// -----------------------------------------------------------------------------
//
// -----------------------------------------------------------------------------
void FlattenImage::dataCheck(bool preflight, size_t voxels, size_t fields, size_t ensembles)
{
  setErrorCondition(0);
  std::stringstream ss;
  VoxelDataContainer* m = getVoxelDataContainer();
  //int err = 0;

  int numImageComp = 1;
  IDataArray::Pointer iDataArray = m->getCellData(m_ImageDataArrayName);
  if(NULL != iDataArray.get())
  {
    UInt8ArrayType* imageDataPtr = UInt8ArrayType::SafePointerDownCast(iDataArray.get());
    if (NULL != imageDataPtr)
    {
      numImageComp = imageDataPtr->GetNumberOfComponents();
    }
  }

  GET_PREREQ_DATA(m, DREAM3D, CellData, ImageData, ss, -301, unsigned char, UCharArrayType, voxels, numImageComp)
//  if(err == -301)
//  {
//    setErrorCondition(0);
//    err = 0;
//    GET_PREREQ_DATA(m, DREAM3D, CellData, ImageData, ss, -302, unsigned char, UCharArrayType, voxels, 3)
//  }

  CREATE_NON_PREREQ_DATA(m, DREAM3D, CellData, FlatImageData, ss, int32_t, Int32ArrayType, 0, voxels, 1)
}

// -----------------------------------------------------------------------------
//
// -----------------------------------------------------------------------------
void AlignSectionsList::find_shifts(std::vector<int> &xshifts, std::vector<int> &yshifts)
{
  VoxelDataContainer* m = getVoxelDataContainer();
  //int64_t totalPoints = m->totalPoints();

  std::ifstream inFile;
  inFile.open(m_InputFile.c_str());

  size_t udims[3] = {0,0,0};
  m->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]),
  };

  int slice;
  int newxshift, newyshift;
  for (DimType iter = 1; iter < dims[2]; iter++)
  {
  inFile >> slice >> newxshift >> newyshift;
    xshifts[iter] = xshifts[iter-1] + newxshift;
    yshifts[iter] = yshifts[iter-1] + newyshift;
  }

  inFile.close();
}

// -----------------------------------------------------------------------------
//
// -----------------------------------------------------------------------------
void AddOrientationNoise::execute()
{
  int err = 0;
  setErrorCondition(err);
  DREAM3D_RANDOMNG_NEW()
  VoxelDataContainer* m = getVoxelDataContainer();

  if(NULL == m)
  {
    setErrorCondition(-999);
    notifyErrorMessage("The DataContainer Object was NULL", -999);
    return;
  }

  int64_t totalPoints = m->getTotalPoints();
  size_t totalFields = m->getNumFieldTuples();

  dataCheck(false, totalPoints, totalFields, m->getNumEnsembleTuples());
  if (getErrorCondition() < 0)
  {
    return;
  }

  m_Magnitude = m_Magnitude*m_pi/180.0;

  add_orientation_noise();

  // If there is an error set this to something negative and also set a message
 notifyStatusMessage("AddOrientationNoises Completed");
}

// -----------------------------------------------------------------------------
//
// -----------------------------------------------------------------------------
void  AddOrientationNoise::add_orientation_noise()
{
 notifyStatusMessage("Adding Orientation Noise");
  DREAM3D_RANDOMNG_NEW()

  VoxelDataContainer* m = getVoxelDataContainer();

  //float ea1, ea2, ea3;
  float g[3][3];
  float newg[3][3];
  float rot[3][3];
  float w, n1, n2, n3;
  int64_t totalPoints = m->getTotalPoints();
  for (size_t i = 0; i < static_cast<size_t>(totalPoints); ++i)
  {
    float ea1 = m_CellEulerAngles[3*i+0];
    float ea2 = m_CellEulerAngles[3*i+1];
    float ea3 = m_CellEulerAngles[3*i+2];
    OrientationMath::EulertoMat(ea1, ea2, ea3, g);
    n1 = static_cast<float>( rg.genrand_res53() );
    n2 = static_cast<float>( rg.genrand_res53() );
    n3 = static_cast<float>( rg.genrand_res53() );
    w = static_cast<float>( rg.genrand_res53() );
    w = 2.0*(w-0.5);
    w = (m_Magnitude*w);
    OrientationMath::AxisAngletoMat(w, n1, n2, n3, rot);
    MatrixMath::Multiply3x3with3x3(g, rot, newg);
    OrientationMath::MattoEuler(newg, ea1, ea2, ea3);
    m_CellEulerAngles[3*i+0] = ea1;
    m_CellEulerAngles[3*i+1] = ea2;
    m_CellEulerAngles[3*i+2] = ea3;
  }
}

// -----------------------------------------------------------------------------
//
// -----------------------------------------------------------------------------
void AdjustVolumeOrigin::execute()
{
  VoxelDataContainer* m = getVoxelDataContainer();
  if(NULL == m)
  {
    setErrorCondition(-999);
    notifyErrorMessage("The DataContainer Object was NULL", -999);
    return;
  }
  setErrorCondition(0);
  std::stringstream ss;

  // Set the Voxel Volume First, since this is easy
  if (m_ApplyToVoxelVolume ==true)
  {
    m->setOrigin(m_Origin.x, m_Origin.y, m_Origin.z);
  }

  if (m_ApplyToSurfaceMesh == true)
  {
    updateSurfaceMesh();
  }

  if (m_ApplyToSolidMesh == true)
  {
    updatesSolidMesh();
  }
  notifyStatusMessage("Complete");
}

// -----------------------------------------------------------------------------
//
// -----------------------------------------------------------------------------
void Threshold::dataCheck(bool preflight, size_t voxels, size_t fields, size_t ensembles)
{
  setErrorCondition(0);
  std::stringstream ss;
  VoxelDataContainer* m = getVoxelDataContainer();

  if(m_SelectedCellArrayName.empty() == true)
  {
    setErrorCondition(-11000);
    ss << "An array from the Voxel Data Container must be selected.";
    addErrorMessage(getHumanLabel(),ss.str(),getErrorCondition());
  }
  else
  {
    m_RawImageDataArrayName=m_SelectedCellArrayName;
    GET_PREREQ_DATA(m, DREAM3D, CellData, RawImageData, ss, -300, ImageProcessing::DefaultPixelType, ImageProcessing::DefaultArrayType, voxels, 1)

    if(m_OverwriteArray)
    {

    }
    else
    {
      CREATE_NON_PREREQ_DATA(m, DREAM3D, CellData, ProcessedImageData, ss, ImageProcessing::DefaultPixelType, ImageProcessing::DefaultArrayType, 0, voxels, 1)
      m->renameCellData(m_ProcessedImageDataArrayName, m_NewCellArrayName);
    }
  }
}

// -----------------------------------------------------------------------------
//
// -----------------------------------------------------------------------------
void AlignSectionsFeature::execute()
{
  setErrorCondition(0);
  VoxelDataContainer* m = getVoxelDataContainer();
  if(NULL == m)
  {
    setErrorCondition(-999);
    notifyErrorMessage("The DataContainer Object was NULL", -999);
    return;
  }

  int64_t totalPoints = m->getTotalPoints();
  size_t numgrains = m->getNumFieldTuples();
  size_t numensembles = m->getNumEnsembleTuples();
  dataCheck(false, totalPoints, numgrains, numensembles);
  if (getErrorCondition() < 0)
  {
    return;
  }

  AlignSections::execute();

  // If there is an error set this to something negative and also set a message
 notifyStatusMessage("Aligning Sections Complete");
}

// -----------------------------------------------------------------------------
//
// -----------------------------------------------------------------------------
void FlattenImage::execute()
{
  VoxelDataContainer* m = getVoxelDataContainer();
  if(NULL == m)
  {
    setErrorCondition(-999);
    notifyErrorMessage("The DataContainer Object was NULL", -999);
    return;
  }
  setErrorCondition(0);
  int64_t totalPoints = m->getTotalPoints();
  size_t numgrains = m->getNumFieldTuples();
  size_t numensembles = m->getNumEnsembleTuples();
  dataCheck(false, totalPoints, numgrains, numensembles);
  if (getErrorCondition() < 0)
  {
    return;
  }

  float Rfactor = 1.0;
  float Gfactor = 1.0;
  float Bfactor = 1.0;
  if (m_FlattenMethod == DREAM3D::FlattenImageMethod::Average)
  {
    Rfactor = 1.0/3.0;
    Gfactor = 1.0/3.0;
    Bfactor = 1.0/3.0;
  }
  else if (m_FlattenMethod == DREAM3D::FlattenImageMethod::Luminosity)
  {
    Rfactor = 0.21;
    Gfactor = 0.72;
    Bfactor = 0.07;
  }

#ifdef DREAM3D_USE_PARALLEL_ALGORITHMS
  tbb::task_scheduler_init init;
  bool doParallel = true;
#endif

  size_t comp = m->getCellData(m_ImageDataArrayName)->GetNumberOfComponents();

  //  std::cout << "FlattenImage: " << m_ConversionFactor << std::endl;
#ifdef DREAM3D_USE_PARALLEL_ALGORITHMS
  if (doParallel == true)
  {
    tbb::parallel_for(tbb::blocked_range<size_t>(0, totalPoints),
                      FlattenImageImpl(m_ImageData, m_FlatImageData, Rfactor, Gfactor, Bfactor, comp), tbb::auto_partitioner());

  }
  else
#endif
  {
    FlattenImageImpl serial(m_ImageData, m_FlatImageData, Rfactor, Gfactor, Bfactor, comp);
    serial.convert(0, totalPoints);
  }

  notifyStatusMessage("Complete");
}

// -----------------------------------------------------------------------------
//
// -----------------------------------------------------------------------------
void DxReader::dataCheck(bool preflight, size_t voxels, size_t fields, size_t ensembles)
{

  setErrorCondition(0);
  std::stringstream ss;
  VoxelDataContainer* m = getVoxelDataContainer();

  if (getInputFile().empty() == true)
  {
    ss << ClassName() << " needs the Input File Set and it was not.";
    setErrorCondition(-387);
    addErrorMessage(getHumanLabel(), ss.str(), getErrorCondition());
  }
  else if (MXAFileInfo::exists(getInputFile()) == false)
  {
    ss << "The input file does not exist.";
    setErrorCondition(-388);
    addErrorMessage(getHumanLabel(), ss.str(), getErrorCondition());
  }
  CREATE_NON_PREREQ_DATA(m, DREAM3D, CellData, GrainIds, ss, int32_t, Int32ArrayType, 0, voxels, 1)

  m->setResolution(m_Resolution.x, m_Resolution.y, m_Resolution.z);
  m->setOrigin(m_Origin.x, m_Origin.y, m_Origin.z);

  if (m_InStream.is_open() == true)
  {
    m_InStream.close();
  }
// We need to read the header of the input file to get the dimensions
  m_InStream.open(getInputFile().c_str(), std::ios_base::binary);
  if(!m_InStream)
  {
    ss.clear();
    ss << " Runtime Error. The input file '" << getInputFile() << "' could not be"
        << " opened for reading. Do you have access to this file?";
    setErrorCondition(-49800);
    addErrorMessage(getHumanLabel(), ss.str(), getErrorCondition());
    return;
  }

  int error = readHeader();
  m_InStream.close();
  if (error < 0)
  {
    setErrorCondition(error);
    ss.clear();
    ss << "Error occurred trying to parse the dimensions from the input file. Is the input file a Dx file?";
    addErrorMessage(getHumanLabel(), ss.str(), -11000);
  }

}

// -----------------------------------------------------------------------------
//
// -----------------------------------------------------------------------------
int VoxelDataContainerWriter::writeEnsembleData(hid_t dcGid)
{
  std::stringstream ss;
  int err = 0;
  VoxelDataContainer* m = getVoxelDataContainer();

  // Write the Ensemble data
  err = H5Utilities::createGroupsFromPath(H5_ENSEMBLE_DATA_GROUP_NAME, dcGid);
  if(err < 0)
  {
    ss.str("");
    ss << "Error creating HDF Group " << H5_ENSEMBLE_DATA_GROUP_NAME << std::endl;
    setErrorCondition(-66);
    notifyErrorMessage( ss.str(), err);
    H5Gclose(dcGid); // Close the Data Container Group
    return err;
  }
  err = H5Lite::writeStringAttribute(dcGid, H5_ENSEMBLE_DATA_GROUP_NAME, H5_NAME, H5_ENSEMBLE_DATA_DEFAULT);

  hid_t ensembleGid = H5Gopen(dcGid, H5_ENSEMBLE_DATA_GROUP_NAME, H5P_DEFAULT);
  if(err < 0)
  {
    ss.str("");
    ss << "Error opening ensemble Group " << H5_ENSEMBLE_DATA_GROUP_NAME << std::endl;
    setErrorCondition(-67);
    notifyErrorMessage( ss.str(), err);
    H5Gclose(dcGid); // Close the Data Container Group
    return err;
  }
  NameListType names = m->getEnsembleArrayNameList();
  for (NameListType::iterator iter = names.begin(); iter != names.end(); ++iter)
  {
    IDataArray::Pointer array = m->getEnsembleData(*iter);
    err = array->writeH5Data(ensembleGid);
    if(err < 0)
    {
      ss.str("");
      ss << "Error writing Ensemble array '" << *iter << "' to the HDF5 File";
      notifyErrorMessage( ss.str(), err);
      setErrorCondition(err);
      H5Gclose(ensembleGid); // Close the Cell Group
      H5Gclose(dcGid); // Close the Data Container Group
      return err;
    }
  }

  H5Gclose(ensembleGid);

  return err;
}

// -----------------------------------------------------------------------------
//
// -----------------------------------------------------------------------------
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 AvizoRectilinearCoordinateWriter::execute()
{
  int err = 0;
  setErrorCondition(err);
  VoxelDataContainer* m = getVoxelDataContainer();
  if(NULL == m)
  {
    setErrorCondition(-999);
    notifyErrorMessage("The DataContainer Object was NULL", -999);
    return;
  }
  setErrorCondition(0);

  // 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(m_OutputFile);
  if(!MXADir::mkdir(parentPath, true))
  {
    std::stringstream ss;
    ss << "Error creating parent path '" << parentPath << "'";
    notifyErrorMessage(ss.str(), -1);
    setErrorCondition(-1);
    return;
  }

  int64_t totalPoints = m->getTotalPoints();
  size_t totalFields = m->getNumFieldTuples();
  size_t totalEnsembleTuples = m->getNumEnsembleTuples();

  dataCheck(false, totalPoints, totalFields, totalEnsembleTuples);

  MXAFileWriter64 writer(m_OutputFile);
  if(false == writer.initWriter())
  {
    std::stringstream ss;
    ss << "Error opening file '" << parentPath << "'";
    notifyErrorMessage(ss.str(), -1);
    setErrorCondition(-1);
    return;
  }

  std::string header = generateHeader();
  writer.writeString(header);

  err = writeData(writer);

  /* Let the GUI know we are done with this filter */
  notifyStatusMessage("Complete");
}

// -----------------------------------------------------------------------------
//
// -----------------------------------------------------------------------------
void YSChoiAbaqusReader::dataCheck(bool preflight, size_t voxels, size_t fields, size_t ensembles)
{
  setErrorCondition(0);
  std::stringstream ss;
  VoxelDataContainer* m = getVoxelDataContainer();

  if (getInputFile().empty() == true)
  {
    ss << ClassName() << " needs the Input File Set and it was not.";
    setErrorCondition(-387);
    addErrorMessage(getHumanLabel(), ss.str(), getErrorCondition());
  }
  else if (MXAFileInfo::exists(getInputFile()) == false)
  {
    ss << "The input file does not exist.";
    setErrorCondition(-388);
    addErrorMessage(getHumanLabel(), ss.str(), getErrorCondition());
  }
  else
  {
    const unsigned int size(1024);
    char buf[size];
    // Read header from data file to figure out how many points there are
    std::ifstream in(getInputFile().c_str());
    std::string word;
    bool headerdone = false;
    int xpoints, ypoints, zpoints;
    float resx, resy, resz;
    while (headerdone == false)
    {
      in.getline(buf, size);
      std::string line = buf;
      in >> word;
      if (DIMS == word)
      {
        in >> xpoints >> ypoints >> zpoints;
        size_t dims[3] = {xpoints, ypoints, zpoints};
        m->setDimensions(dims);
        m->setOrigin(0,0,0);
      }
      if (RES == word)
      {
        in >> resx >> resy >> resz;
        float res[3] = {resx, resy, resz};
        m->setResolution(res);
      }
    }

// -----------------------------------------------------------------------------
//
// -----------------------------------------------------------------------------
void UpdateCellQuats::execute()
{
  setErrorCondition(0);
  VoxelDataContainer* m = getVoxelDataContainer();
  if(NULL == m)
  {
    setErrorCondition(-999);
    notifyErrorMessage("The DataContainer Object was NULL", -999);
    return;
  }
  setErrorCondition(0);
  std::stringstream ss;

  int64_t totalPoints = m->getTotalPoints();

  //getting the 5 component quaternions from the data container and down-casting them
  IDataArray::Pointer Quats5 = m->getCellData(DREAM3D::CellData::Quats);
  if(Quats5->GetNumberOfComponents() != 5)
  {
    notifyErrorMessage("The Quats array did not contain 5 components", -999);
    return;
  }
  DataArray<float>* quats5 = DataArray<float>::SafePointerDownCast(Quats5.get());
  float* quats5ptr = quats5->GetPointer(0);
  //creating the 4 component quaternions in the data container
  CREATE_NON_PREREQ_DATA(m, DREAM3D, CellData, Quats, ss, float, FloatArrayType, 0, totalPoints, 4)

  if (getErrorCondition() < 0)
  {
    return;
  }

  //copying the 5 component quaternions into the new 4 component quaternions
  // This is a special case for dealing with this conversion. If you are dealing with
  // quaternions then DO NOT USE THIS CODE as an example. Use another filter instead.
  for (int i = 0; i < totalPoints; i++)
  {
    for(int j=0;j<4;j++)
    {
      m_Quats[4*i+j] = quats5ptr[5*i+(j+1)];
    }
  }

  notifyStatusMessage("Complete");
}

// -----------------------------------------------------------------------------
//
// -----------------------------------------------------------------------------
void FindAxisODF::dataCheck(bool preflight, size_t voxels, size_t fields, size_t ensembles)
{
  setErrorCondition(0);
  std::stringstream ss;
  VoxelDataContainer* m = getVoxelDataContainer();
  int err = 0;

  GET_PREREQ_DATA(m, DREAM3D, FieldData, AxisEulerAngles, ss, -301, float, FloatArrayType, fields, 3)

  TEST_PREREQ_DATA(m, DREAM3D, FieldData, SurfaceFields, err, -302, bool, BoolArrayType, fields, 1)
  if(err == -302)
  {
    setErrorCondition(0);
    FindSurfaceGrains::Pointer find_surfacefields = FindSurfaceGrains::New();
    find_surfacefields->setObservers(this->getObservers());
    find_surfacefields->setVoxelDataContainer(getVoxelDataContainer());
    if(preflight == true) find_surfacefields->preflight();
    if(preflight == false) find_surfacefields->execute();
  }
  GET_PREREQ_DATA(m, DREAM3D, FieldData, SurfaceFields, ss, -302, bool, BoolArrayType, fields, 1)

  err = 0;
  TEST_PREREQ_DATA(m, DREAM3D, FieldData, FieldPhases, err, -303, int32_t, Int32ArrayType, fields, 1)
  if(err == -303)
  {
    setErrorCondition(0);
    FindGrainPhases::Pointer find_grainphases = FindGrainPhases::New();
    find_grainphases->setObservers(this->getObservers());
    find_grainphases->setVoxelDataContainer(getVoxelDataContainer());
    if(preflight == true) find_grainphases->preflight();
    if(preflight == false) find_grainphases->execute();
  }
  GET_PREREQ_DATA(m, DREAM3D, FieldData, FieldPhases, ss, -303, int32_t, Int32ArrayType, fields, 1)

  typedef DataArray<unsigned int> PhaseTypeArrayType;
  GET_PREREQ_DATA(m, DREAM3D, EnsembleData, PhaseTypes, ss, -307, unsigned int, PhaseTypeArrayType, ensembles, 1)
  m_StatsDataArray = StatsDataArray::SafeObjectDownCast<IDataArray*, StatsDataArray*>(m->getEnsembleData(DREAM3D::EnsembleData::Statistics).get());
  if(m_StatsDataArray == NULL)
  {
    StatsDataArray::Pointer p = StatsDataArray::New();
    m_StatsDataArray = p.get();
    m_StatsDataArray->fillArrayWithNewStatsData(ensembles, m_PhaseTypes);
    m->addEnsembleData(DREAM3D::EnsembleData::Statistics, p);
  }
}

// -----------------------------------------------------------------------------
//
// -----------------------------------------------------------------------------
void RotateEulerRefFrame::execute()
{
  VoxelDataContainer* m = getVoxelDataContainer();
  if(NULL == m)
  {
    setErrorCondition(-999);
    notifyErrorMessage("The DataContainer Object was NULL", -999);
    return;
  }
  setErrorCondition(0);
  int64_t totalPoints = m->getTotalPoints();
  size_t numgrains = m->getNumFieldTuples();
  size_t numensembles = m->getNumEnsembleTuples();
  dataCheck(false, totalPoints, numgrains, numensembles);
  if (getErrorCondition() < 0)
  {
    return;
  }


#ifdef DREAM3D_USE_PARALLEL_ALGORITHMS
  tbb::task_scheduler_init init;
  bool doParallel = true;
#endif

#ifdef DREAM3D_USE_PARALLEL_ALGORITHMS
  if (doParallel == true)
  {
    tbb::parallel_for(tbb::blocked_range<size_t>(0, totalPoints),
                      RotateEulerRefFrameImpl(m_CellEulerAngles, m_RotationAngle, m_RotationAxis), tbb::auto_partitioner());

  }
  else
#endif
  {
    RotateEulerRefFrameImpl serial(m_CellEulerAngles, m_RotationAngle, m_RotationAxis);
    serial.convert(0, totalPoints);
  }

  notifyStatusMessage("Complete");
}

// -----------------------------------------------------------------------------
//
// -----------------------------------------------------------------------------
void FindCellQuats::execute()
{
  setErrorCondition(0);
  VoxelDataContainer* m = getVoxelDataContainer();
  if(NULL == m)
  {
    setErrorCondition(-999);
    notifyErrorMessage("The DataContainer Object was NULL", -999);
    return;
  }
  setErrorCondition(0);
  std::stringstream ss;

  int64_t totalPoints = m->getTotalPoints();
  size_t totalFields = m->getNumFieldTuples();
  size_t totalEnsembles = m->getNumEnsembleTuples();
  dataCheck(false, totalPoints, totalFields, totalEnsembles);
  if (getErrorCondition() < 0)
  {
    return;
  }

  QuatF* quats = reinterpret_cast<QuatF*>(m_Quats);
  QuatF qr;
  int phase = -1;
  for (int i = 0; i < totalPoints; i++)
  {
    phase = m_CellPhases[i];
    OrientationMath::EulertoQuat(qr, m_CellEulerAngles[3 * i], m_CellEulerAngles[3 * i + 1], m_CellEulerAngles[3 * i + 2]);
    QuaternionMathF::UnitQuaternion(qr);
    if (m_CrystalStructures[phase] == Ebsd::CrystalStructure::UnknownCrystalStructure)
    {
      QuaternionMathF::Identity(qr);
    }
    QuaternionMathF::Copy(qr, quats[i]);
  }

  notifyStatusMessage("Complete");
}

// -----------------------------------------------------------------------------
//
// -----------------------------------------------------------------------------
void PerPhaseMinSize::remove_smallgrains()
{
  VoxelDataContainer* m = getVoxelDataContainer();
  int64_t totalPoints = m->getTotalPoints();

  bool good = false;

  int gnum;

  int numgrains = m->getNumFieldTuples();

  std::vector<int> voxcounts;
  voxcounts.resize(numgrains,0);
  for (int64_t i = 0; i < totalPoints; i++)
  {
    gnum = m_GrainIds[i];
    if(gnum >= 0) voxcounts[gnum]++;
  }
  for (size_t i = 1; i <  static_cast<size_t>(numgrains); i++)
  {
    m_Active[i] = true;
    if(voxcounts[i] >= getMinAllowedGrainSize() || m_FieldPhases[i] != m_PhaseNumber) good = true;
  }
  if(good == false)
  {
    setErrorCondition(-1);
    notifyErrorMessage("The minimum size is larger than the largest Field.  All Fields would be removed.  The filter has quit.", -1);
    return;
  }
  for (int64_t i = 0; i < totalPoints; i++)
  {
    gnum = m_GrainIds[i];
    if(voxcounts[gnum] < getMinAllowedGrainSize() && m_CellPhases[i] == m_PhaseNumber && gnum > 0)
    {
      m_GrainIds[i] = -1;
      m_Active[gnum] = false;
    }
  }
}

// -----------------------------------------------------------------------------
//
// -----------------------------------------------------------------------------
void LinkFieldMapToCellArray::dataCheck(bool preflight, size_t voxels, size_t fields, size_t ensembles)
{
  setErrorCondition(0);
  std::stringstream ss;
  VoxelDataContainer* m = getVoxelDataContainer();

  IDataArray::Pointer data = m->getCellData(m_SelectedCellDataArrayName);
  if (NULL == data.get())
  {
    ss.str("");
    ss << "Selected array '" << m_SelectedCellDataArrayName << "' does not exist in the Voxel Data Container. Was it spelled correctly?";
    setErrorCondition(-11001);
    addErrorMessage(getHumanLabel(),ss.str(),getErrorCondition());
    return;
  }

  std::string dType = data->getTypeAsString();
  IDataArray::Pointer p = IDataArray::NullPointer();
  if (dType.compare("int32_t") == 0)
  {
    DataArray<int32_t>* field = DataArray<int32_t>::SafePointerDownCast(data.get());
    m_SelectedCellData = field->GetPointer(0);
  }
  else
  {
    ss.str("");
    ss << "Selected array '" << m_SelectedCellDataArrayName << "' is not an Integer array. Is this the array you want to use?";
    setErrorCondition(-11001);
    addErrorMessage(getHumanLabel(),ss.str(),getErrorCondition());
    return;
  }

  m->clearFieldData();
  BoolArrayType::Pointer active = BoolArrayType::CreateArray(fields, 1, DREAM3D::FieldData::Active);
  // bool* mActive = m_Active->GetPointer(0);
  m->addFieldData(DREAM3D::FieldData::Active, active);

}

// -----------------------------------------------------------------------------
//
// -----------------------------------------------------------------------------
void ClearData::execute()
{
  int err = 0;
  setErrorCondition(err);
  VoxelDataContainer* m = getVoxelDataContainer();
  if(NULL == m)
  {
    setErrorCondition(-999);
    notifyErrorMessage("The DataContainer Object was NULL", -999);
    return;
  }

  setErrorCondition(0);
  dataCheck(false, m->getTotalPoints(), m->getNumFieldTuples(), m->getNumEnsembleTuples());
  if(getErrorCondition() < 0)
  {
    return;
  }

  size_t udims[3] =
  { 0, 0, 0 };
  m->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]), };



  int index;
  std::list<std::string> voxelArrayNames = m->getCellArrayNameList();
  for (int k = m_ZMin; k < m_ZMax+1; k++)
  {
    for (int j = m_YMin; j < m_YMax+1; j++)
    {
      for (int i = m_XMin; i < m_XMax+1; i++)
      {
        index = (k * dims[0] * dims[1]) + (j * dims[0]) + i;
        for (std::list<std::string>::iterator iter = voxelArrayNames.begin(); iter != voxelArrayNames.end(); ++iter)
        {
          std::string name = *iter;
          IDataArray::Pointer p = m->getCellData(*iter);
          p->InitializeTuple(index,0);
        }
      }
    }
  }

  notifyStatusMessage("Completed");
}