Beispiel #1
0
// -----------------------------------------------------------------------------
//
// -----------------------------------------------------------------------------
void InsertAtoms::assign_points(QVector<VertexGeom::Pointer> points, QVector<BoolArrayType::Pointer> inFeature)
{
  size_t count = 0;
  int32_t numFeatures = points.size();
  for (int32_t i = 0; i < numFeatures; i++)
  {
    int64_t numPoints = points[i]->getNumberOfVertices();
    bool* inside = inFeature[i]->getPointer(0);
    for (int64_t j = 0; j < numPoints; j++)
    {
      if (inside[j] == true) { count++; }
    }
  }

  DataContainer::Pointer v = getDataContainerArray()->getDataContainer(getVertexDataContainerName());
  VertexGeom::Pointer vertices = VertexGeom::CreateGeometry(count, DREAM3D::VertexData::SurfaceMeshNodes);

  AttributeMatrix::Pointer vertexAttrMat = v->getAttributeMatrix(getVertexAttributeMatrixName());
  QVector<size_t> tDims(1, count);
  vertexAttrMat->resizeAttributeArrays(tDims);
  updateVertexInstancePointers();

  count = 0;
  float coords[3] = { 0.0f, 0.0f, 0.0f };
  for (int32_t i = 0; i < numFeatures; i++)
  {
    int64_t numPoints = points[i]->getNumberOfVertices();
    bool* inside = inFeature[i]->getPointer(0);
    for (int64_t j = 0; j < numPoints; j++)
    {
      if (inside[j] == true)
      {
        coords[0] = points[i]->getVertexPointer(j)[0];
        coords[1] = points[i]->getVertexPointer(j)[1];
        coords[2] = points[i]->getVertexPointer(j)[2];
        vertices->setCoords(count, coords);
        m_AtomFeatureLabels[count] = i;
        count++;
      }
    }
  }
  v->setGeometry(vertices);
}
// -----------------------------------------------------------------------------
//
// -----------------------------------------------------------------------------
VertexGeom::Pointer RegularGridSampleSurfaceMesh::generate_points()
{
  VertexGeom::Pointer points = VertexGeom::CreateGeometry((m_XPoints * m_YPoints * m_ZPoints), "_INTERNAL_USE_ONLY_points");

  int64_t count = 0;
  float coords[3] = { 0.0f, 0.0f, 0.0f };
  for (int64_t k = 0; k < m_ZPoints; k++)
  {
    for (int64_t j = 0; j < m_YPoints; j++)
    {
      for (int64_t i = 0; i < m_XPoints; i++)
      {
        coords[0] = (float(i) + 0.5f) * m_Resolution.x + m_Origin.x;
        coords[1] = (float(j) + 0.5f) * m_Resolution.y + m_Origin.y;
        coords[2] = (float(k) + 0.5f) * m_Resolution.z + m_Origin.z;
        points->setCoords(count, coords);
        count++;
      }
    }
  }

  return points;
}
Beispiel #3
0
// -----------------------------------------------------------------------------
//
// -----------------------------------------------------------------------------
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");
}
Beispiel #4
0
// -----------------------------------------------------------------------------
//
// -----------------------------------------------------------------------------
void SampleSurfaceMesh::execute()
{
  setErrorCondition(0);
  dataCheck();
  if(getErrorCondition() < 0) { return; }

  DataContainer::Pointer sm = getDataContainerArray()->getDataContainer(m_SurfaceMeshFaceLabelsArrayPath.getDataContainerName());
  SIMPL_RANDOMNG_NEW()

#ifdef SIMPLib_USE_PARALLEL_ALGORITHMS
  tbb::task_scheduler_init init;
  bool doParallel = true;
#endif

  TriangleGeom::Pointer triangleGeom = sm->getGeometryAs<TriangleGeom>();

  // pull down faces
  int64_t numFaces = m_SurfaceMeshFaceLabelsPtr.lock()->getNumberOfTuples();

  // create array to hold bounding vertices for each face
  FloatArrayType::Pointer llPtr = FloatArrayType::CreateArray(3, "_INTERNAL_USE_ONLY_Lower_Left");
  FloatArrayType::Pointer urPtr = FloatArrayType::CreateArray(3, "_INTERNAL_USE_ONLY_Upper_Right");
  float* ll = llPtr->getPointer(0);
  float* ur = urPtr->getPointer(0);
  VertexGeom::Pointer faceBBs = VertexGeom::CreateGeometry(2 * numFaces, "_INTERNAL_USE_ONLY_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();
  std::vector<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 from subclass
  VertexGeom::Pointer points = generate_points();
  if(getErrorCondition() < 0 || NULL == points.get()) { return; }
  int64_t numPoints = points->getNumberOfVertices();

  // create array to hold which polyhedron (feature) each point falls in
  Int32ArrayType::Pointer iArray = Int32ArrayType::NullPointer();
  iArray = Int32ArrayType::CreateArray(numPoints, "_INTERNAL_USE_ONLY_polyhedronIds");
  iArray->initializeWithZeros();
  int32_t* polyIds = iArray->getPointer(0);

#ifdef SIMPLib_USE_PARALLEL_ALGORITHMS
  if (doParallel == true)
  {
    tbb::parallel_for(tbb::blocked_range<size_t>(0, numFeatures),
                      SampleSurfaceMeshImpl(triangleGeom, faceLists, faceBBs, points, polyIds), tbb::auto_partitioner());
  }
  else
#endif
  {
    SampleSurfaceMeshImpl serial(triangleGeom, faceLists, faceBBs, points, polyIds);
    serial.checkPoints(0, numFeatures);
  }

  assign_points(iArray);

  notifyStatusMessage(getHumanLabel(), "Complete");
}