMatrixType::CellFeature, DREAM3D::GeometryType::ImageGeometry);
parameters.push_back(DataArraySelectionFilterParameter::New("Average Quaternions", "AvgQuatsArrayPath", getAvgQuatsArrayPath(), FilterParameter::RequiredArray, req));
}
parameters.push_back(StringFilterParameter::New("Data Container", "VertexDataContainerName", getVertexDataContainerName(), FilterParameter::CreatedArray));
parameters.push_back(SeparatorFilterParameter::New("Vertex Data", FilterParameter::CreatedArray));
parameters.push_back(StringFilterParameter::New("Vertex Attribute Matrix", "VertexAttributeMatrixName", getVertexAttributeMatrixName(), FilterParameter::CreatedArray));
parameters.push_back(StringFilterParameter::New("Atom Feature Labels", "AtomFeatureLabelsArrayName", getAtomFeatureLabelsArrayName(), FilterParameter::CreatedArray));
setFilterParameters(parameters);
}
// -----------------------------------------------------------------------------
//
// -----------------------------------------------------------------------------
int SurfaceMeshToNonconformalVtk::writeCellData(FILE* vtkFile, QMap<int32_t, int32_t>& featureIds)
{
int err = 0;
if (NULL == vtkFile)
{
return -1;
}
DataContainer::Pointer sm = getDataContainerArray()->getDataContainer(m_SurfaceMeshFaceLabelsArrayPath.getDataContainerName());
// Write the triangle region ids
TriangleGeom::Pointer triangleGeom = getDataContainerArray()->getDataContainer(getSurfaceMeshFaceLabelsArrayPath().getDataContainerName())->getGeometryAs<TriangleGeom>();
int64_t numTriangles = triangleGeom->getNumberOfTris();
int swapped;
// This is like a "section header"
fprintf(vtkFile, "\n");
fprintf(vtkFile, "CELL_DATA %lld\n", (long long int)(numTriangles * 2));
int32_t totalCellsWritten = 0;
// Write the FeatureId Data to the file
fprintf(vtkFile, "SCALARS FeatureID int 1\n");
fprintf(vtkFile, "LOOKUP_TABLE default\n");
// Loop over all the features
for(QMap<int32_t, int32_t>::iterator featureIter = featureIds.begin(); featureIter != featureIds.end(); ++featureIter)
{
int32_t gid = featureIter.key(); // The current Feature Id
size_t size = featureIter.value(); // The number of triangles for this feature id
std::vector<int32_t> buffer(size, 0);
totalCellsWritten += size;
// Endian Swap our current feature Id since we are going to write it a bunch of times.
swapped = gid;
SIMPLib::Endian::FromSystemToBig::convert(swapped);
size_t index = 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++)
{
if (m_SurfaceMeshFaceLabels[j * 2] == gid || m_SurfaceMeshFaceLabels[j * 2 + 1] == gid)
{
if(m_WriteBinaryFile == true)
{
buffer[index] = swapped;
++index;
}
else
{
fprintf(vtkFile, "%d\n", gid);
}
}
}
// Write the Buffer
if(m_WriteBinaryFile == true)
{
fwrite(&(buffer.front()), sizeof(int32_t), size, vtkFile);
}
}
#if 0
// Write the Original Triangle ID Data to the file
fprintf(vtkFile, "\n");
fprintf(vtkFile, "SCALARS TriangleID int 1\n");
fprintf(vtkFile, "LOOKUP_TABLE default\n");
for(int i = 0; i < triangleCount * 2; ++i)
{
//Triangle& t = triangles[i]; // Get the current Node
if(m_WriteBinaryFile == true)
{
swapped = i;
SIMPLib::Endian::FromSystemToBig::convert(swapped);
fwrite(&swapped, sizeof(int), 1, vtkFile);
fwrite(&swapped, sizeof(int), 1, vtkFile);
}
else
{
fprintf(vtkFile, "%d\n", i);
fprintf(vtkFile, "%d\n", i);
}
}
#endif
QString attrMatName = m_SurfaceMeshFaceLabelsArrayPath.getAttributeMatrixName();
notifyStatusMessage(getHumanLabel(), "Writing Face Normals...");
writeCellNormalData<double>(sm, attrMatName, SIMPL::FaceData::SurfaceMeshFaceNormals,
"double", m_WriteBinaryFile, vtkFile, featureIds, m_SurfaceMeshFaceLabels);
notifyStatusMessage(getHumanLabel(), "Writing Principal Curvature 1");
writeCellScalarData<double>(sm, attrMatName, SIMPL::FaceData::SurfaceMeshPrincipalCurvature1,
"double", m_WriteBinaryFile, vtkFile, featureIds, m_SurfaceMeshFaceLabels);
notifyStatusMessage(getHumanLabel(), "Writing Principal Curvature 2");
writeCellScalarData<double>(sm, attrMatName, SIMPL::FaceData::SurfaceMeshPrincipalCurvature2,
"double", m_WriteBinaryFile, vtkFile, featureIds, m_SurfaceMeshFaceLabels);
notifyStatusMessage(getHumanLabel(), "Writing Feature Face Id");
writeCellScalarData<int32_t>(sm, attrMatName, SIMPL::FaceData::SurfaceMeshFeatureFaceId,
"int", m_WriteBinaryFile, vtkFile, featureIds, m_SurfaceMeshFaceLabels);
notifyStatusMessage(getHumanLabel(), "Writing Gaussian Curvature");
writeCellScalarData<double>(sm, attrMatName, SIMPL::FaceData::SurfaceMeshGaussianCurvatures,
"double", m_WriteBinaryFile, vtkFile, featureIds, m_SurfaceMeshFaceLabels);
notifyStatusMessage(getHumanLabel(), "Writing Mean Curvature");
writeCellScalarData<double>(sm, attrMatName, SIMPL::FaceData::SurfaceMeshMeanCurvatures,
"double", m_WriteBinaryFile, vtkFile, featureIds, m_SurfaceMeshFaceLabels);
#if 0
writeCellVectorData<double>(sm, attrMatName, SIMPL::CellData::SurfaceMeshPrincipalDirection1,
"double", m_WriteBinaryFile, "VECTORS", vtkFile, nT);
writeCellVectorData<double>(sm, attrMatName, SIMPL::CellData::SurfaceMeshPrincipalDirection2,
"double", m_WriteBinaryFile, "VECTORS", vtkFile, nT);
writeCellNormalData<double>(sm, attrMatName, "Goldfeather_Triangle_Normals",
"double", m_WriteBinaryFile, vtkFile, nT);
#endif
return err;
}
// -----------------------------------------------------------------------------
//
// -----------------------------------------------------------------------------
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 SurfaceMeshToNonconformalVtk::readFilterParameters(AbstractFilterParametersReader* reader, int index)
{
reader->openFilterGroup(this, index);
setSurfaceMeshNodeTypeArrayPath(reader->readDataArrayPath("SurfaceMeshNodeTypeArrayPath", getSurfaceMeshNodeTypeArrayPath() ) );
setSurfaceMeshFaceLabelsArrayPath(reader->readDataArrayPath("SurfaceMeshFaceLabelsArrayPath", getSurfaceMeshFaceLabelsArrayPath() ) );
setOutputVtkFile( reader->readString( "OutputVtkFile", getOutputVtkFile() ) );
setWriteBinaryFile( reader->readValue("WriteBinaryFile", getWriteBinaryFile()) );
reader->closeFilterGroup();
}
// -----------------------------------------------------------------------------
//
// -----------------------------------------------------------------------------
int SurfaceMeshToVtk::writeCellData(FILE* vtkFile)
{
int err = 0;
if (NULL == vtkFile)
{
return -1;
}
DataContainer::Pointer sm = getDataContainerArray()->getDataContainer(m_SurfaceMeshFaceLabelsArrayPath.getDataContainerName());
// Write the triangle region ids
TriangleGeom::Pointer triangleGeom = getDataContainerArray()->getDataContainer(getSurfaceMeshFaceLabelsArrayPath().getDataContainerName())->getGeometryAs<TriangleGeom>();
int64_t nT = triangleGeom->getNumberOfTris();
int numTriangles = nT;
int swapped;
if (false == m_WriteConformalMesh)
{
numTriangles = nT * 2;
}
// This is like a "section header"
fprintf(vtkFile, "\n");
fprintf(vtkFile, "CELL_DATA %d\n", numTriangles);
// Write the FeatureId Data to the file
fprintf(vtkFile, "SCALARS FeatureID int 1\n");
fprintf(vtkFile, "LOOKUP_TABLE default\n");
for(int i = 0; i < nT; ++i)
{
//FaceArray::Face_t& t = triangles[i]; // Get the current Node
if(m_WriteBinaryFile == true)
{
swapped = m_SurfaceMeshFaceLabels[i * 2];
SIMPLib::Endian::FromSystemToBig::convert(swapped);
fwrite(&swapped, sizeof(int), 1, vtkFile);
if(false == m_WriteConformalMesh)
{
swapped = m_SurfaceMeshFaceLabels[i * 2 + 1];
SIMPLib::Endian::FromSystemToBig::convert(swapped);
fwrite(&swapped, sizeof(int), 1, vtkFile);
}
}
else
{
fprintf(vtkFile, "%d\n", m_SurfaceMeshFaceLabels[i * 2]);
if(false == m_WriteConformalMesh)
{
fprintf(vtkFile, "%d\n", m_SurfaceMeshFaceLabels[i * 2 + 1]);
}
}
}
#if 0
// Write the Original Triangle ID Data to the file
fprintf(vtkFile, "\n");
fprintf(vtkFile, "SCALARS TriangleID int 1\n");
fprintf(vtkFile, "LOOKUP_TABLE default\n");
for(int i = 0; i < nT; ++i)
{
//Triangle& t = triangles[i]; // Get the current Node
if(m_WriteBinaryFile == true)
{
swapped = i;
SIMPLib::Endian::FromSystemToBig::convert(swapped);
fwrite(&swapped, sizeof(int), 1, vtkFile);
if(false == m_WriteConformalMesh)
{
fwrite(&swapped, sizeof(int), 1, vtkFile);
}
}
else
{
fprintf(vtkFile, "%d\n", i);
if(false == m_WriteConformalMesh)
{
fprintf(vtkFile, "%d\n", i);
}
}
}
#endif
QString attrMatName = m_SurfaceMeshFaceLabelsArrayPath.getAttributeMatrixName();
writeCellScalarData<int32_t>(sm, attrMatName, DREAM3D::FaceData::SurfaceMeshFeatureFaceId,
"int", m_WriteBinaryFile, m_WriteConformalMesh, vtkFile, nT);
writeCellScalarData<double>(sm, attrMatName, DREAM3D::FaceData::SurfaceMeshPrincipalCurvature1,
"double", m_WriteBinaryFile, m_WriteConformalMesh, vtkFile, nT);
writeCellScalarData<double>(sm, attrMatName, DREAM3D::FaceData::SurfaceMeshPrincipalCurvature2,
"double", m_WriteBinaryFile, m_WriteConformalMesh, vtkFile, nT);
writeCellVectorData<double>(sm, attrMatName, DREAM3D::FaceData::SurfaceMeshPrincipalDirection1,
"double", m_WriteBinaryFile, m_WriteConformalMesh, "VECTORS", vtkFile, nT);
writeCellVectorData<double>(sm, attrMatName, DREAM3D::FaceData::SurfaceMeshPrincipalDirection2,
"double", m_WriteBinaryFile, m_WriteConformalMesh, "VECTORS", vtkFile, nT);
writeCellScalarData<double>(sm, attrMatName, DREAM3D::FaceData::SurfaceMeshGaussianCurvatures,
"double", m_WriteBinaryFile, m_WriteConformalMesh, vtkFile, nT);
writeCellScalarData<double>(sm, attrMatName, DREAM3D::FaceData::SurfaceMeshMeanCurvatures,
"double", m_WriteBinaryFile, m_WriteConformalMesh, vtkFile, nT);
writeCellNormalData<double>(sm, attrMatName, DREAM3D::FaceData::SurfaceMeshFaceNormals,
"double", m_WriteBinaryFile, m_WriteConformalMesh, vtkFile, nT);
writeCellNormalData<double>(sm, attrMatName, "Goldfeather_Triangle_Normals",
"double", m_WriteBinaryFile, m_WriteConformalMesh, vtkFile, nT);
return err;
}
// -----------------------------------------------------------------------------
//
// -----------------------------------------------------------------------------
void AbaqusSurfaceMeshWriter::setupFilterParameters()
{
FilterParameterVector parameters;
parameters.push_back(OutputFileFilterParameter::New("Output File", "OutputFile", getOutputFile(), FilterParameter::Parameter, "*.inp"));
parameters.push_back(SeparatorFilterParameter::New("Face Data", FilterParameter::RequiredArray));
{
DataArraySelectionFilterParameter::RequirementType req = DataArraySelectionFilterParameter::CreateRequirement(DREAM3D::TypeNames::Int32, 2, DREAM3D::AttributeMatrixType::Face, DREAM3D::GeometryType::TriangleGeometry);
parameters.push_back(DataArraySelectionFilterParameter::New("Face Labels", "SurfaceMeshFaceLabelsArrayPath", getSurfaceMeshFaceLabelsArrayPath(), FilterParameter::RequiredArray, req));
}
setFilterParameters(parameters);
}
// -----------------------------------------------------------------------------
//
// -----------------------------------------------------------------------------
int32_t AbaqusSurfaceMeshWriter::writeFeatures(FILE* f)
{
//*Elset, elset=Feature1
//1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16
int32_t err = 0;
TriangleGeom::Pointer triangleGeo = getDataContainerArray()->getDataContainer(getSurfaceMeshFaceLabelsArrayPath().getDataContainerName())->getGeometryAs<TriangleGeom>();
int64_t nTriangles = triangleGeo->getNumberOfTris();
// Store all the unique Spins
std::set<int32_t> uniqueSpins;
for (int64_t i = 0; i < nTriangles; i++)
{
uniqueSpins.insert(m_SurfaceMeshFaceLabels[i * 2]);
uniqueSpins.insert(m_SurfaceMeshFaceLabels[i * 2 + 1]);
}
int32_t spin = 0;
//Loop over the unique Spins
for (std::set<int32_t>::iterator spinIter = uniqueSpins.begin(); spinIter != uniqueSpins.end(); ++spinIter )
{
spin = *spinIter;
if (spin < 0) { continue; }
fprintf(f, "*ELSET, ELSET=Feature%d\n", spin);
{
QString ss = QObject::tr("Writing ELSET for Feature Id %1").arg(spin);
notifyStatusMessage(getMessagePrefix(), getHumanLabel(), ss);
}
// Loop over all the triangles for this spin
int64_t lineCount = 0;
for (int64_t t = 0; t < nTriangles; ++t)
{
if (m_SurfaceMeshFaceLabels[t * 2] != spin && m_SurfaceMeshFaceLabels[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, ", %lld\n", (long long int)(t));
lineCount = 0;
}
else if(lineCount == 0) // First value on the line
{
fprintf(f, "%lld", (long long int)(t));
lineCount++;
}
else
{
fprintf(f, ", %lld", (long long int)(t));
lineCount++;
}
}
// Make sure we have a new line at the end of the section
if (lineCount != 0)
{
fprintf(f, "\n");
}
}
return err;
}
// -----------------------------------------------------------------------------
//
// -----------------------------------------------------------------------------
void AbaqusSurfaceMeshWriter::execute()
{
int32_t err = 0;
setErrorCondition(err);
dataCheck();
if(getErrorCondition() < 0) { return; }
DataContainer::Pointer sm = getDataContainerArray()->getDataContainer(getSurfaceMeshFaceLabelsArrayPath().getDataContainerName());
// 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(getOutputFile());
QDir parentPath = fi.path();
if(!parentPath.mkpath("."))
{
QString ss = QObject::tr("Error creating parent path '%1'").arg(parentPath.absolutePath());
setErrorCondition(-8005);
notifyErrorMessage(getHumanLabel(), ss, getErrorCondition());
return;
}
TriangleGeom::Pointer triangleGeom = sm->getGeometryAs<TriangleGeom>();
// Store all the unique Spins
std::set<int32_t> uniqueSpins;
for (int64_t i = 0; i < triangleGeom->getNumberOfTris(); i++)
{
uniqueSpins.insert(m_SurfaceMeshFaceLabels[i * 2]);
uniqueSpins.insert(m_SurfaceMeshFaceLabels[i * 2 + 1]);
}
FILE* f = fopen(m_OutputFile.toLatin1().data(), "wb");
ScopedFileMonitor fileMonitor(f);
err = writeHeader(f, triangleGeom->getNumberOfVertices(), triangleGeom->getNumberOfTris(), uniqueSpins.size() - 1);
if(err < 0)
{
QString ss = QObject::tr("Error writing header for file '%1'").arg(m_OutputFile);
setErrorCondition(-8001);
notifyErrorMessage(getHumanLabel(), ss, getErrorCondition());
return;
}
err = writeNodes(f);
if(err < 0)
{
QString ss = QObject::tr("Error writing nodes for file '%1'").arg(m_OutputFile);
setErrorCondition(-8002);
notifyErrorMessage(getHumanLabel(), ss, getErrorCondition());
return;
}
err = writeTriangles(f);
if(err < 0)
{
QString ss = QObject::tr("Error writing triangles for file '%1'").arg(m_OutputFile);
setErrorCondition(-8003);
notifyErrorMessage(getHumanLabel(), ss, getErrorCondition());
return;
}
err = writeFeatures(f);
if(err < 0)
{
QString ss = QObject::tr("Error writing Features for file '%1'").arg(m_OutputFile);
setErrorCondition(-8004);
notifyErrorMessage(getHumanLabel(), ss, getErrorCondition());
return;
}
notifyStatusMessage(getHumanLabel(), "Complete");
}
// -----------------------------------------------------------------------------
//
// -----------------------------------------------------------------------------
void AbaqusSurfaceMeshWriter::dataCheck()
{
setErrorCondition(0);
if (m_OutputFile.isEmpty() == true)
{
setErrorCondition(-1003);
notifyErrorMessage(getHumanLabel(), "The output file must be set", getErrorCondition());
}
QFileInfo fi(m_OutputFile);
QDir parentPath = fi.path();
if (parentPath.exists() == false)
{
QString ss = QObject::tr( "The directory path for the output file does not exist. DREAM.3D will attempt to create this path during execution of the filter");
notifyWarningMessage(getHumanLabel(), ss, -1);
}
QVector<IDataArray::Pointer> dataArrays;
TriangleGeom::Pointer triangles = getDataContainerArray()->getPrereqGeometryFromDataContainer<TriangleGeom, AbstractFilter>(this, getSurfaceMeshFaceLabelsArrayPath().getDataContainerName());
if(getErrorCondition() >= 0) { dataArrays.push_back(triangles->getTriangles()); }
QVector<size_t> cDims(1, 2);
m_SurfaceMeshFaceLabelsPtr = getDataContainerArray()->getPrereqArrayFromPath<DataArray<int32_t>, AbstractFilter>(this, getSurfaceMeshFaceLabelsArrayPath(), cDims); /* Assigns the shared_ptr<> to an instance variable that is a weak_ptr<> */
if( NULL != m_SurfaceMeshFaceLabelsPtr.lock().get() ) /* Validate the Weak Pointer wraps a non-NULL pointer to a DataArray<T> object */
{ m_SurfaceMeshFaceLabels = m_SurfaceMeshFaceLabelsPtr.lock()->getPointer(0); } /* Now assign the raw pointer to data from the DataArray<T> object */
if(getErrorCondition() >= 0) { dataArrays.push_back(m_SurfaceMeshFaceLabelsPtr.lock()); }
getDataContainerArray()->validateNumberOfTuples<AbstractFilter>(this, dataArrays);
}
// -----------------------------------------------------------------------------
//
// -----------------------------------------------------------------------------
void GenerateFaceSchuhMisorientationColoring::dataCheckSurfaceMesh()
{
DataArrayPath tempPath;
setErrorCondition(0);
DataContainer::Pointer sm = getDataContainerArray()->getPrereqDataContainer<AbstractFilter>(this, m_SurfaceMeshFaceLabelsArrayPath.getDataContainerName(), false);
if(getErrorCondition() < 0) { return; }
QVector<size_t> dims(1, 2);
m_SurfaceMeshFaceLabelsPtr = getDataContainerArray()->getPrereqArrayFromPath<DataArray<int32_t>, AbstractFilter>(this, getSurfaceMeshFaceLabelsArrayPath(), dims); /* Assigns the shared_ptr<> to an instance variable that is a weak_ptr<> */
if( NULL != m_SurfaceMeshFaceLabelsPtr.lock().get() ) /* Validate the Weak Pointer wraps a non-NULL pointer to a DataArray<T> object */
{ m_SurfaceMeshFaceLabels = m_SurfaceMeshFaceLabelsPtr.lock()->getPointer(0); } /* Now assign the raw pointer to data from the DataArray<T> object */
dims[0] = 3;
tempPath.update(m_SurfaceMeshFaceLabelsArrayPath.getDataContainerName(), m_SurfaceMeshFaceLabelsArrayPath.getAttributeMatrixName(), getSurfaceMeshFaceSchuhMisorientationColorsArrayName() );
m_SurfaceMeshFaceSchuhMisorientationColorsPtr = getDataContainerArray()->createNonPrereqArrayFromPath<DataArray<uint8_t>, AbstractFilter, uint8_t>(this, tempPath, 0, dims); /* Assigns the shared_ptr<> to an instance variable that is a weak_ptr<> */
if( NULL != m_SurfaceMeshFaceSchuhMisorientationColorsPtr.lock().get() ) /* Validate the Weak Pointer wraps a non-NULL pointer to a DataArray<T> object */
{ m_SurfaceMeshFaceSchuhMisorientationColors = m_SurfaceMeshFaceSchuhMisorientationColorsPtr.lock()->getPointer(0); } /* Now assign the raw pointer to data from the DataArray<T> object */
}
// -----------------------------------------------------------------------------
//
// -----------------------------------------------------------------------------
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");
}
// -----------------------------------------------------------------------------
//
// -----------------------------------------------------------------------------
int SurfaceMeshToVtk::writePointData(FILE* vtkFile)
{
int err = 0;
if (NULL == vtkFile)
{
return -1;
}
DataContainer::Pointer sm = getDataContainerArray()->getDataContainer(m_SurfaceMeshFaceLabelsArrayPath.getDataContainerName());
TriangleGeom::Pointer triangleGeom = getDataContainerArray()->getDataContainer(getSurfaceMeshFaceLabelsArrayPath().getDataContainerName())->getGeometryAs<TriangleGeom>();
qint64 numNodes = triangleGeom->getNumberOfVertices();
int64_t numberWrittenumNodes = 0;
// Write the Node Type Data to the file
for (int i = 0; i < numNodes; i++)
{
if (m_SurfaceMeshNodeType[i] > 0) { ++numberWrittenumNodes; }
}
// This is the section header
fprintf(vtkFile, "\n");
fprintf(vtkFile, "POINT_DATA %lld\n", (long long int)(numberWrittenumNodes));
fprintf(vtkFile, "SCALARS Node_Type char 1\n");
fprintf(vtkFile, "LOOKUP_TABLE default\n");
for(int i = 0; i < numNodes; ++i)
{
if(m_SurfaceMeshNodeType[i] > 0)
{
if(m_WriteBinaryFile == true)
{
// Normally, we would byte swap to big endian but since we are only writing
// 1 byte Char values, nothing to swap.
fwrite(m_SurfaceMeshNodeType + i, sizeof(char), 1, vtkFile);
}
else
{
fprintf(vtkFile, "%d ", m_SurfaceMeshNodeType[i]);
}
}
}
QString attrMatName = m_SurfaceMeshNodeTypeArrayPath.getAttributeMatrixName();
#if 1
// This is from the Goldfeather Paper
writePointVectorData<double>(sm, attrMatName, "Principal_Direction_1",
"double", m_WriteBinaryFile, m_WriteConformalMesh, "VECTORS", vtkFile, numNodes);
// This is from the Goldfeather Paper
writePointVectorData<double>(sm, attrMatName, "Principal_Direction_2",
"double", m_WriteBinaryFile, m_WriteConformalMesh, "VECTORS", vtkFile, numNodes);
// This is from the Goldfeather Paper
writePointScalarData<double>(sm, attrMatName, "Principal_Curvature_1",
"double", m_WriteBinaryFile, m_WriteConformalMesh, vtkFile, numNodes);
// This is from the Goldfeather Paper
writePointScalarData<double>(sm, attrMatName, "Principal_Curvature_2",
"double", m_WriteBinaryFile, m_WriteConformalMesh, vtkFile, numNodes);
#endif
// This is from the Goldfeather Paper
writePointVectorData<double>(sm, attrMatName, DREAM3D::VertexData::SurfaceMeshNodeNormals,
"double", m_WriteBinaryFile, m_WriteConformalMesh, "VECTORS", vtkFile, numNodes);
return err;
}
// -----------------------------------------------------------------------------
//
// -----------------------------------------------------------------------------
void AbaqusSurfaceMeshWriter::readFilterParameters(AbstractFilterParametersReader* reader, int index)
{
reader->openFilterGroup(this, index);
setSurfaceMeshFaceLabelsArrayPath(reader->readDataArrayPath("SurfaceMeshFaceLabelsArrayPath", getSurfaceMeshFaceLabelsArrayPath() ) );
setOutputFile( reader->readString( "OutputFile", getOutputFile() ) );
reader->closeFilterGroup();
}
// -----------------------------------------------------------------------------
//
// -----------------------------------------------------------------------------
void SurfaceMeshToVtk::setupFilterParameters()
{
QVector<FilterParameter::Pointer> parameters;
parameters.push_back(OutputFileFilterParameter::New("Output Vtk File", "OutputVtkFile", getOutputVtkFile(), FilterParameter::Parameter));
parameters.push_back(BooleanFilterParameter::New("Write Binary Vtk File", "WriteBinaryFile", getWriteBinaryFile(), FilterParameter::Parameter));
parameters.push_back(BooleanFilterParameter::New("Write Conformal Mesh", "WriteConformalMesh", getWriteConformalMesh(), FilterParameter::Parameter));
{
DataArraySelectionFilterParameter::RequirementType req;
parameters.push_back(DataArraySelectionFilterParameter::New("SurfaceMeshFaceLabels", "SurfaceMeshFaceLabelsArrayPath", getSurfaceMeshFaceLabelsArrayPath(), FilterParameter::RequiredArray, req));
}
{
DataArraySelectionFilterParameter::RequirementType req;
parameters.push_back(DataArraySelectionFilterParameter::New("SurfaceMeshNodeType", "SurfaceMeshNodeTypeArrayPath", getSurfaceMeshNodeTypeArrayPath(), FilterParameter::RequiredArray, req));
}
parameters.push_back(SeparatorFilterParameter::New("Vertex Data", FilterParameter::RequiredArray));
{
MultiDataArraySelectionFilterParameter::RequirementType req;
req.dcGeometryTypes = QVector<unsigned int>(1, DREAM3D::GeometryType::TriangleGeometry);
req.amTypes = QVector<unsigned int>(1, DREAM3D::AttributeMatrixType::Vertex);
parameters.push_back(MultiDataArraySelectionFilterParameter::New("Vertex Arrays", "SelectedVertexArrays", getSelectedVertexArrays(), FilterParameter::RequiredArray, req));
}
parameters.push_back(SeparatorFilterParameter::New("Face Data", FilterParameter::RequiredArray));
{
MultiDataArraySelectionFilterParameter::RequirementType req;
req.dcGeometryTypes = QVector<unsigned int>(1, DREAM3D::GeometryType::TriangleGeometry);
req.amTypes = QVector<unsigned int>(1, DREAM3D::AttributeMatrixType::Face);
parameters.push_back(MultiDataArraySelectionFilterParameter::New("Face Arrays", "SelectedFaceArrays", getSelectedFaceArrays(), FilterParameter::RequiredArray, req));
}
setFilterParameters(parameters);
}
// -----------------------------------------------------------------------------
//
// -----------------------------------------------------------------------------
void FindModulusMismatch::setupFilterParameters()
{
FilterParameterVector parameters;
{
DataArraySelectionFilterParameter::RequirementType req = DataArraySelectionFilterParameter::CreateCategoryRequirement(DREAM3D::Defaults::AnyPrimitive, 1, DREAM3D::AttributeMatrixObjectType::Any);
parameters.push_back(DataArraySelectionFilterParameter::New("Moduli", "ModuliArrayPath", getModuliArrayPath(), FilterParameter::RequiredArray, req));
}
{
DataArraySelectionFilterParameter::RequirementType req = DataArraySelectionFilterParameter::CreateCategoryRequirement(DREAM3D::Defaults::AnyPrimitive, 2, DREAM3D::AttributeMatrixObjectType::Any);
parameters.push_back(DataArraySelectionFilterParameter::New("SurfaceMeshFaceLabels", "SurfaceMeshFaceLabelsArrayPath", getSurfaceMeshFaceLabelsArrayPath(), FilterParameter::RequiredArray, req));
}
parameters.push_back(StringFilterParameter::New("SurfaceMeshDeltaModulus", "SurfaceMeshDeltaModulusArrayName", getSurfaceMeshDeltaModulusArrayName(), FilterParameter::CreatedArray));
setFilterParameters(parameters);
}
// -----------------------------------------------------------------------------
//
// -----------------------------------------------------------------------------
void SurfaceMeshToNonconformalVtk::dataCheck()
{
setErrorCondition(0);
QString ss;
if (m_OutputVtkFile.isEmpty() == true)
{
setErrorCondition(-1003);
notifyErrorMessage(getHumanLabel(), "Vtk Output file is Not set correctly", -1003);
}
DataContainer::Pointer sm = getDataContainerArray()->getPrereqDataContainer<AbstractFilter>(this, m_SurfaceMeshFaceLabelsArrayPath.getDataContainerName(), false);
if(getErrorCondition() < 0) { return; }
TriangleGeom::Pointer triangles = sm->getPrereqGeometry<TriangleGeom, AbstractFilter>(this);
if(getErrorCondition() < 0) { return; }
// We MUST have Nodes
if (NULL == triangles->getVertices().get())
{
setErrorCondition(-386);
notifyErrorMessage(getHumanLabel(), "DataContainer Geometry missing Vertices", getErrorCondition());
}
// We MUST have Triangles defined also.
if (NULL == triangles->getTriangles().get())
{
setErrorCondition(-387);
notifyErrorMessage(getHumanLabel(), "DataContainer Geometry missing Triangles", getErrorCondition());
}
QVector<size_t> dims(1, 2);
m_SurfaceMeshFaceLabelsPtr = getDataContainerArray()->getPrereqArrayFromPath<DataArray<int32_t>, AbstractFilter>(this, getSurfaceMeshFaceLabelsArrayPath(), dims); /* Assigns the shared_ptr<> to an instance variable that is a weak_ptr<> */
if( NULL != m_SurfaceMeshFaceLabelsPtr.lock().get() ) /* Validate the Weak Pointer wraps a non-NULL pointer to a DataArray<T> object */
{ m_SurfaceMeshFaceLabels = m_SurfaceMeshFaceLabelsPtr.lock()->getPointer(0); } /* Now assign the raw pointer to data from the DataArray<T> object */
dims[0] = 1;
m_SurfaceMeshNodeTypePtr = getDataContainerArray()->getPrereqArrayFromPath<DataArray<int8_t>, AbstractFilter>(this, getSurfaceMeshNodeTypeArrayPath(), dims); /* Assigns the shared_ptr<> to an instance variable that is a weak_ptr<> */
if( NULL != m_SurfaceMeshNodeTypePtr.lock().get() ) /* Validate the Weak Pointer wraps a non-NULL pointer to a DataArray<T> object */
{ m_SurfaceMeshNodeType = m_SurfaceMeshNodeTypePtr.lock()->getPointer(0); } /* Now assign the raw pointer to data from the DataArray<T> object */
}
// -----------------------------------------------------------------------------
void FindModulusMismatch::readFilterParameters(AbstractFilterParametersReader* reader, int index)
{
reader->openFilterGroup(this, index);
setSurfaceMeshDeltaModulusArrayName(reader->readString("SurfaceMeshDeltaModulusArrayName", getSurfaceMeshDeltaModulusArrayName() ) );
setSurfaceMeshFaceLabelsArrayPath(reader->readDataArrayPath("SurfaceMeshFaceLabelsArrayPath", getSurfaceMeshFaceLabelsArrayPath() ) );
setModuliArrayPath(reader->readDataArrayPath("ModuliArrayPath", getModuliArrayPath() ) );
reader->closeFilterGroup();
}
// -----------------------------------------------------------------------------
//
// -----------------------------------------------------------------------------
int SurfaceMeshToNonconformalVtk::writePointData(FILE* vtkFile)
{
int err = 0;
if (NULL == vtkFile)
{
return -1;
}
DataContainer::Pointer sm = getDataContainerArray()->getDataContainer(m_SurfaceMeshNodeTypeArrayPath.getDataContainerName());
TriangleGeom::Pointer triangleGeom = getDataContainerArray()->getDataContainer(getSurfaceMeshFaceLabelsArrayPath().getDataContainerName())->getGeometryAs<TriangleGeom>();
//Get the Number of Vertex points in the mesh with a valid node type
qint64 numNodes = triangleGeom->getNumberOfVertices();
int nNodes = 0;
// int swapped;
for (int i = 0; i < numNodes; i++)
{
if (m_SurfaceMeshNodeType[i] > 0) { ++nNodes; }
else { qDebug() << "Node Type Invalid: " << i << "::" << (int)(m_SurfaceMeshNodeType[i]) ;}
}
// This is the section header
fprintf(vtkFile, "\n");
fprintf(vtkFile, "POINT_DATA %d\n", nNodes);
fprintf(vtkFile, "SCALARS Node_Type char 1\n");
fprintf(vtkFile, "LOOKUP_TABLE default\n");
for(int i = 0; i < numNodes; ++i)
{
if(m_SurfaceMeshNodeType[i] > 0)
{
if(m_WriteBinaryFile == true)
{
// swapped = m_SurfaceMeshNodeType[i];
// SIMPLib::Endian::FromSystemToBig::convert(swapped);
fwrite(m_SurfaceMeshNodeType + i, sizeof(char), 1, vtkFile);
}
else
{
fprintf(vtkFile, "%d ", m_SurfaceMeshNodeType[i]);
}
}
}
QString attrMatName = m_SurfaceMeshNodeTypeArrayPath.getAttributeMatrixName();
#if 1
// This is from the Goldfeather Paper
writePointVectorData<double>(sm, attrMatName, "Principal_Direction_1",
"double", m_WriteBinaryFile, "VECTORS", vtkFile, numNodes);
// This is from the Goldfeather Paper
writePointVectorData<double>(sm, attrMatName, "Principal_Direction_2",
"double", m_WriteBinaryFile, "VECTORS", vtkFile, numNodes);
// This is from the Goldfeather Paper
writePointScalarData<double>(sm, attrMatName, "Principal_Curvature_1",
"double", m_WriteBinaryFile, vtkFile, numNodes);
// This is from the Goldfeather Paper
writePointScalarData<double>(sm, attrMatName, "Principal_Curvature_2",
"double", m_WriteBinaryFile, vtkFile, numNodes);
#endif
// This is from the Goldfeather Paper
writePointVectorData<double>(sm, attrMatName, SIMPL::VertexData::SurfaceMeshNodeNormals,
"double", m_WriteBinaryFile, "VECTORS", vtkFile, numNodes);
return err;
}
// -----------------------------------------------------------------------------
//
// -----------------------------------------------------------------------------
void FindModulusMismatch::dataCheckSurfaceMesh()
{
DataArrayPath tempPath;
setErrorCondition(0);
DataContainer::Pointer sm = getDataContainerArray()->getPrereqDataContainer<AbstractFilter>(this, getSurfaceMeshFaceLabelsArrayPath().getDataContainerName());
if(getErrorCondition() < 0 || NULL == sm.get()) { return; }
QVector<size_t> dims(1, 2);
m_SurfaceMeshFaceLabelsPtr = getDataContainerArray()->getPrereqArrayFromPath<DataArray<int32_t>, AbstractFilter>(this, getSurfaceMeshFaceLabelsArrayPath(), dims); /* Assigns the shared_ptr<> to an instance variable that is a weak_ptr<> */
if( NULL != m_SurfaceMeshFaceLabelsPtr.lock().get() ) /* Validate the Weak Pointer wraps a non-NULL pointer to a DataArray<T> object */
{ m_SurfaceMeshFaceLabels = m_SurfaceMeshFaceLabelsPtr.lock()->getPointer(0); } /* Now assign the raw pointer to data from the DataArray<T> object */
dims[0] = 1;
tempPath.update(m_SurfaceMeshFaceLabelsArrayPath.getDataContainerName(), m_SurfaceMeshFaceLabelsArrayPath.getAttributeMatrixName(), getSurfaceMeshDeltaModulusArrayName() );
m_SurfaceMeshDeltaModulusPtr = getDataContainerArray()->createNonPrereqArrayFromPath<DataArray<float>, AbstractFilter, float>(this, tempPath, 180.0, dims); /* Assigns the shared_ptr<> to an instance variable that is a weak_ptr<> */
if( NULL != m_SurfaceMeshDeltaModulusPtr.lock().get() ) /* Validate the Weak Pointer wraps a non-NULL pointer to a DataArray<T> object */
{ m_SurfaceMeshDeltaModulus = m_SurfaceMeshDeltaModulusPtr.lock()->getPointer(0); } /* Now assign the raw pointer to data from the DataArray<T> object */
}
// -----------------------------------------------------------------------------
//
// -----------------------------------------------------------------------------
void SurfaceMeshToNonconformalVtk::setupFilterParameters()
{
QVector<FilterParameter::Pointer> parameters;
parameters.push_back(OutputFileFilterParameter::New("Output Vtk File", "OutputVtkFile", getOutputVtkFile(), FilterParameter::Parameter));
parameters.push_back(BooleanFilterParameter::New("Write Binary Vtk File", "WriteBinaryFile", getWriteBinaryFile(), FilterParameter::Parameter));
{
DataArraySelectionFilterParameter::RequirementType req;
parameters.push_back(DataArraySelectionFilterParameter::New("SurfaceMeshFaceLabels", "SurfaceMeshFaceLabelsArrayPath", getSurfaceMeshFaceLabelsArrayPath(), FilterParameter::RequiredArray, req));
}
{
DataArraySelectionFilterParameter::RequirementType req;
parameters.push_back(DataArraySelectionFilterParameter::New("SurfaceMeshNodeType", "SurfaceMeshNodeTypeArrayPath", getSurfaceMeshNodeTypeArrayPath(), FilterParameter::RequiredArray, req));
}
setFilterParameters(parameters);
}
// -----------------------------------------------------------------------------
//
// -----------------------------------------------------------------------------
void SharedFeatureFaceFilter::dataCheck()
{
setErrorCondition(0);
DataArrayPath tempPath;
getDataContainerArray()->getPrereqGeometryFromDataContainer<TriangleGeom, AbstractFilter>(this, getSurfaceMeshFaceLabelsArrayPath().getDataContainerName());
DataContainer::Pointer sm = getDataContainerArray()->getPrereqDataContainer<AbstractFilter>(this, m_SurfaceMeshFaceLabelsArrayPath.getDataContainerName(), false);
if(getErrorCondition() < 0) { return; }
QVector<size_t> tDims(1, 0);
AttributeMatrix::Pointer facefeatureAttrMat = sm->createNonPrereqAttributeMatrix<AbstractFilter>(this, getFaceFeatureAttributeMatrixName(), tDims, DREAM3D::AttributeMatrixType::FaceFeature);
if(getErrorCondition() < 0 || NULL == facefeatureAttrMat.get()) { return; }
QVector<size_t> cDims(1, 2);
m_SurfaceMeshFaceLabelsPtr = getDataContainerArray()->getPrereqArrayFromPath<DataArray<int32_t>, AbstractFilter>(this, getSurfaceMeshFaceLabelsArrayPath(), cDims); /* Assigns the shared_ptr<> to an instance variable that is a weak_ptr<> */
if( NULL != m_SurfaceMeshFaceLabelsPtr.lock().get() ) /* Validate the Weak Pointer wraps a non-NULL pointer to a DataArray<T> object */
{ m_SurfaceMeshFaceLabels = m_SurfaceMeshFaceLabelsPtr.lock()->getPointer(0); } /* Now assign the raw pointer to data from the DataArray<T> object */
cDims[0] = 1;
tempPath.update(m_SurfaceMeshFaceLabelsArrayPath.getDataContainerName(), m_SurfaceMeshFaceLabelsArrayPath.getAttributeMatrixName(), getSurfaceMeshFeatureFaceIdsArrayName() );
m_SurfaceMeshFeatureFaceIdsPtr = getDataContainerArray()->createNonPrereqArrayFromPath<DataArray<int32_t>, AbstractFilter, int32_t>(this, tempPath, 0, cDims); /* Assigns the shared_ptr<> to an instance variable that is a weak_ptr<> */
if( NULL != m_SurfaceMeshFeatureFaceIdsPtr.lock().get() ) /* Validate the Weak Pointer wraps a non-NULL pointer to a DataArray<T> object */
{ m_SurfaceMeshFeatureFaceIds = m_SurfaceMeshFeatureFaceIdsPtr.lock()->getPointer(0); } /* Now assign the raw pointer to data from the DataArray<T> object */
tempPath.update(m_SurfaceMeshFaceLabelsArrayPath.getDataContainerName(), getFaceFeatureAttributeMatrixName(), getSurfaceMeshFeatureFaceNumTrianglesArrayName() );
m_SurfaceMeshFeatureFaceNumTrianglesPtr = getDataContainerArray()->createNonPrereqArrayFromPath<DataArray<int32_t>, AbstractFilter, int32_t>(this, tempPath, 0, cDims); /* Assigns the shared_ptr<> to an instance variable that is a weak_ptr<> */
if( NULL != m_SurfaceMeshFeatureFaceNumTrianglesPtr.lock().get() ) /* Validate the Weak Pointer wraps a non-NULL pointer to a DataArray<T> object */
{ m_SurfaceMeshFeatureFaceNumTriangles = m_SurfaceMeshFeatureFaceNumTrianglesPtr.lock()->getPointer(0); } /* Now assign the raw pointer to data from the DataArray<T> object */
cDims[0] = 2;
tempPath.update(m_SurfaceMeshFaceLabelsArrayPath.getDataContainerName(), getFaceFeatureAttributeMatrixName(), getSurfaceMeshFeatureFaceLabelsArrayName() );
m_SurfaceMeshFeatureFaceLabelsPtr = getDataContainerArray()->createNonPrereqArrayFromPath<DataArray<int32_t>, AbstractFilter, int32_t>(this, tempPath, 0, cDims); /* Assigns the shared_ptr<> to an instance variable that is a weak_ptr<> */
if( NULL != m_SurfaceMeshFeatureFaceLabelsPtr.lock().get() ) /* Validate the Weak Pointer wraps a non-NULL pointer to a DataArray<T> object */
{ m_SurfaceMeshFeatureFaceLabels = m_SurfaceMeshFeatureFaceLabelsPtr.lock()->getPointer(0); } /* Now assign the raw pointer to data from the DataArray<T> object */
}
// -----------------------------------------------------------------------------
//
// -----------------------------------------------------------------------------
void InsertAtoms::readFilterParameters(AbstractFilterParametersReader* reader, int index)
{
reader->openFilterGroup(this, index);
setVertexDataContainerName(reader->readString("VertexDataContainerName", getVertexDataContainerName() ) );
setVertexAttributeMatrixName(reader->readString("VertexAttributeMatrixName", getVertexAttributeMatrixName() ) );
setAtomFeatureLabelsArrayName(reader->readString("AtomFeatureLabelsArrayName", getAtomFeatureLabelsArrayName() ) );
setAvgQuatsArrayPath(reader->readDataArrayPath("AvgQuatsArrayPath", getAvgQuatsArrayPath() ) );
setSurfaceMeshFaceLabelsArrayPath(reader->readDataArrayPath("SurfaceMeshFaceLabelsArrayPath", getSurfaceMeshFaceLabelsArrayPath() ) );
setLatticeConstants( reader->readFloatVec3("LatticeConstants", getLatticeConstants() ) );
setBasis( reader->readValue("Basis", getBasis() ) );
reader->closeFilterGroup();
}
// -----------------------------------------------------------------------------
//
// -----------------------------------------------------------------------------
void SharedFeatureFaceFilter::setupFilterParameters()
{
FilterParameterVector parameters;
parameters.push_back(SeparatorFilterParameter::New("Face Data", FilterParameter::RequiredArray));
{
DataArraySelectionFilterParameter::RequirementType req = DataArraySelectionFilterParameter::CreateRequirement(DREAM3D::TypeNames::Int32, 2, DREAM3D::AttributeMatrixType::Face, DREAM3D::GeometryType::TriangleGeometry);
parameters.push_back(DataArraySelectionFilterParameter::New("Face Labels", "SurfaceMeshFaceLabelsArrayPath", getSurfaceMeshFaceLabelsArrayPath(), FilterParameter::RequiredArray, req));
}
parameters.push_back(SeparatorFilterParameter::New("Face Data", FilterParameter::CreatedArray));
parameters.push_back(StringFilterParameter::New("Feature Face Ids", "SurfaceMeshFeatureFaceIdsArrayName", getSurfaceMeshFeatureFaceIdsArrayName(), FilterParameter::CreatedArray));
parameters.push_back(SeparatorFilterParameter::New("Face Feature Data", FilterParameter::CreatedArray));
parameters.push_back(StringFilterParameter::New("Face Feature Attribute Matrix", "FaceFeatureAttributeMatrixName", getFaceFeatureAttributeMatrixName(), FilterParameter::CreatedArray));
parameters.push_back(StringFilterParameter::New("Face Labels", "SurfaceMeshFeatureFaceLabelsArrayName", getSurfaceMeshFeatureFaceLabelsArrayName(), FilterParameter::CreatedArray));
parameters.push_back(StringFilterParameter::New("Number of Triangles", "SurfaceMeshFeatureFaceNumTrianglesArrayName", getSurfaceMeshFeatureFaceNumTrianglesArrayName(), FilterParameter::CreatedArray));
setFilterParameters(parameters);
}
// -----------------------------------------------------------------------------
//
// -----------------------------------------------------------------------------
void InsertAtoms::execute()
{
setErrorCondition(0);
dataCheck();
if(getErrorCondition() < 0) { return; }
// Validate that the selected AvgQuats array has tuples equal to the largest
// Feature Id; the filter would not crash otherwise, but the user should
// be notified of unanticipated behavior ; this cannot be done in the dataCheck since
// we don't have acces to the data yet
int32_t numFeaturesIn = static_cast<int32_t>(m_AvgQuatsPtr.lock()->getNumberOfTuples());
bool mismatchedFeatures = true;
int32_t largestFeature = 0;
size_t numTuples = m_SurfaceMeshFaceLabelsPtr.lock()->getNumberOfTuples();
for (size_t i = 0; i < numTuples; i++)
{
if (m_SurfaceMeshFaceLabels[2 * i] > largestFeature)
{
largestFeature = m_SurfaceMeshFaceLabels[2 * i];
if (largestFeature >= numFeaturesIn)
{
mismatchedFeatures = true;
break;
}
}
else if (m_SurfaceMeshFaceLabels[2 * i + 1] > largestFeature)
{
largestFeature = m_SurfaceMeshFaceLabels[2 * i + 1];
if (largestFeature >= numFeaturesIn)
{
mismatchedFeatures = true;
break;
}
}
}
if (mismatchedFeatures == true)
{
QString ss = QObject::tr("The number of Features in the AvgQuats array (%1) is larger than the largest Feature Id in the SurfaceMeshFaceLabels array").arg(numFeaturesIn);
setErrorCondition(-5555);
notifyErrorMessage(getHumanLabel(), ss, getErrorCondition());
return;
}
if (largestFeature != (numFeaturesIn - 1))
{
QString ss = QObject::tr("The number of Features in the AvgQuats array (%1) does not match the largest Feature Id in the SurfaceMeshFaceLabels array").arg(numFeaturesIn);
setErrorCondition(-5555);
notifyErrorMessage(getHumanLabel(), ss, getErrorCondition());
return;
}
FloatVec3_t latticeConstants;
latticeConstants.x = m_LatticeConstants.x / 10000.0;
latticeConstants.y = m_LatticeConstants.y / 10000.0;
latticeConstants.z = m_LatticeConstants.z / 10000.0;
DataContainer::Pointer sm = getDataContainerArray()->getDataContainer(getSurfaceMeshFaceLabelsArrayPath().getDataContainerName());
SIMPL_RANDOMNG_NEW()
#ifdef SIMPLib_USE_PARALLEL_ALGORITHMS
tbb::task_scheduler_init init;
bool doParallel = true;
#endif
// pull down faces
TriangleGeom::Pointer triangleGeom = sm->getGeometryAs<TriangleGeom>();
int64_t numFaces = m_SurfaceMeshFaceLabelsPtr.lock()->getNumberOfTuples();
// create array to hold bounding vertices for each face
FloatArrayType::Pointer llPtr = FloatArrayType::CreateArray(3, "Lower_Left_Internal_Use_Only");
FloatArrayType::Pointer urPtr = FloatArrayType::CreateArray(3, "Upper_Right_Internal_Use_Only");
float* ll = llPtr->getPointer(0);
float* ur = urPtr->getPointer(0);
VertexGeom::Pointer faceBBs = VertexGeom::CreateGeometry(2 * numFaces, "faceBBs");
// walk through faces to see how many features there are
int32_t g1 = 0, g2 = 0;
int32_t maxFeatureId = 0;
for (int64_t i = 0; i < numFaces; i++)
{
g1 = m_SurfaceMeshFaceLabels[2 * i];
g2 = m_SurfaceMeshFaceLabels[2 * i + 1];
if (g1 > maxFeatureId) { maxFeatureId = g1; }
if (g2 > maxFeatureId) { maxFeatureId = g2; }
}
// add one to account for feature 0
int32_t numFeatures = maxFeatureId + 1;
// create a dynamic list array to hold face lists
Int32Int32DynamicListArray::Pointer faceLists = Int32Int32DynamicListArray::New();
QVector<int32_t> linkCount(numFeatures, 0);
// fill out lists with number of references to cells
typedef boost::shared_array<int32_t> SharedInt32Array_t;
SharedInt32Array_t linkLocPtr(new int32_t[numFaces]);
int32_t* linkLoc = linkLocPtr.get();
::memset(linkLoc, 0, numFaces * sizeof(int32_t));
// traverse data to determine number of faces belonging to each feature
for (int64_t i = 0; i < numFaces; i++)
{
g1 = m_SurfaceMeshFaceLabels[2 * i];
g2 = m_SurfaceMeshFaceLabels[2 * i + 1];
if (g1 > 0) { linkCount[g1]++; }
if (g2 > 0) { linkCount[g2]++; }
}
// now allocate storage for the faces
faceLists->allocateLists(linkCount);
// traverse data again to get the faces belonging to each feature
for (int64_t i = 0; i < numFaces; i++)
{
g1 = m_SurfaceMeshFaceLabels[2 * i];
g2 = m_SurfaceMeshFaceLabels[2 * i + 1];
if (g1 > 0) { faceLists->insertCellReference(g1, (linkLoc[g1])++, i); }
if (g2 > 0) { faceLists->insertCellReference(g2, (linkLoc[g2])++, i); }
// find bounding box for each face
GeometryMath::FindBoundingBoxOfFace(triangleGeom, i, ll, ur);
faceBBs->setCoords(2 * i, ll);
faceBBs->setCoords(2 * i + 1, ur);
}
// generate the list of sampling points fom subclass
QVector<VertexGeom::Pointer> points(numFeatures);
QVector<BoolArrayType::Pointer> inFeature(numFeatures);
for (int32_t i = 0; i < numFeatures; i++)
{
points[i] = VertexGeom::CreateGeometry(0, "_INTERNAL_USE_ONLY_points");
inFeature[i] = BoolArrayType::CreateArray(0, "_INTERNAL_USE_ONLY_inside");
}
QuatF* avgQuats = reinterpret_cast<QuatF*>(m_AvgQuats);
#ifdef SIMPLib_USE_PARALLEL_ALGORITHMS
if (doParallel == true)
{
tbb::parallel_for(tbb::blocked_range<size_t>(0, numFeatures),
InsertAtomsImpl(triangleGeom, faceLists, faceBBs, avgQuats, latticeConstants, m_Basis, points, inFeature), tbb::auto_partitioner());
}
else
#endif
{
InsertAtomsImpl serial(triangleGeom, faceLists, faceBBs, avgQuats, latticeConstants, m_Basis, points, inFeature);
serial.checkPoints(0, numFeatures);
}
assign_points(points, inFeature);
notifyStatusMessage(getHumanLabel(), "Complete");
}
// -----------------------------------------------------------------------------
//
// -----------------------------------------------------------------------------
void SharedFeatureFaceFilter::readFilterParameters(AbstractFilterParametersReader* reader, int index)
{
reader->openFilterGroup(this, index);
setFaceFeatureAttributeMatrixName(reader->readString("FaceFeatureAttributeMatrixName", getFaceFeatureAttributeMatrixName() ) );
setSurfaceMeshFeatureFaceIdsArrayName(reader->readString("SurfaceMeshFeatureFaceIdsArrayName", getSurfaceMeshFeatureFaceIdsArrayName() ) );
setSurfaceMeshFeatureFaceLabelsArrayName(reader->readString("SurfaceMeshFeatureFaceLabelsArrayName", getSurfaceMeshFeatureFaceLabelsArrayName() ) );
setSurfaceMeshFeatureFaceNumTrianglesArrayName(reader->readString("SurfaceMeshFeatureFaceNumTrianglesArrayName", getSurfaceMeshFeatureFaceNumTrianglesArrayName() ) );
setSurfaceMeshFaceLabelsArrayPath(reader->readDataArrayPath("SurfaceMeshFaceLabelsArrayPath", getSurfaceMeshFaceLabelsArrayPath() ) );
reader->closeFilterGroup();
}
