// -----------------------------------------------------------------------------
//
// -----------------------------------------------------------------------------
int VertexGeom::writeXdmf(QTextStream& out, QString dcName, QString hdfFileName)
{
  herr_t err = 0;

  // Always start the grid
  out << "  <!-- *************** START OF " << dcName << " *************** -->" << "\n";
  out << "  <Grid Name=\"" << dcName << "\" GridType=\"Uniform\">" << "\n";

#if 0
  DataArrayPath dap = getTemporalDataPath();
  if(dap.isValid())
  {
    IDataArray::Pointer timeValues = getAttributeMatrix(dap.getAttributeMatrixName())->getAttributeArray(dap.getDataArrayName());
    Int32ArrayType::Pointer timeValuePtr = boost::dynamic_pointer_cast<Int32ArrayType>(timeValues);
    out << "    <Time TimeType=\"Single\" Value=\"" << timeValuePtr->getValue(0) << "\"/>\n";
  }
#endif

  out << "    <Topology TopologyType=\"Polyvertex\" NumberOfElements=\"" << getNumberOfVertices() << "\">" << "\n";
  out << "      <DataItem Format=\"HDF\" NumberType=\"Int\" Dimensions=\"" << getNumberOfVertices() << "\">" << "\n";
  out << "        " << hdfFileName << ":/DataContainers/" << dcName << "/" << DREAM3D::Geometry::Geometry << "/" << "Verts" << "\n";
  out << "      </DataItem>" << "\n";
  out << "    </Topology>" << "\n";

  out << "    <Geometry Type=\"XYZ\">" << "\n";
  out << "      <DataItem Format=\"HDF\"  Dimensions=\"" << getNumberOfVertices() << " 3\" NumberType=\"Float\" Precision=\"4\">" << "\n";
  out << "        " << hdfFileName << ":/DataContainers/" << dcName << "/" << DREAM3D::Geometry::Geometry << "/" << DREAM3D::Geometry::SharedVertexList << "\n";
  out << "      </DataItem>" << "\n";
  out << "    </Geometry>" << "\n";
  out << "" << "\n";

  return err;
}

// -----------------------------------------------------------------------------
//
// -----------------------------------------------------------------------------
void AbaqusSurfaceMeshWriter::execute()
{
  int err = 0;
  std::stringstream ss;

  SurfaceMeshDataContainer* sm = getSurfaceMeshDataContainer();
  dataCheck(false, 1, 1, 1);
  if(getErrorCondition() < 0)
  {
    return;
  }

  // Make sure any directory path is also available as the user may have just typed
  // in a path without actually creating the full path
  std::string parentPath = MXAFileInfo::parentPath(getOutputFile());
  if(!MXADir::mkdir(parentPath, true))
  {
    std::stringstream ss;
    ss << "Error creating parent path '" << parentPath << "'";
    notifyErrorMessage(ss.str(), -1);
    setErrorCondition(-1);
    return;
  }

  DREAM3D::SurfaceMesh::VertListPointer_t nodesPtr = sm->getVertices();
  DREAM3D::SurfaceMesh::FaceListPointer_t trianglePtr = sm->getFaces();

  // Get the Labels(GrainIds or Region Ids) for the triangles
  Int32ArrayType::Pointer faceLabelsPtr = boost::dynamic_pointer_cast<Int32ArrayType>(sm->getFaceData(DREAM3D::FaceData::SurfaceMeshFaceLabels));
  int32_t* faceLabels = faceLabelsPtr->GetPointer(0);

  // Store all the unique Spins
  std::set<int> uniqueSpins;
  for (int i = 0; i < trianglePtr->GetNumberOfTuples(); i++)
  {
    uniqueSpins.insert(faceLabels[i*2]);
    uniqueSpins.insert(faceLabels[i*2+1]);
  }

  FILE* f = fopen(m_OutputFile.c_str(), "wb");
  ScopedFileMonitor fileMonitor(f);

  err = writeHeader(f, nodesPtr->GetNumberOfTuples(), trianglePtr->GetNumberOfTuples(), uniqueSpins.size()-1);
  err = writeNodes(f);
  err = writeTriangles(f);
  err = writeGrains(f);

  setErrorCondition(0);
  notifyStatusMessage("Complete");

  return;
}

// -----------------------------------------------------------------------------
//
// -----------------------------------------------------------------------------
void ReadH5Ebsd::copyHEDMArrays(H5EbsdVolumeReader* ebsdReader)
{
  float* f1 = NULL;
  float* f2 = NULL;
  float* f3 = NULL;
  int* phasePtr = NULL;

  FloatArrayType::Pointer fArray = FloatArrayType::NullPointer();
  Int32ArrayType::Pointer iArray = Int32ArrayType::NullPointer();
  VoxelDataContainer* m = getVoxelDataContainer();
  int64_t totalPoints = m->getTotalPoints();


  if (m_SelectedVoxelCellArrays.find(m_CellEulerAnglesArrayName) != m_SelectedVoxelCellArrays.end() )
  {
    //  radianconversion = M_PI / 180.0;
    f1 = reinterpret_cast<float*>(ebsdReader->getPointerByName(Ebsd::Mic::Euler1));
    f2 = reinterpret_cast<float*>(ebsdReader->getPointerByName(Ebsd::Mic::Euler2));
    f3 = reinterpret_cast<float*>(ebsdReader->getPointerByName(Ebsd::Mic::Euler3));
    fArray = FloatArrayType::CreateArray(totalPoints * 3, DREAM3D::CellData::EulerAngles);
    fArray->SetNumberOfComponents(3);
    float* cellEulerAngles = fArray->GetPointer(0);
    for (int64_t i = 0; i < totalPoints; i++)
    {
      cellEulerAngles[3 * i] = f1[i];
      cellEulerAngles[3 * i + 1] = f2[i];
      cellEulerAngles[3 * i + 2] = f3[i];
    }
    m->addCellData(DREAM3D::CellData::EulerAngles, fArray);
  }

  if (m_SelectedVoxelCellArrays.find(m_CellPhasesArrayName) != m_SelectedVoxelCellArrays.end() )
  {
    phasePtr = reinterpret_cast<int*>(ebsdReader->getPointerByName(Ebsd::Mic::Phase));
    iArray = Int32ArrayType::CreateArray(totalPoints, DREAM3D::CellData::Phases);
    iArray->SetNumberOfComponents(1);
    ::memcpy(iArray->GetPointer(0), phasePtr, sizeof(int32_t) * totalPoints);
    m->addCellData(DREAM3D::CellData::Phases, iArray);
  }

  if (m_SelectedVoxelCellArrays.find(Ebsd::Mic::Confidence) != m_SelectedVoxelCellArrays.end() )
  {
    f1 = reinterpret_cast<float*>(ebsdReader->getPointerByName(Ebsd::Mic::Confidence));
    fArray = FloatArrayType::CreateArray(totalPoints, Ebsd::Mic::Confidence);
    fArray->SetNumberOfComponents(1);
    ::memcpy(fArray->GetPointer(0), f1, sizeof(float) * totalPoints);
    m->addCellData(Ebsd::Mic::Confidence, fArray);
  }
}

// -----------------------------------------------------------------------------
//
// -----------------------------------------------------------------------------
void RegularGridSampleSurfaceMesh::assign_points(Int32ArrayType::Pointer iArray)
{
  int32_t* ids = iArray->getPointer(0);
  for (int64_t i = 0; i < (m_XPoints * m_YPoints * m_ZPoints); i++)
  {
    m_FeatureIds[i] = ids[i];
  }
}

// -----------------------------------------------------------------------------
//
// -----------------------------------------------------------------------------
  void TestDataArray()
  {
    int32_t* ptr = NULL;
    {
      Int32ArrayType::Pointer d = Int32ArrayType::CreateArray(0, "Test7");
      DREAM3D_REQUIRE_EQUAL(0, d->getSize());
      DREAM3D_REQUIRE_EQUAL(0, d->getNumberOfTuples());
      ptr = d->getPointer(0);
      DREAM3D_REQUIRE_EQUAL(ptr, 0);
      DREAM3D_REQUIRE_EQUAL(d->isAllocated(), false);
    }

    {
      QVector<size_t> dims(1, NUM_COMPONENTS);
      Int32ArrayType::Pointer int32Array = Int32ArrayType::CreateArray(NUM_ELEMENTS, dims, "Test8");
      ptr = int32Array->getPointer(0);
      DREAM3D_REQUIRE_EQUAL(int32Array->isAllocated(), true);
      DREAM3D_REQUIRE_EQUAL(NUM_ELEMENTS, int32Array->getNumberOfTuples());
      DREAM3D_REQUIRE_EQUAL(NUM_ELEMENTS * NUM_COMPONENTS, int32Array->getSize());

      for (int i = 0; i < NUM_TUPLES; ++i)
      {
        for (int c = 0; c < NUM_COMPONENTS; ++c)
        {
          int32Array->setComponent(i, c, i + c);
        }
      }

      // Resize Larger
      int32Array->resize(NUM_TUPLES_2);
      DREAM3D_REQUIRE_EQUAL(NUM_TUPLES_2, int32Array->getNumberOfTuples());
      DREAM3D_REQUIRE_EQUAL(NUM_ELEMENTS_2, int32Array->getSize());
      DREAM3D_REQUIRE_EQUAL(int32Array->isAllocated(), true);

      // This should have saved our data so lets look at the data and compare it
      for (int i = 0; i < NUM_TUPLES; ++i)
      {
        for (int c = 0; c < NUM_COMPONENTS; ++c)
        {
          DREAM3D_REQUIRE_EQUAL( (int32Array->getComponent(i, c)), (i + c))
        }
      }

      // Resize Smaller - Which should have still saved some of our data
      int32Array->resize(NUM_TUPLES_3);
      DREAM3D_REQUIRE_EQUAL(NUM_TUPLES_3, int32Array->getNumberOfTuples());
      DREAM3D_REQUIRE_EQUAL(NUM_ELEMENTS_3, int32Array->getSize());
      DREAM3D_REQUIRE_EQUAL(int32Array->isAllocated(), true);

      // This should have saved our data so lets look at the data and compare it
      for (int i = 0; i < NUM_TUPLES; ++i)
      {
        for (int c = 0; c < NUM_COMPONENTS; ++c)
        {
          DREAM3D_REQUIRE_EQUAL( (int32Array->getComponent(i, c)), (i + c))
        }
      }

      // Change number of components
      //    dims[0] = NUM_COMPONENTS_4;
      //    int32Array->setDims(dims);
      //    DREAM3D_REQUIRE_EQUAL(NUM_TUPLES_4, int32Array->getNumberOfTuples());
      //    DREAM3D_REQUIRE_EQUAL(NUM_ELEMENTS_4, int32Array->getSize());

      double temp = 9999;
      int32Array->initializeTuple(0, temp );
      for (int c = 0; c < NUM_COMPONENTS; ++c)
      {
        DREAM3D_REQUIRE_EQUAL( (int32Array->getComponent(0, c)), (9999))
      }


      ptr = int32Array->getPointer(0);
    }

  }

// -----------------------------------------------------------------------------
//
// -----------------------------------------------------------------------------
void VisualizeGBCDPoleFigure::execute()
{
  setErrorCondition(0);
  dataCheck();
  if(getErrorCondition() < 0) { return; }

  // Make sure any directory path is also available as the user may have just typed
  // in a path without actually creating the full path
  QFileInfo fi(getOutputFile());

  QDir dir(fi.path());
  if(!dir.mkpath("."))
  {
    QString ss;
    ss = QObject::tr("Error creating parent path '%1'").arg(dir.path());
    setErrorCondition(-1);
    notifyErrorMessage(getHumanLabel(), ss, getErrorCondition());
    return;
  }

  QFile file(getOutputFile());
  if (!file.open(QIODevice::WriteOnly | QIODevice::Text))
  {
    QString ss = QObject::tr("Error opening output file '%1'").arg(getOutputFile());
    setErrorCondition(-100);
    notifyErrorMessage(getHumanLabel(), ss, getErrorCondition());
    return;
  }

  FloatArrayType::Pointer gbcdDeltasArray = FloatArrayType::CreateArray(5, "GBCDDeltas");
  gbcdDeltasArray->initializeWithZeros();

  FloatArrayType::Pointer gbcdLimitsArray = FloatArrayType::CreateArray(10, "GBCDLimits");
  gbcdLimitsArray->initializeWithZeros();

  Int32ArrayType::Pointer gbcdSizesArray = Int32ArrayType::CreateArray(5, "GBCDSizes");
  gbcdSizesArray->initializeWithZeros();

  float* gbcdDeltas = gbcdDeltasArray->getPointer(0);
  int* gbcdSizes = gbcdSizesArray->getPointer(0);
  float* gbcdLimits = gbcdLimitsArray->getPointer(0);

  // Original Ranges from Dave R.
  //m_GBCDlimits[0] = 0.0f;
  //m_GBCDlimits[1] = cosf(1.0f*m_pi);
  //m_GBCDlimits[2] = 0.0f;
  //m_GBCDlimits[3] = 0.0f;
  //m_GBCDlimits[4] = cosf(1.0f*m_pi);
  //m_GBCDlimits[5] = 2.0f*m_pi;
  //m_GBCDlimits[6] = cosf(0.0f);
  //m_GBCDlimits[7] = 2.0f*m_pi;
  //m_GBCDlimits[8] = 2.0f*m_pi;
  //m_GBCDlimits[9] = cosf(0.0f);

  // Greg R. Ranges
  gbcdLimits[0] = 0.0f;
  gbcdLimits[1] = 0.0f;
  gbcdLimits[2] = 0.0f;
  gbcdLimits[3] = 0.0f;
  gbcdLimits[4] = 0.0f;
  gbcdLimits[5] = SIMPLib::Constants::k_PiOver2;
  gbcdLimits[6] = 1.0f;
  gbcdLimits[7] = SIMPLib::Constants::k_PiOver2;
  gbcdLimits[8] = 1.0f;
  gbcdLimits[9] = SIMPLib::Constants::k_2Pi;

  // reset the 3rd and 4th dimensions using the square grid approach
  gbcdLimits[3] = -sqrtf(SIMPLib::Constants::k_PiOver2);
  gbcdLimits[4] = -sqrtf(SIMPLib::Constants::k_PiOver2);
  gbcdLimits[8] = sqrtf(SIMPLib::Constants::k_PiOver2);
  gbcdLimits[9] = sqrtf(SIMPLib::Constants::k_PiOver2);

  // get num components of GBCD
  QVector<size_t> cDims = m_GBCDPtr.lock()->getComponentDimensions();

  gbcdSizes[0] = cDims[0];
  gbcdSizes[1] = cDims[1];
  gbcdSizes[2] = cDims[2];
  gbcdSizes[3] = cDims[3];
  gbcdSizes[4] = cDims[4];

  gbcdDeltas[0] = (gbcdLimits[5] - gbcdLimits[0]) / float(gbcdSizes[0]);
  gbcdDeltas[1] = (gbcdLimits[6] - gbcdLimits[1]) / float(gbcdSizes[1]);
  gbcdDeltas[2] = (gbcdLimits[7] - gbcdLimits[2]) / float(gbcdSizes[2]);
  gbcdDeltas[3] = (gbcdLimits[8] - gbcdLimits[3]) / float(gbcdSizes[3]);
  gbcdDeltas[4] = (gbcdLimits[9] - gbcdLimits[4]) / float(gbcdSizes[4]);

  float vec[3] = { 0.0f, 0.0f, 0.0f };
  float vec2[3] = { 0.0f, 0.0f, 0.0f };
  float rotNormal[3] = { 0.0f, 0.0f, 0.0f };
  float rotNormal2[3] = { 0.0f, 0.0f, 0.0f };
  float sqCoord[2] = { 0.0f, 0.0f };
  float dg[3][3] = { { 0.0f, 0.0f, 0.0f }, { 0.0f, 0.0f, 0.0f } };
  float dgt[3][3] = { { 0.0f, 0.0f, 0.0f }, { 0.0f, 0.0f, 0.0f } };
  float dg1[3][3] = { { 0.0f, 0.0f, 0.0f }, { 0.0f, 0.0f, 0.0f } };
  float dg2[3][3] = { { 0.0f, 0.0f, 0.0f }, { 0.0f, 0.0f, 0.0f } };
  float sym1[3][3] = { { 0.0f, 0.0f, 0.0f }, { 0.0f, 0.0f, 0.0f } };
//.........这里部分代码省略.........

    void generate(size_t start, size_t end) const
    {

      // We want to work with the raw pointers for speed so get those pointers.
      float* m_GBCDdeltas = m_GbcdDeltasArray->getPointer(0);
      float* m_GBCDlimits = m_GbcdLimitsArray->getPointer(0);
      int* m_GBCDsizes = m_GbcdSizesArray->getPointer(0);
      int32_t* m_Bins = m_GbcdBinsArray->getPointer(0);
      bool* m_HemiCheck = m_GbcdHemiCheckArray->getPointer(0);

      int32_t* m_Labels = m_LabelsArray->getPointer(0);
      double* m_Normals = m_NormalsArray->getPointer(0);
      int32_t* m_Phases = m_PhasesArray->getPointer(0);
      float* m_Eulers = m_EulersArray->getPointer(0);
      uint32_t* m_CrystalStructures = m_CrystalStructuresArray->getPointer(0);


      int32_t j = 0;//, j4;
      int32_t k = 0;//, k4;
      int32_t m = 0;
      int32_t temp = 0;
      //bool gbcd_indices_good;
      int32_t feature1 = 0, feature2 = 0;
      int32_t inversion = 1;
      float g1ea[3] = { 0.0f, 0.0f, 0.0f }, g2ea[3] = { 0.0f, 0.0f, 0.0f };
      float g1[3][3] = { { 0.0f, 0.0f, 0.0f }, { 0.0f, 0.0f, 0.0f } }, g2[3][3] = { { 0.0f, 0.0f, 0.0f }, { 0.0f, 0.0f, 0.0f } };
      float g1s[3][3] = { { 0.0f, 0.0f, 0.0f }, { 0.0f, 0.0f, 0.0f } }, g2s[3][3] = { { 0.0f, 0.0f, 0.0f }, { 0.0f, 0.0f, 0.0f } };
      float sym1[3][3] = { { 0.0f, 0.0f, 0.0f }, { 0.0f, 0.0f, 0.0f } }, sym2[3][3] = { { 0.0f, 0.0f, 0.0f }, { 0.0f, 0.0f, 0.0f } };
      float g2t[3][3] = { { 0.0f, 0.0f, 0.0f }, { 0.0f, 0.0f, 0.0f } }, dg[3][3] = { { 0.0f, 0.0f, 0.0f }, { 0.0f, 0.0f, 0.0f } };
      float euler_mis[3] = { 0.0f, 0.0f, 0.0f };
      float normal[3] = { 0.0f, 0.0f, 0.0f };
      float xstl1_norm1[3] = { 0.0f, 0.0f, 0.0f };
      int32_t gbcd_index = 0;
      float sqCoord[2] = { 0.0f, 0.0f }, sqCoordInv[2] = { 0.0f, 0.0f };
      bool nhCheck = false, nhCheckInv = true;
      int32_t SYMcounter = 0;
      int64_t TRIcounter = static_cast<int64_t>(start - startOffset);
      int64_t TRIcounterShift = 0;

      for (size_t i = start; i < end; i++)
      {
        SYMcounter = 0;
        feature1 = m_Labels[2 * i];
        feature2 = m_Labels[2 * i + 1];
        normal[0] = m_Normals[3 * i];
        normal[1] = m_Normals[3 * i + 1];
        normal[2] = m_Normals[3 * i + 2];

        if (feature1 < 0 || feature2 < 0) { continue; }

        if (m_Phases[feature1] == m_Phases[feature2] && m_Phases[feature1] > 0)
        {
          TRIcounterShift = (TRIcounter * numEntriesPerTri);
          uint32_t cryst = m_CrystalStructures[m_Phases[feature1]];
          for (int32_t q = 0; q < 2; q++)
          {
            if (q == 1)
            {
              temp = feature1;
              feature1 = feature2;
              feature2 = temp;
              normal[0] = -normal[0];
              normal[1] = -normal[1];
              normal[2] = -normal[2];
            }
            for (m = 0; m < 3; m++)
            {
              g1ea[m] = m_Eulers[3 * feature1 + m];
              g2ea[m] = m_Eulers[3 * feature2 + m];
            }

            FOrientArrayType om(9, 0.0f);
            FOrientTransformsType::eu2om(FOrientArrayType(g1ea, 3), om);
            om.toGMatrix(g1);

            FOrientTransformsType::eu2om(FOrientArrayType(g2ea, 3), om);
            om.toGMatrix(g2);

            int32_t nsym = m_OrientationOps[cryst]->getNumSymOps();
            for (j = 0; j < nsym; j++)
            {
              // rotate g1 by symOp
              m_OrientationOps[cryst]->getMatSymOp(j, sym1);
              MatrixMath::Multiply3x3with3x3(sym1, g1, g1s);
              // get the crystal directions along the triangle normals
              MatrixMath::Multiply3x3with3x1(g1s, normal, xstl1_norm1);
              // get coordinates in square projection of crystal normal parallel to boundary normal
              nhCheck = getSquareCoord(xstl1_norm1, sqCoord);
              if (inversion == 1)
              {
                sqCoordInv[0] = -sqCoord[0];
                sqCoordInv[1] = -sqCoord[1];
                if (nhCheck == false) { nhCheckInv = true; }
                else { nhCheckInv = false; }
              }

              for (k = 0; k < nsym; k++)
              {
                // calculate the symmetric misorienation
                m_OrientationOps[cryst]->getMatSymOp(k, sym2);
//.........这里部分代码省略.........

// -----------------------------------------------------------------------------
//
// -----------------------------------------------------------------------------
void ErodeDilateBadData::execute()
{
  setErrorCondition(0);
  dataCheck();
  if(getErrorCondition() < 0) { return; }

  DataContainer::Pointer m = getDataContainerArray()->getDataContainer(getFeatureIdsArrayPath().getDataContainerName());
  size_t totalPoints = m_FeatureIdsPtr.lock()->getNumberOfTuples();

  Int32ArrayType::Pointer neighborsPtr = Int32ArrayType::CreateArray(totalPoints, "_INTERNAL_USE_ONLY_Neighbors");
  m_Neighbors = neighborsPtr->getPointer(0);
  neighborsPtr->initializeWithValue(-1);

  size_t udims[3] = {0, 0, 0};
  m->getGeometryAs<ImageGeom>()->getDimensions(udims);
#if (CMP_SIZEOF_SIZE_T == 4)
  typedef int32_t DimType;
#else
  typedef int64_t DimType;
#endif
  DimType dims[3] =
  {
    static_cast<DimType>(udims[0]),
    static_cast<DimType>(udims[1]),
    static_cast<DimType>(udims[2]),
  };

  int32_t good = 1;
  int64_t count = 0;
  int64_t kstride = 0, jstride = 0;
  int32_t featurename = 0, feature = 0;
  int32_t current = 0;
  int32_t most = 0;
  int64_t neighpoint = 0;
  size_t numfeatures = 0;

  for (size_t i = 0; i < totalPoints; i++)
  {
    featurename = m_FeatureIds[i];
    if (featurename > numfeatures) { numfeatures = featurename; }
  }

  DimType neighpoints[6] = { 0, 0, 0, 0, 0, 0 };
  neighpoints[0] = -dims[0] * dims[1];
  neighpoints[1] = -dims[0];
  neighpoints[2] = -1;
  neighpoints[3] = 1;
  neighpoints[4] = dims[0];
  neighpoints[5] = dims[0] * dims[1];

  QVector<int32_t> n(numfeatures + 1, 0);

  for (int32_t iteration = 0; iteration < m_NumIterations; iteration++)
  {
    for (DimType k = 0; k < dims[2]; k++)
    {
      kstride = dims[0] * dims[1] * k;
      for (DimType j = 0; j < dims[1]; j++)
      {
        jstride = dims[0] * j;
        for (DimType i = 0; i < dims[0]; i++)
        {
          count = kstride + jstride + i;
          featurename = m_FeatureIds[count];
          if (featurename == 0)
          {
            current = 0;
            most = 0;
            for (int32_t l = 0; l < 6; l++)
            {
              good = 1;
              neighpoint = count + neighpoints[l];
              if (l == 0 && (k == 0 || m_ZDirOn == false)) { good = 0; }
              else if (l == 5 && (k == (dims[2] - 1) || m_ZDirOn == false)) { good = 0; }
              else if (l == 1 && (j == 0 || m_YDirOn == false)) { good = 0; }
              else if (l == 4 && (j == (dims[1] - 1) || m_YDirOn == false)) { good = 0; }
              else if (l == 2 && (i == 0 || m_XDirOn == false)) { good = 0; }
              else if (l == 3 && (i == (dims[0] - 1) || m_XDirOn == false)) { good = 0; }
              if (good == 1)
              {
                feature = m_FeatureIds[neighpoint];
                if (m_Direction == 0 && feature > 0)
                {
                  m_Neighbors[neighpoint] = count;
                }
                if (feature > 0 && m_Direction == 1)
                {
                  n[feature]++;
                  current = n[feature];
                  if (current > most)
                  {
                    most = current;
                    m_Neighbors[count] = neighpoint;
                  }
                }
              }
            }
//.........这里部分代码省略.........

// -----------------------------------------------------------------------------
//
// -----------------------------------------------------------------------------
void VisualizeGBCDGMT::execute()
{
  setErrorCondition(0);
  dataCheck();
  if(getErrorCondition() < 0) { return; }

  DataContainer::Pointer sm = getDataContainerArray()->getDataContainer(getGBCDArrayPath().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 dir(fi.path());
  if (!dir.mkpath("."))
  {
    QString ss;
    ss = QObject::tr("Error creating parent path '%1'").arg(dir.path());
    setErrorCondition(-1);
    notifyErrorMessage(getHumanLabel(), ss, getErrorCondition());
    return;
  }

  QFile file(getOutputFile());
  if (!file.open(QIODevice::WriteOnly | QIODevice::Text))
  {
    QString ss = QObject::tr("Error opening output file '%1'").arg(getOutputFile());
    setErrorCondition(-100);
    notifyErrorMessage(getHumanLabel(), ss, getErrorCondition());
    return;
  }

  FloatArrayType::Pointer gbcdDeltasArray = FloatArrayType::CreateArray(5, "GBCDDeltas");
  gbcdDeltasArray->initializeWithZeros();

  FloatArrayType::Pointer gbcdLimitsArray = FloatArrayType::CreateArray(10, "GBCDLimits");
  gbcdLimitsArray->initializeWithZeros();

  Int32ArrayType::Pointer gbcdSizesArray = Int32ArrayType::CreateArray(5, "GBCDSizes");
  gbcdSizesArray->initializeWithZeros();

  float* gbcdDeltas = gbcdDeltasArray->getPointer(0);
  int32_t* gbcdSizes = gbcdSizesArray->getPointer(0);
  float* gbcdLimits = gbcdLimitsArray->getPointer(0);

  // Original Ranges from Dave R.
  //m_GBCDlimits[0] = 0.0f;
  //m_GBCDlimits[1] = cosf(1.0f*m_pi);
  //m_GBCDlimits[2] = 0.0f;
  //m_GBCDlimits[3] = 0.0f;
  //m_GBCDlimits[4] = cosf(1.0f*m_pi);
  //m_GBCDlimits[5] = 2.0f*m_pi;
  //m_GBCDlimits[6] = cosf(0.0f);
  //m_GBCDlimits[7] = 2.0f*m_pi;
  //m_GBCDlimits[8] = 2.0f*m_pi;
  //m_GBCDlimits[9] = cosf(0.0f);

  // Greg R. Ranges
  gbcdLimits[0] = 0.0f;
  gbcdLimits[1] = 0.0f;
  gbcdLimits[2] = 0.0f;
  gbcdLimits[3] = -sqrtf(SIMPLib::Constants::k_Pi / 2.0f);
  gbcdLimits[4] = -sqrtf(SIMPLib::Constants::k_Pi / 2.0f);
  gbcdLimits[5] = SIMPLib::Constants::k_Pi / 2.0f;
  gbcdLimits[6] = 1.0f;
  gbcdLimits[7] = SIMPLib::Constants::k_Pi / 2.0f;
  gbcdLimits[8] = sqrtf(SIMPLib::Constants::k_Pi / 2.0f);
  gbcdLimits[9] = sqrtf(SIMPLib::Constants::k_Pi / 2.0f);

  // get num components of GBCD
  QVector<size_t> cDims = m_GBCDPtr.lock()->getComponentDimensions();

  gbcdSizes[0] = cDims[0];
  gbcdSizes[1] = cDims[1];
  gbcdSizes[2] = cDims[2];
  gbcdSizes[3] = cDims[3];
  gbcdSizes[4] = cDims[4];

  gbcdDeltas[0] = (gbcdLimits[5] - gbcdLimits[0]) / float(gbcdSizes[0]);
  gbcdDeltas[1] = (gbcdLimits[6] - gbcdLimits[1]) / float(gbcdSizes[1]);
  gbcdDeltas[2] = (gbcdLimits[7] - gbcdLimits[2]) / float(gbcdSizes[2]);
  gbcdDeltas[3] = (gbcdLimits[8] - gbcdLimits[3]) / float(gbcdSizes[3]);
  gbcdDeltas[4] = (gbcdLimits[9] - gbcdLimits[4]) / float(gbcdSizes[4]);

  float vec[3] = { 0.0f, 0.0f, 0.0f };
  float vec2[3] = { 0.0f, 0.0f, 0.0f };
  float rotNormal[3] = { 0.0f, 0.0f, 0.0f };
  float rotNormal2[3] = { 0.0f, 0.0f, 0.0f };
  float sqCoord[2] = { 0.0f, 0.0f };
  float dg[3][3] = { { 0.0f, 0.0f, 0.0f }, { 0.0f, 0.0f, 0.0f } };
  float dgt[3][3] = { { 0.0f, 0.0f, 0.0f }, { 0.0f, 0.0f, 0.0f } };
  float dg1[3][3] = { { 0.0f, 0.0f, 0.0f }, { 0.0f, 0.0f, 0.0f } };
  float dg2[3][3] = { { 0.0f, 0.0f, 0.0f }, { 0.0f, 0.0f, 0.0f } };
  float sym1[3][3] = { { 0.0f, 0.0f, 0.0f }, { 0.0f, 0.0f, 0.0f } };
  float sym2[3][3] = { { 0.0f, 0.0f, 0.0f }, { 0.0f, 0.0f, 0.0f } };
  float sym2t[3][3] = { { 0.0f, 0.0f, 0.0f }, { 0.0f, 0.0f, 0.0f } };
  float mis_euler1[3] = { 0.0f, 0.0f, 0.0f };

//.........这里部分代码省略.........

  /**
   * @brief ConvertData Templated function that converts an IDataArray to a given primitive type
   * @param ptr IDataArray instance pointer
   * @param dims Component dimensions
   * @param m DataContainer instance pointer
   * @param scalarType Primitive type to convert to
   * @param attributeMatrixName Name of target AttributeMatrix
   * @param name Name of converted array
   */
  void ConvertData(T* ptr, QVector<size_t> dims, DataContainer::Pointer m, int32_t scalarType, const QString attributeMatrixName, const QString& name)
  {
    int voxels = ptr->getNumberOfTuples();
    size_t size = ptr->getSize();

    if (scalarType == Detail::Int8)
    {
      Int8ArrayType::Pointer p = Int8ArrayType::CreateArray(voxels, dims, name);
      m->getAttributeMatrix(attributeMatrixName)->addAttributeArray(p->getName(), p);
      for(size_t v = 0; v < size; ++v)
      {
        p->setValue(v, ptr->getValue(v) );
      }
    }
    else if (scalarType == Detail::UInt8)
    {
      UInt8ArrayType::Pointer p = UInt8ArrayType::CreateArray(voxels, dims, name);
      m->getAttributeMatrix(attributeMatrixName)->addAttributeArray(p->getName(), p);
      for(size_t v = 0; v < size; ++v)
      {
        p->setValue(v, ptr->getValue(v) );
      }
    }
    else if (scalarType == Detail::Int16)
    {
      Int16ArrayType::Pointer p = Int16ArrayType::CreateArray(voxels, dims, name);
      m->getAttributeMatrix(attributeMatrixName)->addAttributeArray(p->getName(), p);
      for(size_t v = 0; v < size; ++v)
      {
        p->setValue(v, ptr->getValue(v) );
      }
    }
    else if (scalarType == Detail::UInt16)
    {
      UInt16ArrayType::Pointer p = UInt16ArrayType::CreateArray(voxels, dims, name);
      m->getAttributeMatrix(attributeMatrixName)->addAttributeArray(p->getName(), p);
      for(size_t v = 0; v < size; ++v)
      {
        p->setValue(v, ptr->getValue(v) );
      }
    }
    else if (scalarType == Detail::Int32)
    {
      Int32ArrayType::Pointer p = Int32ArrayType::CreateArray(voxels, dims, name);
      m->getAttributeMatrix(attributeMatrixName)->addAttributeArray(p->getName(), p);
      for(size_t v = 0; v < size; ++v)
      {
        p->setValue(v, ptr->getValue(v) );
      }
    }
    else if (scalarType == Detail::UInt32)
    {
      UInt32ArrayType::Pointer p = UInt32ArrayType::CreateArray(voxels, dims, name);
      m->getAttributeMatrix(attributeMatrixName)->addAttributeArray(p->getName(), p);
      for(size_t v = 0; v < size; ++v)
      {
        p->setValue(v, ptr->getValue(v) );
      }
    }
    else if (scalarType == Detail::Int64)
    {
      Int64ArrayType::Pointer p = Int64ArrayType::CreateArray(voxels, dims, name);
      m->getAttributeMatrix(attributeMatrixName)->addAttributeArray(p->getName(), p);
      for(size_t v = 0; v < size; ++v)
      {
        p->setValue(v, ptr->getValue(v) );
      }
    }
    else if (scalarType == Detail::UInt64)
    {
      UInt64ArrayType::Pointer p = UInt64ArrayType::CreateArray(voxels, dims, name);
      m->getAttributeMatrix(attributeMatrixName)->addAttributeArray(p->getName(), p);
      for(size_t v = 0; v < size; ++v)
      {
        p->setValue(v, ptr->getValue(v) );
      }
    }
    else if (scalarType == Detail::Float)
    {
      FloatArrayType::Pointer p = FloatArrayType::CreateArray(voxels, dims, name);
      m->getAttributeMatrix(attributeMatrixName)->addAttributeArray(p->getName(), p);
      for(size_t v = 0; v < size; ++v)
      {
        p->setValue(v, ptr->getValue(v) );
      }
    }
    else if (scalarType == Detail::Double)
    {
      DoubleArrayType::Pointer p = DoubleArrayType::CreateArray(voxels, dims, name);
      m->getAttributeMatrix(attributeMatrixName)->addAttributeArray(p->getName(), p);
      for(size_t v = 0; v < size; ++v)
//.........这里部分代码省略.........

// -----------------------------------------------------------------------------
//
// -----------------------------------------------------------------------------
void ImportR3DStack::execute()
{
  int err = 0;
  setErrorCondition(err);
  dataCheck(false,1,1,1);
  if (getErrorCondition() < 0) { notifyErrorMessage("There is a problem with the data check", getErrorCondition()); }
  VoxelDataContainer* m = getVoxelDataContainer();
  if(NULL == m)
  {
    setErrorCondition(-999);
    notifyErrorMessage("The DataContainer Object was NULL", -999);
    return;
  }
  setErrorCondition(0);
  std::stringstream ss;

  m->setResolution(m_Resolution.x, m_Resolution.y, m_Resolution.z);
  m->setOrigin(m_Origin.x, m_Origin.y, m_Origin.z);
  int x = 0;
  int y = 0;
  readXYSize(x, y);

  if (x < 1 || y < 1)
  {  
	setErrorCondition(-1000);
	notifyErrorMessage("At least one dimension is less than 1", getErrorCondition());
  }
  size_t numSlices = m_ZEndIndex - m_ZStartIndex + 1;
  size_t totalVoxels = numSlices * x * y;
  // Create a new array, eventually substituting this into the DataContainer later on.
  Int32ArrayType::Pointer grainIdsPtr = Int32ArrayType::CreateArray(totalVoxels, 1, DREAM3D::CellData::GrainIds);
  grainIdsPtr->initializeWithZeros();
  m_GrainIds = grainIdsPtr->GetPointer(0); // Get the pointer to the front of the array
  int32_t* currentPositionPtr = m_GrainIds;

  bool ok = false;

  int pixelBytes = 0;
  int totalPixels = 0;
  int height = 0;
  int width = 0;

  size_t index = 0;

  int64_t z = m_ZStartIndex;

  m->setDimensions(x,y,numSlices);

  for (std::vector<std::string>::iterator filepath = m_R3DFileList.begin(); filepath != m_R3DFileList.end(); ++filepath)
  {
    QString R3DFName = QString::fromStdString(*filepath);

    ss.str("");
    ss << "Importing file " << R3DFName.toStdString();
    notifyStatusMessage(ss.str());

    QByteArray buf;
    QFile in(R3DFName);

    if (!in.open(QIODevice::ReadOnly | QIODevice::Text))
    {
      QString msg = QString("R3D file could not be opened: ") + R3DFName;
      setErrorCondition(-14000);
      notifyErrorMessage(msg.toStdString(), getErrorCondition());
    }

    buf = in.readLine(); // Read first line which is the x and y sizes

    QList<QByteArray> tokens = buf.split(',');

    width = tokens.at(0).toInt();
    height = tokens.at(1).toInt();

    int32_t value = 0;

    for(qint32 i = 0; i < height; ++i)
    {
      buf = in.readLine();
      tokens = buf.split(',');
      if (tokens.size() != width+2)
      {
		notifyStatusMessage("A file did not have the correct width partilcuar line");
		break;
      }
      for(int j = 1; j < width+1; j++)
      {
        currentPositionPtr[index] = tokens[j].toInt(&ok, 10);
        ++index;
		if (!ok) 
		{
		  setErrorCondition(-2004);
		  notifyErrorMessage("Width dimension entry was not an integer", getErrorCondition());
		  break;
		}
      }

      if (in.atEnd() == true && i < height - 2)
//.........这里部分代码省略.........

// -----------------------------------------------------------------------------
//
// -----------------------------------------------------------------------------
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);
//.........这里部分代码省略.........

// -----------------------------------------------------------------------------
//
// -----------------------------------------------------------------------------
int AbaqusSurfaceMeshWriter::writeGrains(FILE* f)
{

  //*Elset, elset=Grain1
  //1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16

  int err = 0;

  std::stringstream ss;
  SurfaceMeshDataContainer* sm = getSurfaceMeshDataContainer();
  DREAM3D::SurfaceMesh::VertListPointer_t nodesPtr = sm->getVertices();
  DREAM3D::SurfaceMesh::FaceListPointer_t trianglePtr = sm->getFaces();

  // Get the Labels(GrainIds or Region Ids) for the triangles
  Int32ArrayType::Pointer faceLabelsPtr = boost::dynamic_pointer_cast<Int32ArrayType>(sm->getFaceData(DREAM3D::FaceData::SurfaceMeshFaceLabels));
  int32_t* faceLabels = faceLabelsPtr->GetPointer(0);

  int nTriangles = trianglePtr->GetNumberOfTuples();

  // Store all the unique Spins
  std::set<int> uniqueSpins;
  for (int i = 0; i < nTriangles; i++)
  {
    uniqueSpins.insert(faceLabels[i*2]);
    uniqueSpins.insert(faceLabels[i*2+1]);
  }

  int spin = 0;

  //Loop over the unique Spins
  for (std::set<int>::iterator spinIter = uniqueSpins.begin(); spinIter != uniqueSpins.end(); ++spinIter )
  {
    spin = *spinIter;
    if(spin < 0) { continue; }

    fprintf(f, "*ELSET, ELSET=Grain%d\n", spin);

    ss.str("");
    ss << "Writing ELSET for Grain Id " << spin;
    notifyStatusMessage(ss.str());


    // Loop over all the triangles for this spin
    int lineCount = 0;
    for(int t = 0; t < nTriangles; ++t)
    {
      if (faceLabels[t*2] != spin && faceLabels[t*2+1] != spin)
      {
        continue; // We do not match either spin so move to the next triangle
      }

      // Only print 15 Triangles per line
      if (lineCount == 15)
      {
        fprintf(f, ", %d\n", t);
        lineCount = 0;
      }
      else if(lineCount == 0) // First value on the line
      {
        fprintf(f,"%d", t);
        lineCount++;
      }
      else
      {
        fprintf(f,", %d", t);
        lineCount++;
      }

    }
    // Make sure we have a new line at the end of the section
    if (lineCount != 0)
    {
      fprintf(f, "\n");
    }
  }
  return err;
}

// -----------------------------------------------------------------------------
//
// -----------------------------------------------------------------------------
void ErodeDilateCoordinationNumber::execute()
{
  setErrorCondition(0);
  dataCheck();
  if(getErrorCondition() < 0) { return; }

  DataContainer::Pointer m = getDataContainerArray()->getDataContainer(getFeatureIdsArrayPath().getDataContainerName());
  size_t totalPoints = m_FeatureIdsPtr.lock()->getNumberOfTuples();

  Int32ArrayType::Pointer neighborsPtr = Int32ArrayType::CreateArray(totalPoints, "Neighbors");
  m_Neighbors = neighborsPtr->getPointer(0);
  neighborsPtr->initializeWithValue(-1);

  size_t udims[3] = {0, 0, 0};
  m->getGeometryAs<ImageGeom>()->getDimensions(udims);

  int64_t dims[3] =
  {
    static_cast<int64_t>(udims[0]),
    static_cast<int64_t>(udims[1]),
    static_cast<int64_t>(udims[2]),
  };

  int32_t good = 1;
  int64_t point = 0;
  int64_t kstride = 0, jstride = 0;
  int32_t featurename = 0, feature = 0;
  int32_t coordination = 0;
  int32_t current = 0;
  int32_t most = 0;
  int64_t neighpoint = 0;
  size_t numfeatures = 0;

  for(size_t i = 0; i < totalPoints; i++)
  {
    featurename = m_FeatureIds[i];
    if (featurename > numfeatures) { numfeatures = featurename; }
  }

  int64_t neighpoints[6] = { 0, 0, 0, 0, 0, 0 };
  neighpoints[0] = -dims[0] * dims[1];
  neighpoints[1] = -dims[0];
  neighpoints[2] = -1;
  neighpoints[3] = 1;
  neighpoints[4] = dims[0];
  neighpoints[5] = dims[0] * dims[1];

  QString attrMatName = m_FeatureIdsArrayPath.getAttributeMatrixName();
  QList<QString> voxelArrayNames = m->getAttributeMatrix(attrMatName)->getAttributeArrayNames();

  QVector<int32_t> n(numfeatures + 1, 0);
  QVector<int32_t> coordinationNumber(totalPoints, 0);
  bool keepgoing = true;
  int32_t counter = 1;

  while (counter > 0 && keepgoing == true)
  {
    counter = 0;
    if (m_Loop == false) { keepgoing = false; }

    for (int64_t k = 0; k < dims[2]; k++)
    {
      kstride = dims[0] * dims[1] * k;
      for (int64_t j = 0; j < dims[1]; j++)
      {
        jstride = dims[0] * j;
        for (int64_t i = 0; i < dims[0]; i++)
        {
          point = kstride + jstride + i;
          featurename = m_FeatureIds[point];
          coordination = 0;
          current = 0;
          most = 0;
          for (int32_t l = 0; l < 6; l++)
          {
            good = 1;
            neighpoint = point + neighpoints[l];
            if (l == 0 && k == 0) { good = 0; }
            if (l == 5 && k == (dims[2] - 1)) { good = 0; }
            if (l == 1 && j == 0) { good = 0; }
            if (l == 4 && j == (dims[1] - 1)) { good = 0; }
            if (l == 2 && i == 0) { good = 0; }
            if (l == 3 && i == (dims[0] - 1)) { good = 0; }
            if (good == 1)
            {
              feature = m_FeatureIds[neighpoint];
              if ((featurename > 0 && feature == 0) || (featurename == 0 && feature > 0))
              {
                coordination = coordination + 1;
                n[feature]++;
                current = n[feature];
                if (current > most)
                {
                  most = current;
                  m_Neighbors[point] = neighpoint;
                }
              }
//.........这里部分代码省略.........

// -----------------------------------------------------------------------------
//
// -----------------------------------------------------------------------------
bool AttributeMatrix::removeInactiveObjects(QVector<bool> activeObjects, Int32ArrayType::Pointer Ids)
{
    bool acceptableMatrix = false;
    //Only valid for feature or ensemble type matrices
    if(m