コード例 #1
0
// -----------------------------------------------------------------------------
//
// -----------------------------------------------------------------------------
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();
}
コード例 #2
0
// -----------------------------------------------------------------------------
//
// -----------------------------------------------------------------------------
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");
}
コード例 #3
0
ファイル: ChangeResolution.cpp プロジェクト: tuks188/DREAM3D
// -----------------------------------------------------------------------------
//
// -----------------------------------------------------------------------------
void ChangeResolution::preflight()
{
  VoxelDataContainer* m = getVoxelDataContainer();

  size_t dims[3];
  m->getDimensions(dims);

  float sizex = (dims[0])*m->getXRes();
  float sizey = (dims[1])*m->getYRes();
  float sizez = (dims[2])*m->getZRes();
  int m_XP = int(sizex / m_Resolution.x);
  int m_YP = int(sizey / m_Resolution.y);
  int m_ZP = int(sizez / m_Resolution.z);

  m->setDimensions(m_XP, m_YP, m_ZP);
  m->setResolution(m_Resolution.x, m_Resolution.y, m_Resolution.z);
}
コード例 #4
0
// -----------------------------------------------------------------------------
//
// -----------------------------------------------------------------------------
void SegmentGrains::execute()
{
  setErrorCondition(0);
  VoxelDataContainer* m = getVoxelDataContainer();
  std::stringstream ss;
  if(NULL == m)
  {
    setErrorCondition(-1);
    ss << " DataContainer was NULL";
    addErrorMessage(getHumanLabel(), ss.str(), -1);
    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]), };

  size_t gnum = 1;
  int seed = 0;
  int neighbor;
  bool good = 0;
  DimType col, row, plane;
  size_t size = 0;
  size_t initialVoxelsListSize = 1000;
  std::vector<int> voxelslist(initialVoxelsListSize, -1);
  DimType neighpoints[6];
  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]);

  // Burn volume with tight orientation tolerance to simulate simultaneous growth/aglomeration
  while (seed >= 0)
  {
    seed = getSeed(gnum);
    if(seed >= 0)
    {
      size = 0;
      voxelslist[size] = seed;
      size++;
      for (size_t j = 0; j < size; ++j)
      {
        // Get the current Voxel
        size_t currentpoint = voxelslist[j];
        // Figure out the Row, Col & Plane the voxel is located in
        col = currentpoint % dims[0];
        row = (currentpoint / dims[0]) % dims[1];
        plane = currentpoint / (dims[0] * dims[1]);

        // Now loop over its 6 neighbors
        for (int i = 0; i < 6; i++)
        {
          good = true;
          neighbor = currentpoint + neighpoints[i];
          // Make sure we have a valid neighbor taking into account the edges of the volume
          if(i == 0 && plane == 0) good = false;
          if(i == 5 && plane == (dims[2] - 1)) good = false;
          if(i == 1 && row == 0) good = false;
          if(i == 4 && row == (dims[1] - 1)) good = false;
          if(i == 2 && col == 0) good = false;
          if(i == 3 && col == (dims[0] - 1)) good = false;

          if(good == true)
          {
            // We got a good voxel to check so check to see if it can be grouped with this point
            if(determineGrouping(currentpoint, neighbor, gnum) == true)
            {
              // The voxel can be grouped with this voxel so add it to the list of voxels for this grain
              voxelslist[size] = neighbor;
              // Increment the size of the list which affects the "j" loop
              size++;
              // Sanity check the size of the voxelslist vector. If it is not large enough, double the size of the vector
              if(size >= voxelslist.size())
              {
                voxelslist.resize(size + size, -1); // The resize is a hit but the doubling mitigates the penalty somewhat
              }
            }
          }
        }
      }
      voxelslist.clear();
      voxelslist.resize(initialVoxelsListSize, -1);
      gnum++;
      ss.str("");
      ss << "Total Grains: " << gnum;
      if(gnum%100 == 0) notifyStatusMessage(ss.str());
      if (getCancel() == true)
      {
        setErrorCondition(-1);
        break;
      }
    }
  }


  // If there is an error set this to something negative and also set a message
 notifyStatusMessage("Completed");
}
コード例 #5
0
// -----------------------------------------------------------------------------
//
// -----------------------------------------------------------------------------
void IdentifySample::execute()
{
  setErrorCondition(0);
  // int err = 0;
  VoxelDataContainer* m = getVoxelDataContainer();
  if(NULL == m)
  {
    setErrorCondition(-999);
    notifyErrorMessage("The DataContainer Object was NULL", -999);
    return;
  }

  int64_t totalPoints = m->getTotalPoints();
  dataCheck(false, totalPoints, m->getNumFieldTuples(), m->getNumEnsembleTuples());
  if (getErrorCondition() < 0 && getErrorCondition() != -305)
  {
    return;
  }
  setErrorCondition(0);

  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]),
  };

  DimType neighpoints[6];
  DimType xp = dims[0];
  DimType yp = dims[1];
  DimType zp = dims[2];

  neighpoints[0] = -(xp * yp);
  neighpoints[1] = -xp;
  neighpoints[2] = -1;
  neighpoints[3] = 1;
  neighpoints[4] = xp;
  neighpoints[5] = (xp * yp);
  std::vector<int> currentvlist;
  std::vector<bool> checked;
  checked.resize(totalPoints,false);
  std::vector<bool> Sample;
  Sample.resize(totalPoints,false);
  std::vector<bool> notSample;
  notSample.resize(totalPoints,false);
  int biggestBlock = 0;
  size_t count;
  int good;
  int neighbor;
  DimType column, row, plane;
  int index;

  for (int i = 0; i < totalPoints; i++)
  {
    if(checked[i] == false && m_GoodVoxels[i] == false)
    {
      currentvlist.push_back(i);
      count = 0;
      while (count < currentvlist.size())
      {
        index = currentvlist[count];
        column = index % xp;
        row = (index / xp) % yp;
        plane = index / (xp * yp);
        for (int j = 0; j < 6; j++)
        {
          good = 1;
          neighbor = static_cast<int>( index + neighpoints[j] );
          if(j == 0 && plane == 0) good = 0;
          if(j == 5 && plane == (zp - 1)) good = 0;
          if(j == 1 && row == 0) good = 0;
          if(j == 4 && row == (yp - 1)) good = 0;
          if(j == 2 && column == 0) good = 0;
          if(j == 3 && column == (xp - 1)) good = 0;
          if(good == 1 && checked[neighbor] == false && m_GoodVoxels[neighbor] == false)
          {
            currentvlist.push_back(neighbor);
            checked[neighbor] = true;
          }
        }
        count++;
      }
      if(static_cast<int>(currentvlist.size()) >= biggestBlock)
      {
        biggestBlock = currentvlist.size();
        for(int j = 0; j < totalPoints; j++)
        {
          notSample[j] = false;
        }
        for(size_t j = 0; j < currentvlist.size(); j++)
        {
          notSample[currentvlist[j]] = true;
        }
      }
      currentvlist.clear();
    }
  }
  for (int i = 0; i < totalPoints; i++)
  {
    if (notSample[i] == false && m_GoodVoxels[i] == false) m_GoodVoxels[i] = true;
    else if (notSample[i] == true && m_GoodVoxels[i] == true) m_GoodVoxels[i] = false;
  }
  notSample.clear();
  checked.clear();

  biggestBlock = 0;
  checked.resize(totalPoints,false);
  for (int i = 0; i < totalPoints; i++)
  {
    if(checked[i] == false && m_GoodVoxels[i] == true)
    {
      currentvlist.push_back(i);
      count = 0;
      while (count < currentvlist.size())
      {
        index = currentvlist[count];
        column = index % xp;
        row = (index / xp) % yp;
        plane = index / (xp * yp);
        for (int j = 0; j < 6; j++)
        {
          good = 1;
          neighbor = static_cast<int>( index + neighpoints[j] );
          if(j == 0 && plane == 0) good = 0;
          if(j == 5 && plane == (zp - 1)) good = 0;
          if(j == 1 && row == 0) good = 0;
          if(j == 4 && row == (yp - 1)) good = 0;
          if(j == 2 && column == 0) good = 0;
          if(j == 3 && column == (xp - 1)) good = 0;
          if(good == 1 && checked[neighbor] == false && m_GoodVoxels[neighbor] == true)
          {
            currentvlist.push_back(neighbor);
            checked[neighbor] = true;
          }
        }
        count++;
      }
      if(static_cast<int>(currentvlist.size()) >= biggestBlock)
      {
        biggestBlock = currentvlist.size();
        for(int j = 0; j < totalPoints; j++)
        {
          Sample[j] = false;
        }
        for(size_t j = 0; j < currentvlist.size(); j++)
        {
          Sample[currentvlist[j]] = true;
        }
      }
      currentvlist.clear();
    }
  }
  for (int i = 0; i < totalPoints; i++)
  {
    if (Sample[i] == false && m_GoodVoxels[i] == true) m_GoodVoxels[i] = false;
    else if (Sample[i] == true && m_GoodVoxels[i] == false) m_GoodVoxels[i] = true;
  }
  Sample.clear();
  checked.clear();

  /*  std::vector<bool> change;
  change.resize(totalPoints,false);
  for (int i = 0; i < totalPoints; i++)
  {
    if(m_GoodVoxels[i] == false)
    {
        column = i % xp;
        row = (i / xp) % yp;
        plane = i / (xp * yp);
        for (int j = 0; j < 6; j++)
        {
          good = 1;
          neighbor = static_cast<int>( i + neighpoints[j] );
          if(j == 0 && plane == 0) good = 0;
          if(j == 5 && plane == (zp - 1)) good = 0;
          if(j == 1 && row == 0) good = 0;
          if(j == 4 && row == (yp - 1)) good = 0;
          if(j == 2 && column == 0) good = 0;
          if(j == 3 && column == (xp - 1)) good = 0;
          if(good == 1 && m_GoodVoxels[neighbor] == true)
          {
            change[i] = true;
          }
        }
  }
  }
  for(int j = 0; j < totalPoints; j++)
  {
  if(change[j] == true) m_GoodVoxels[j] = true;
  }
  change.clear();
  */
  // If there is an error set this to something negative and also set a message
  notifyStatusMessage("Identifying Sample Complete");
}
コード例 #6
0
ファイル: ChangeResolution.cpp プロジェクト: tuks188/DREAM3D
// -----------------------------------------------------------------------------
//
// -----------------------------------------------------------------------------
void ChangeResolution::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;
  }

  setErrorCondition(0);


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

  if(m->getXRes() == m_Resolution.x
      && m->getYRes() == m_Resolution.y
      && m->getZRes() == m_Resolution.z)
  {
    return;
  }

  size_t dims[3];
  m->getDimensions(dims);


  float sizex = (dims[0])*m->getXRes();
  float sizey = (dims[1])*m->getYRes();
  float sizez = (dims[2])*m->getZRes();
  int m_XP = int(sizex / m_Resolution.x);
  int m_YP = int(sizey / m_Resolution.y);
  int m_ZP = int(sizez / m_Resolution.z);
  int64_t totalPoints = m_XP*m_YP*m_ZP;

  float x, y, z;
  int col, row, plane;
  int index;
  int index_old;
  std::vector<size_t> newindicies;
  newindicies.resize(totalPoints);
  for (int i = 0; i < m_ZP; i++)
  {
    std::stringstream ss;
    ss << "Changing Resolution - " << ((float)i/m->getZPoints())*100 << " Percent Complete";
    notifyStatusMessage(ss.str());
    for (int j = 0; j < m_YP; j++)
    {
      for (int k = 0; k < m_XP; k++)
      {
        x = (k * m_Resolution.x);
        y = (j * m_Resolution.y);
        z = (i * m_Resolution.z);
        col = int(x / m->getXRes());
        row = int(y / m->getYRes());
        plane = int(z / m->getZRes());
        index_old = (plane * m->getXPoints() * m->getYPoints()) + (row * m->getXPoints()) + col;
        index = (i * m_XP * m_YP) + (j * m_XP) + k;
    newindicies[index] = index_old;
      }
    }
  }

  std::list<std::string> voxelArrayNames = m->getCellArrayNameList();
  for (std::list<std::string>::iterator iter = voxelArrayNames.begin(); iter != voxelArrayNames.end(); ++iter)
  {
    std::string name = *iter;
    IDataArray::Pointer p = m->getCellData(*iter);
    // Make a copy of the 'p' array that has the same name. When placed into
    // the data container this will over write the current array with
    // the same name. At least in theory
    IDataArray::Pointer data = p->createNewArray(p->GetNumberOfTuples(), p->GetNumberOfComponents(), p->GetName());
    data->Resize(totalPoints);
    void* source = NULL;
    void* destination = NULL;
    size_t newIndicies_I = 0;
    int nComp = data->GetNumberOfComponents();
    for (size_t i = 0; i < static_cast<size_t>(totalPoints); i++)
    {
      newIndicies_I = newindicies[i];

      source = p->GetVoidPointer((nComp * newIndicies_I));
      destination = data->GetVoidPointer((data->GetNumberOfComponents() * i));
      ::memcpy(destination, source, p->GetTypeSize() * data->GetNumberOfComponents());
    }
    m->addCellData(*iter, data);
  }
  m->setResolution(m_Resolution.x, m_Resolution.y, m_Resolution.z);
  m->setDimensions(m_XP, m_YP, m_ZP);

  notifyStatusMessage("Complete");
}
コード例 #7
0
// -----------------------------------------------------------------------------
//
// -----------------------------------------------------------------------------
void AlignSectionsFeature::find_shifts(std::vector<int> &xshifts, std::vector<int> &yshifts)
{
  VoxelDataContainer* m = getVoxelDataContainer();
  //int64_t totalPoints = m->totalPoints();

  std::ofstream outFile;
  if (getWriteAlignmentShifts() == true) {
    outFile.open(getAlignmentShiftFileName().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]),
  };

  float disorientation = 0;
  float mindisorientation = 100000000;
  int newxshift = 0;
  int newyshift = 0;
  int oldxshift = 0;
  int oldyshift = 0;
  float count = 0;
  int slice = 0;
//  int xspot, yspot;
  int refposition = 0;
  int curposition = 0;

  std::vector<std::vector<float> >  misorients;
  misorients.resize(dims[0]);
  for (DimType a = 0; a < dims[0]; a++)
  {
    misorients[a].resize(dims[1], 0.0);
  }
  for (DimType iter = 1; iter < dims[2]; iter++)
  {
    std::stringstream ss;
    ss << "Aligning Sections - Determining Shifts - " << ((float)iter/dims[2])*100 << " Percent Complete";
  //  notifyStatusMessage(ss.str());
    mindisorientation = 100000000;
    slice = static_cast<int>( (dims[2] - 1) - iter );
    oldxshift = -1;
    oldyshift = -1;
    newxshift = 0;
    newyshift = 0;
    for (DimType a = 0; a < dims[0]; a++)
    {
      for (DimType b = 0; b < dims[1]; b++)
      {
        misorients[a][b] = 0;
      }
    }
    while (newxshift != oldxshift || newyshift != oldyshift)
    {
      oldxshift = newxshift;
      oldyshift = newyshift;
      for (int j = -3; j < 4; j++)
      {
        for (int k = -3; k < 4; k++)
        {
          disorientation = 0;
          count = 0;
          if(misorients[k + oldxshift + size_t(dims[0] / 2)][j + oldyshift + (size_t)(dims[1] / 2)] == 0 && abs(k + oldxshift) < (dims[0] / 2)
              && (j + oldyshift) < (dims[1] / 2))
          {
            for (DimType l = 0; l < dims[1]; l = l + 4)
            {
              for (DimType n = 0; n < dims[0]; n = n + 4)
              {
                if((l + j + oldyshift) >= 0 && (l + j + oldyshift) < dims[1] && (n + k + oldxshift) >= 0 && (n + k + oldxshift) < dims[0])
                {
                  refposition = static_cast<int>( ((slice + 1) * dims[0] * dims[1]) + (l * dims[0]) + n );
                  curposition = static_cast<int>( (slice * dims[0] * dims[1]) + ((l + j + oldyshift) * dims[0]) + (n + k + oldxshift) );
                  if(m_GoodVoxels[refposition] != m_GoodVoxels[curposition]) disorientation++;
                count++;
                }
                else
                {

        }
              }
            }
            disorientation = disorientation/count;
            misorients[k + oldxshift + int(dims[0] / 2)][j + oldyshift + int(dims[1] / 2)] = disorientation;
            if(disorientation < mindisorientation)
            {
              newxshift = k + oldxshift;
              newyshift = j + oldyshift;
              mindisorientation = disorientation;
            }
          }
        }
      }
    }
    xshifts[iter] = xshifts[iter-1] + newxshift;
    yshifts[iter] = yshifts[iter-1] + newyshift;
    if (getWriteAlignmentShifts() == true) {
      outFile << slice << "	" << slice+1 << "	" << newxshift << "	" << newyshift << "	" << xshifts[iter] << "	" << yshifts[iter] << std::endl;
    }
  }
  if (getWriteAlignmentShifts() == true) {
    outFile.close();
  }
}
コード例 #8
0
ファイル: Threshold.cpp プロジェクト: leavy/DREAM3D
// -----------------------------------------------------------------------------
//
// -----------------------------------------------------------------------------
void Threshold::execute()
{
  std::stringstream ss;
  int err = 0;
  setErrorCondition(err);
  VoxelDataContainer* m = getVoxelDataContainer();
  if(NULL == m)
  {
    setErrorCondition(-999);
    notifyErrorMessage("The DataContainer Object was NULL", getErrorCondition());
    return;
  }
  setErrorCondition(0);
  int64_t totalPoints = m->getTotalPoints();
  size_t totalFields = m->getNumFieldTuples();
  size_t totalEnsembles = m->getNumEnsembleTuples();
  dataCheck(false, totalPoints, totalFields, totalEnsembles);
  if(m_OverwriteArray)
  {
    CREATE_NON_PREREQ_DATA(m, DREAM3D, CellData, ProcessedImageData, ss, ImageProcessing::DefaultPixelType, ImageProcessing::DefaultArrayType, 0, totalPoints, 1)
  }
  if (getErrorCondition() < 0)
  {
    return;
  }

  //get dims
  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]),
  };

    //wrap input as itk image
    ImageProcessing::DefaultImageType::Pointer inputImage=ITKUtilities::Dream3DtoITK(m, m_RawImageData);

    //define threshold filters
    typedef itk::BinaryThresholdImageFilter <ImageProcessing::DefaultImageType, ImageProcessing::DefaultImageType> BinaryThresholdImageFilterType;
    typedef itk::BinaryThresholdImageFilter <ImageProcessing::DefaultSliceType, ImageProcessing::DefaultSliceType> BinaryThresholdImageFilterType2D;

  if(m_Method>=0 && m_Method<=11)
  {
     //define hitogram generator (will make the same kind of histogram for 2 and 3d images
    typedef itk::Statistics::ImageToHistogramFilter<ImageProcessing::DefaultImageType> HistogramGenerator;

    //find threshold value w/ histogram
    itk::HistogramThresholdCalculator< HistogramGenerator::HistogramType, uint8_t >::Pointer calculator;

    typedef itk::HuangThresholdCalculator< HistogramGenerator::HistogramType, uint8_t > HuangCalculatorType;
    typedef itk::IntermodesThresholdCalculator< HistogramGenerator::HistogramType, uint8_t > IntermodesCalculatorType;
    typedef itk::IsoDataThresholdCalculator< HistogramGenerator::HistogramType, uint8_t > IsoDataCalculatorType;
    typedef itk::KittlerIllingworthThresholdCalculator< HistogramGenerator::HistogramType, uint8_t > KittlerIllingowrthCalculatorType;
    typedef itk::LiThresholdCalculator< HistogramGenerator::HistogramType, uint8_t > LiCalculatorType;
    typedef itk::MaximumEntropyThresholdCalculator< HistogramGenerator::HistogramType, uint8_t > MaximumEntropyCalculatorType;
    typedef itk::MomentsThresholdCalculator< HistogramGenerator::HistogramType, uint8_t > MomentsCalculatorType;
    typedef itk::OtsuThresholdCalculator< HistogramGenerator::HistogramType, uint8_t > OtsuCalculatorType;
    typedef itk::RenyiEntropyThresholdCalculator< HistogramGenerator::HistogramType, uint8_t > RenyiEntropyCalculatorType;
    typedef itk::ShanbhagThresholdCalculator< HistogramGenerator::HistogramType, uint8_t > ShanbhagCalculatorType;
    typedef itk::TriangleThresholdCalculator< HistogramGenerator::HistogramType, uint8_t > TriangleCalculatorType;
    typedef itk::YenThresholdCalculator< HistogramGenerator::HistogramType, uint8_t > YenCalculatorType;

    switch(m_Method)
    {
      case 0:
        {
          calculator = HuangCalculatorType::New();
        }
        break;

      case 1:
        {
          calculator = IntermodesCalculatorType::New();
        }
        break;

      case 2:
        {
          calculator = IsoDataCalculatorType::New();
        }
        break;

      case 3:
        {
          calculator = KittlerIllingowrthCalculatorType::New();
        }
        break;

      case 4:
        {
          calculator = LiCalculatorType::New();
        }
        break;

      case 5:
        {
          calculator = MaximumEntropyCalculatorType::New();
        }
        break;

      case 6:
        {
          calculator = MomentsCalculatorType::New();
        }
        break;

      case 7:
        {
          calculator = OtsuCalculatorType::New();
        }
        break;

      case 8:
        {
          calculator = RenyiEntropyCalculatorType::New();
        }
        break;

      case 9:
        {
          calculator = ShanbhagCalculatorType::New();
        }
        break;

      case 10:
        {
          calculator = TriangleCalculatorType::New();
        }
        break;

      case 11:
        {
          calculator = YenCalculatorType::New();
        }
        break;
    }

    if(m_Slice)
    {
      //define 2d histogram generator
      typedef itk::Statistics::ImageToHistogramFilter<ImageProcessing::DefaultSliceType> HistogramGenerator2D;
      HistogramGenerator2D::Pointer histogramFilter2D = HistogramGenerator2D::New();

      //specify number of bins / bounds
      typedef HistogramGenerator2D::HistogramSizeType SizeType;
      SizeType size( 1 );
      size[0] = 255;
      histogramFilter2D->SetHistogramSize( size );
      histogramFilter2D->SetMarginalScale( 10.0 );
      HistogramGenerator2D::HistogramMeasurementVectorType lowerBound( 1 );
      HistogramGenerator2D::HistogramMeasurementVectorType upperBound( 1 );
      lowerBound[0] = 0;
      upperBound[0] = 256;
      histogramFilter2D->SetHistogramBinMinimum( lowerBound );
      histogramFilter2D->SetHistogramBinMaximum( upperBound );

      //wrap output buffer as image
      ImageProcessing::DefaultImageType::Pointer outputImage=ITKUtilities::Dream3DtoITK(m, m_ProcessedImageData);

      //loop over slices
      for(int i=0; i<dims[2]; i++)
      {
        //get slice
        ImageProcessing::DefaultSliceType::Pointer slice = ITKUtilities::ExtractSlice<ImageProcessing::DefaultPixelType>(inputImage, ImageProcessing::ZSlice, i);

        //find histogram
        histogramFilter2D->SetInput( slice );
        histogramFilter2D->Update();
        const HistogramGenerator::HistogramType * histogram = histogramFilter2D->GetOutput();

        //calculate threshold level
        calculator->SetInput(histogram);
        calculator->Update();
        const uint8_t thresholdValue = calculator->GetThreshold();

        //threshold
        BinaryThresholdImageFilterType2D::Pointer thresholdFilter = BinaryThresholdImageFilterType2D::New();
        thresholdFilter->SetInput(slice);
        thresholdFilter->SetLowerThreshold(thresholdValue);
        thresholdFilter->SetUpperThreshold(255);
        thresholdFilter->SetInsideValue(255);
        thresholdFilter->SetOutsideValue(0);
        thresholdFilter->Update();

        //copy back into volume
        ITKUtilities::SetSlice<ImageProcessing::DefaultPixelType>(outputImage, thresholdFilter->GetOutput(), ImageProcessing::ZSlice, i);
      }
    }
    else
    {
      //specify number of bins / bounds
      HistogramGenerator::Pointer histogramFilter = HistogramGenerator::New();
      typedef HistogramGenerator::HistogramSizeType SizeType;
      SizeType size( 1 );
      size[0] = 255;
      histogramFilter->SetHistogramSize( size );
      histogramFilter->SetMarginalScale( 10.0 );
      HistogramGenerator::HistogramMeasurementVectorType lowerBound( 1 );
      HistogramGenerator::HistogramMeasurementVectorType upperBound( 1 );
      lowerBound[0] = 0;
      upperBound[0] = 256;
      histogramFilter->SetHistogramBinMinimum( lowerBound );
      histogramFilter->SetHistogramBinMaximum( upperBound );

      //find histogram
      histogramFilter->SetInput( inputImage );
      histogramFilter->Update();
      const HistogramGenerator::HistogramType * histogram = histogramFilter->GetOutput();

      //calculate threshold level
      calculator->SetInput(histogram);
      calculator->Update();
      const uint8_t thresholdValue = calculator->GetThreshold();

      //threshold
      BinaryThresholdImageFilterType::Pointer thresholdFilter = BinaryThresholdImageFilterType::New();
      thresholdFilter->SetInput(inputImage);
      thresholdFilter->SetLowerThreshold(thresholdValue);
      thresholdFilter->SetUpperThreshold(255);
      thresholdFilter->SetInsideValue(255);
      thresholdFilter->SetOutsideValue(0);
      thresholdFilter->GetOutput()->GetPixelContainer()->SetImportPointer(m_ProcessedImageData, totalPoints, false);
      thresholdFilter->Update();
    }
  }
  else if(m_Method==12)//manual
  {
    //threshold
    BinaryThresholdImageFilterType::Pointer thresholdFilter = BinaryThresholdImageFilterType::New();
    thresholdFilter->SetInput(inputImage);
    thresholdFilter->SetLowerThreshold(m_ManualParameter);
    thresholdFilter->SetUpperThreshold(255);
    thresholdFilter->SetInsideValue(255);
    thresholdFilter->SetOutsideValue(0);
    thresholdFilter->GetOutput()->GetPixelContainer()->SetImportPointer(m_ProcessedImageData, totalPoints, false);
    thresholdFilter->Update();
  }
  /*
  else if(m_Method==13)//robust automatic
  {
    typedef itk::GradientMagnitudeImageFilter<ImageProcessing::DefaultImageType, ImageProcessing::DefaultImageType>  GradientMagnitudeType;
    typedef itk::GradientMagnitudeImageFilter<ImageProcessing::DefaultSliceType, ImageProcessing::DefaultSliceType>  GradientMagnitudeType2D;

    typedef itk::itkRobustAutomaticThresholdCalculator<ImageProcessing::DefaultImageType,ImageProcessing::DefaultImageType> SelectionType;
    typedef itk::itkRobustAutomaticThresholdCalculator<ImageProcessing::DefaultSliceType,ImageProcessing::DefaultSliceType> SelectionType2D;

    if(m_slice)
    {
      //wrap output buffer as image
      ImageProcessing::DefaultImageType::Pointer outputImage=ITKUtilities::Dream3DtoITK(m, m_ProcessedImageData);

      //loop over slices
      for(int i=0; i<dims[2]; i++)
      {
        //get slice
        ImageProcessing::DefaultSliceType::Pointer slice = ITKUtilities::ExtractSlice<ImageProcessing::DefaultPixelType>(inputImage, ImageProcessing::ZSlice, i);

        //find gradient
        GradientMagnitudeType2D::Pointer gradientFilter = GradientMagnitudeType2D::New();
        gradientFilter->setInput(slice);
        gradientFilter->Update();

        //calculate thershold
        SelectionType2D::Pointer calculatorFilter = SelectionType2D::New();
        calculatorFilter->SetInput(slice);
        calculatorFilter->SetGradientImage(gradientFilter->GetOutput());
        calculatorFilter->SetPow(m_ManualParameter);
        calculatorFilter->Update();
        const uint8_t thresholdValue = calculatorFilter->GetOutput();

        //threshold
        BinaryThresholdImageFilterType::Pointer thresholdFilter = BinaryThresholdImageFilterType::New();
        thresholdFilter->SetInput(inputImage);
        thresholdFilter->SetLowerThreshold(thresholdValue);
        thresholdFilter->SetUpperThreshold(255);
        thresholdFilter->SetInsideValue(255);
        thresholdFilter->SetOutsideValue(0);
        thresholdFilter->Update();

        //copy back into volume
        ITKUtilities::SetSlice<ImageProcessing::DefaultPixelType>(outputImage, thresholdFilter->GetOutput(), ImageProcessing::ZSlice, i);
      }
    }
    else
    {
      //find gradient
      GradientMagnitudeType::Pointer gradientFilter = GradientMagnitudeType::New();
      gradientFilter->setInput(inputImage);
      gradientFilter->Update();

      //calculate threshold
      SelectionType::Pointer calculatorFilter = SelectionType::New();
      calculatorFilter->SetInput(inputImage);
      calculatorFilter->SetGradientImage(gradientFilter->GetOutput());
      calculatorFilter->SetPow(m_ManualParameter);
      calculatorFilter->Update();
      const uint8_t thresholdValue = calculatorFilter->GetOutput();

      //threshold
      BinaryThresholdImageFilterType::Pointer thresholdFilter = BinaryThresholdImageFilterType::New();
      thresholdFilter->SetInput(inputImage);
      thresholdFilter->SetLowerThreshold(thresholdValue);
      thresholdFilter->SetUpperThreshold(255);
      thresholdFilter->SetInsideValue(255);
      thresholdFilter->SetOutsideValue(0);
      thresholdFilter->GetOutput()->GetPixelContainer()->SetImportPointer(m_ProcessedImageData, totalPoints, false);
      thresholdFilter->Update();
    }
  }
  */


  //array name changing/cleanup
  if(m_OverwriteArray)
  {
    m->removeCellData(m_SelectedCellArrayName);
    bool check = m->renameCellData(m_ProcessedImageDataArrayName, m_SelectedCellArrayName);
  }

  /* Let the GUI know we are done with this filter */
   notifyStatusMessage("Complete");
}
コード例 #9
0
// -----------------------------------------------------------------------------
//
// -----------------------------------------------------------------------------
void AlignSections::execute()
{
  setErrorCondition(0);
  VoxelDataContainer* m = getVoxelDataContainer();
  if (NULL == m)
  {
    setErrorCondition(-1);
    std::stringstream ss;
    ss << " DataContainer was NULL";
    notifyErrorMessage(ss.str(), -1);
    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;
  }

  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 xspot, yspot;
  DimType newPosition;
  DimType currentPosition;
  //  unsigned int  phase2;

  std::vector<int> xshifts;
  std::vector<int> yshifts;
  xshifts.resize(dims[2],0);
  yshifts.resize(dims[2],0);

  find_shifts(xshifts, yshifts);

  std::list<std::string> voxelArrayNames = m->getCellArrayNameList();
  DimType progIncrement = dims[2]/100;
  DimType prog = 1;
  int progressInt = 0;
  std::stringstream ss;

  for (DimType i = 1; i < dims[2]; i++)
  {
    if (i > prog)
    {
      ss.str("");
      progressInt = ((float)i/dims[2])*100.0;
      ss << "Transferring Cell Data - " << progressInt << "% Complete";
      notifyStatusMessage(ss.str());
      prog = prog + progIncrement;
    }
    if (getCancel() == true)
    {
      return;
    }
    slice = static_cast<int>( (dims[2] - 1) - i );
    for (DimType l = 0; l < dims[1]; l++)
    {
      for (DimType n = 0; n < dims[0]; n++)
      {
        if(yshifts[i] >= 0) yspot = static_cast<int>(l);
        else if(yshifts[i] < 0) yspot = static_cast<int>( dims[1] - 1 - l );
        if(xshifts[i] >= 0) xspot = static_cast<int>(n);
        else if(xshifts[i] < 0) xspot = static_cast<int>( dims[0] - 1 - n );
        newPosition = (slice * dims[0] * dims[1]) + (yspot * dims[0]) + xspot;
        currentPosition = (slice * dims[0] * dims[1]) + ((yspot + yshifts[i]) * dims[0]) + (xspot + xshifts[i]);
        if((yspot + yshifts[i]) >= 0 && (yspot + yshifts[i]) <= dims[1] - 1 && (xspot + xshifts[i]) >= 0
           && (xspot + xshifts[i]) <= dims[0] - 1)
        {
          for(std::list<std::string>::iterator iter = voxelArrayNames.begin(); iter != voxelArrayNames.end(); ++iter)
          {
            std::string name = *iter;
            IDataArray::Pointer p = m->getCellData(*iter);
            p->CopyTuple(currentPosition, newPosition);
          }
        }
        if((yspot + yshifts[i]) < 0 || (yspot + yshifts[i]) > dims[1] - 1 || (xspot + xshifts[i]) < 0
           || (xspot + xshifts[i]) > dims[0] - 1)
        {
          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(newPosition, 0.0);          }
        }
      }
    }
  }

  // If there is an error set this to something negative and also set a message
  notifyStatusMessage("Complete");
}
コード例 #10
0
ファイル: OpenCloseBadData.cpp プロジェクト: tuks188/DREAM3D
// -----------------------------------------------------------------------------
//
// -----------------------------------------------------------------------------
void OpenCloseBadData::execute()
{
  setErrorCondition(0);
 // int err = 0;
  VoxelDataContainer* m = getVoxelDataContainer();
  if(NULL == m)
  {
    setErrorCondition(-999);
    notifyErrorMessage("The DataContainer Object was NULL", -999);
    return;
  }


  int64_t totalPoints = m->getTotalPoints();
  dataCheck(false, totalPoints, m->getNumFieldTuples(), m->getNumEnsembleTuples());
  if (getErrorCondition() < 0 && getErrorCondition() != -305)
  {
    return;
  }
  setErrorCondition(0);

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

  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]),
  };

//  size_t count = 1;
  int good = 1;
//  int neighbor;
//  int index = 0;
//  float x, y, z;
//  DimType row, plane;
  int neighpoint;
  size_t numgrains = m->getNumFieldTuples();

  int neighpoints[6];
  neighpoints[0] = static_cast<int>(-dims[0] * dims[1]);
  neighpoints[1] = static_cast<int>(-dims[0]);
  neighpoints[2] = static_cast<int>(-1);
  neighpoints[3] = static_cast<int>(1);
  neighpoints[4] = static_cast<int>(dims[0]);
  neighpoints[5] = static_cast<int>(dims[0] * dims[1]);
  std::vector<int> currentvlist;

  size_t count = 0;
  int kstride, jstride;
  int grainname, grain;

  int current;
  int most;

  std::vector<int > n(numgrains + 1,0);
  for (int iteration = 0; iteration < m_NumIterations; iteration++)
  {
    for (int k = 0; k < dims[2]; k++)
    {
    kstride = static_cast<int>( dims[0]*dims[1]*k );
      for (int j = 0; j < dims[1]; j++)
      {
      jstride = static_cast<int>( dims[0]*j );
        for (int i = 0; i < dims[0]; i++)
        {
        count = kstride+jstride+i;
        std::stringstream ss;
        grainname = m_GrainIds[count];
        if (grainname == 0)
        {
			current = 0;
			most = 0;
			for (int l = 0; l < 6; l++)
			{
			  good = 1;
			  neighpoint = static_cast<int>( count + 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)
			  {
				  grain = m_GrainIds[neighpoint];
				  if (m_Direction == 0 && grain > 0)
				  {
					m_Neighbors[neighpoint] = count;
				  }
				  if ((grain > 0 && m_Direction == 1))
				  {
					n[grain]++;
					current = n[grain];
					if (current > most)
					{
					  most = current;
					  m_Neighbors[count] = neighpoint;
					}
				  }
			  }
			}
			if (m_Direction == 1)
			{
			  for (int l = 0; l < 6; l++)
			  {
  				good = 1;
				neighpoint = static_cast<int>( count + 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)
				{
					grain = m_GrainIds[neighpoint];
					n[grain] = 0;
				}
			  }
			}
        }
      }
    }

    }
    std::list<std::string> voxelArrayNames = m->getCellArrayNameList();
    for (int j = 0; j < totalPoints; j++)
    {
      int grainname = m_GrainIds[j];
      int neighbor = m_Neighbors[j];
      if (neighbor >= 0)
      {
        if ( (grainname == 0 && m_GrainIds[neighbor] > 0 && m_Direction == 1)
            || (grainname > 0 && m_GrainIds[neighbor] == 0 && m_Direction == 0))
        {
            for(std::list<std::string>::iterator iter = voxelArrayNames.begin(); iter != voxelArrayNames.end(); ++iter)
            {
              std::string name = *iter;
              IDataArray::Pointer p = m->getCellData(*iter);
              p->CopyTuple(neighbor, j);
            }
        }
      }
    }
  }

  // If there is an error set this to something negative and also set a message
  notifyStatusMessage("Complete");
}
コード例 #11
0
// -----------------------------------------------------------------------------
//
// -----------------------------------------------------------------------------
void QuickSolidMesh::execute()
{
  setErrorCondition(0);
  VoxelDataContainer* m = getVoxelDataContainer();
  SolidMeshDataContainer* sm = getSolidMeshDataContainer();
  if(NULL == m)
  {
    setErrorCondition(-999);
    notifyErrorMessage("The DataContainer Object was NULL", -999);
    return;
  }
  setErrorCondition(0);

  int64_t totalPoints = m->getTotalPoints();
  size_t totalFields = m->getNumFieldTuples();
  size_t totalEnsembles = m->getNumEnsembleTuples();
  dataCheck(false, totalPoints, totalFields, totalEnsembles);
  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]),
  };

  size_t xP = dims[0];
  size_t yP = dims[1];
  size_t zP = dims[2];
  float xRes = m->getXRes();
  float yRes = m->getYRes();
  float zRes = m->getZRes();

  int numNodes = (xP+1)*(yP+1)*(zP+1);
  int numTetrahedrons = 6*(xP*yP*zP);

  size_t point;
  size_t nodeId1, nodeId2, nodeId3, nodeId4, nodeId5, nodeId6, nodeId7, nodeId8;

  StructArray<Node>::Pointer vertices = StructArray<Node>::CreateArray(numNodes, DREAM3D::CellData::SolidMeshNodes);
  StructArray<Tetrahedron>::Pointer tetrahedrons = StructArray<Tetrahedron>::CreateArray(numTetrahedrons, DREAM3D::CellData::SolidMeshTetrahedrons);
  Node* vertex = vertices.get()->GetPointer(0);
  Tetrahedron* tetrahedron = tetrahedrons.get()->GetPointer(0);

  for(size_t k = 0; k < zP; k++)
  {
	  for(size_t j = 0; j < yP; j++)
	  {
		  for(size_t i = 0; i < xP; i++)
		  {
			point = (k*xP*yP)+(j*xP)+i;

			nodeId1 = (k*(xP+1)*(yP+1)) + (j*(xP+1)) + i;
			vertex[nodeId1].coord[0] = (i*xRes) - (xRes/2.0);
			vertex[nodeId1].coord[1] = (j*yRes) - (yRes/2.0);
			vertex[nodeId1].coord[2] = (k*zRes) - (zRes/2.0);

			nodeId2 = (k*(xP+1)*(yP+1)) + (j*(xP+1)) + (i+1);
			vertex[nodeId2].coord[0] = ((i+1)*xRes) - (xRes/2.0);
			vertex[nodeId2].coord[1] = (j*yRes) - (yRes/2.0);
			vertex[nodeId2].coord[2] = (k*zRes) - (zRes/2.0);

			nodeId3 = (k*(xP+1)*(yP+1)) + ((j+1)*(xP+1)) + i;
			vertex[nodeId3].coord[0] = (i*xRes) - (xRes/2.0);
			vertex[nodeId3].coord[1] = ((j+1)*yRes) - (yRes/2.0);
			vertex[nodeId3].coord[2] = (k*zRes) - (zRes/2.0);

			nodeId4 = (k*(xP+1)*(yP+1)) + ((j+1)*(xP+1)) + (i+1);
			vertex[nodeId4].coord[0] = ((i+1)*xRes) - (xRes/2.0);
			vertex[nodeId4].coord[1] = ((j+1)*yRes) - (yRes/2.0);
			vertex[nodeId4].coord[2] = (k*zRes) - (zRes/2.0);

			nodeId5 = ((k+1)*(xP+1)*(yP+1)) + (j*(xP+1)) + i;
			vertex[nodeId5].coord[0] = (i*xRes) - (xRes/2.0);
			vertex[nodeId5].coord[1] = (j*yRes) - (yRes/2.0);
			vertex[nodeId5].coord[2] = ((k+1)*zRes) - (zRes/2.0);

			nodeId6 = ((k+1)*(xP+1)*(yP+1)) + (j*(xP+1)) + (i+1);
			vertex[nodeId6].coord[0] = ((i+1)*xRes) - (xRes/2.0);
			vertex[nodeId6].coord[1] = (j*yRes) - (yRes/2.0);
			vertex[nodeId6].coord[2] = ((k+1)*zRes) - (zRes/2.0);

			nodeId7 = ((k+1)*(xP+1)*(yP+1)) + ((j+1)*(xP+1)) + i;
			vertex[nodeId7].coord[0] = (i*xRes) - (xRes/2.0);
			vertex[nodeId7].coord[1] = ((j+1)*yRes) - (yRes/2.0);
			vertex[nodeId7].coord[2] = ((k+1)*zRes) - (zRes/2.0);

			nodeId8 = ((k+1)*(xP+1)*(yP+1)) + ((j+1)*(xP+1)) + (i+1);
			vertex[nodeId8].coord[0] = ((i+1)*xRes) - (xRes/2.0);
			vertex[nodeId8].coord[1] = ((j+1)*yRes) - (yRes/2.0);
			vertex[nodeId8].coord[2] = ((k+1)*zRes) - (zRes/2.0);

			tetrahedron[6*point].node_id[0] = nodeId1;
			tetrahedron[6*point].node_id[1] = nodeId2;
			tetrahedron[6*point].node_id[2] = nodeId3;
			tetrahedron[6*point].node_id[3] = nodeId7;
			tetrahedron[6*point].nSpin = m_GrainIds[point];

			tetrahedron[6*point+1].node_id[0] = nodeId2;
			tetrahedron[6*point+1].node_id[1] = nodeId4;
			tetrahedron[6*point+1].node_id[2] = nodeId3;
			tetrahedron[6*point+1].node_id[3] = nodeId7;
			tetrahedron[6*point+1].nSpin = m_GrainIds[point];

			tetrahedron[6*point+2].node_id[0] = nodeId1;
			tetrahedron[6*point+2].node_id[1] = nodeId2;
			tetrahedron[6*point+2].node_id[2] = nodeId7;
			tetrahedron[6*point+2].node_id[3] = nodeId5;
			tetrahedron[6*point+2].nSpin = m_GrainIds[point];

			tetrahedron[6*point+3].node_id[0] = nodeId2;
			tetrahedron[6*point+3].node_id[1] = nodeId4;
			tetrahedron[6*point+3].node_id[2] = nodeId7;
			tetrahedron[6*point+3].node_id[3] = nodeId8;
			tetrahedron[6*point+3].nSpin = m_GrainIds[point];

			tetrahedron[6*point+4].node_id[0] = nodeId2;
			tetrahedron[6*point+4].node_id[1] = nodeId5;
			tetrahedron[6*point+4].node_id[2] = nodeId6;
			tetrahedron[6*point+4].node_id[3] = nodeId7;
			tetrahedron[6*point+4].nSpin = m_GrainIds[point];

			tetrahedron[6*point+5].node_id[0] = nodeId6;
			tetrahedron[6*point+5].node_id[1] = nodeId8;
			tetrahedron[6*point+5].node_id[2] = nodeId2;
			tetrahedron[6*point+5].node_id[3] = nodeId7;
			tetrahedron[6*point+5].nSpin = m_GrainIds[point];
		  }

	  }
  }

  sm->setTetrahedrons(tetrahedrons);
  sm->setNodes(vertices);

  notifyStatusMessage("Complete");
}
コード例 #12
0
ファイル: FindNeighbors.cpp プロジェクト: leavy/DREAM3D
// -----------------------------------------------------------------------------
//
// -----------------------------------------------------------------------------
void FindNeighbors::execute()
{
  setErrorCondition(0);
  std::stringstream ss;
  VoxelDataContainer* m = getVoxelDataContainer();
  if(NULL == m)
  {
    setErrorCondition(-999);
    notifyErrorMessage("The DataContainer Object was NULL", -999);
    return;
  }


  int64_t totalPoints = m->getTotalPoints();
  int totalFields = int(m->getNumFieldTuples());
  dataCheck(false, totalPoints, totalFields, 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]),
  };

  DimType neighpoints[6];
  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];

  float column, row, plane;
  int grain;
  size_t nnum;
  int onsurf = 0;
  int good = 0;
  int neighbor = 0;

  //size_t xtalCount = m->getEnsembleData(DREAM3D::EnsembleData::CrystalStructures)->GetNumberOfTuples();

    std::vector<std::vector<int> > neighborlist;
    std::vector<std::vector<float> > neighborsurfacearealist;

  int nListSize = 100;
  neighborlist.resize(totalFields);
  neighborsurfacearealist.resize(totalFields);
  for (int i = 1; i < totalFields; i++)
  {
    std::stringstream ss;
    ss << "Finding Neighbors - Initializing Neighbor Lists - " << (static_cast<float>(i)/totalFields)*100 << " Percent Complete";
 //   notifyStatusMessage(ss.str());
    m_NumNeighbors[i] = 0;
    neighborlist[i].resize(nListSize);
    neighborsurfacearealist[i].resize(nListSize, -1.0);
  m_SurfaceFields[i] = false;
  }

  totalPoints = m->getTotalPoints();

  for (int64_t j = 0; j < totalPoints; j++)
  {
    std::stringstream ss;
    ss << "Finding Neighbors - Determining Neighbor Lists - " << (static_cast<float>(j)/totalPoints)*100 << " Percent Complete";
 //   notifyStatusMessage(ss.str());
    onsurf = 0;
    grain = m_GrainIds[j];
    if(grain > 0)
    {
      column = static_cast<float>( j % m->getXPoints() );
      row = static_cast<float>( (j / m->getXPoints()) % m->getYPoints() );
      plane = static_cast<float>( j / (m->getXPoints() * m->getYPoints()) );
      if((column == 0 || column == (m->getXPoints() - 1) || row == 0 || row == (m->getYPoints() - 1) || plane == 0 || plane == (m->getZPoints() - 1)) && m->getZPoints() != 1)
      {
        m_SurfaceFields[grain] = true;
      }
      if((column == 0 || column == (m->getXPoints() - 1) || row == 0 || row == (m->getYPoints() - 1)) && m->getZPoints() == 1)
      {
        m_SurfaceFields[grain] = true;
      }
      for (int k = 0; k < 6; k++)
      {
        good = 1;
        neighbor = static_cast<int>( j + neighpoints[k] );
        if(k == 0 && plane == 0) good = 0;
        if(k == 5 && plane == (m->getZPoints() - 1)) good = 0;
        if(k == 1 && row == 0) good = 0;
        if(k == 4 && row == (m->getYPoints() - 1)) good = 0;
        if(k == 2 && column == 0) good = 0;
        if(k == 3 && column == (m->getXPoints() - 1)) good = 0;
        if(good == 1 && m_GrainIds[neighbor] != grain && m_GrainIds[neighbor] > 0)
        {
          onsurf++;
          nnum = m_NumNeighbors[grain];
          neighborlist[grain].push_back(m_GrainIds[neighbor]);
          nnum++;
          m_NumNeighbors[grain] = static_cast<int32_t>(nnum);
        }
      }
    }
    m_SurfaceVoxels[j] = onsurf;
  }

  // We do this to create new set of NeighborList objects
  dataCheck(false, totalPoints, totalFields, m->getNumEnsembleTuples());

  for (size_t i = 1; i < m->getNumFieldTuples(); i++)
  {
    std::stringstream ss;
    ss << "Finding Neighbors - Calculating Surface Areas - " << ((float)i/totalFields)*100 << " Percent Complete";
  //  notifyStatusMessage(ss.str());

    std::map<int, int> neighToCount;
    int numneighs = static_cast<int>( neighborlist[i].size() );

    // this increments the voxel counts for each grain
    for (int j = 0; j < numneighs; j++)
    {
      neighToCount[neighborlist[i][j]]++;
    }

    neighToCount.erase(0);
    neighToCount.erase(-1);
    //Resize the grains neighbor list to zero
    neighborlist[i].resize(0);
    neighborsurfacearealist[i].resize(0);

    for (std::map<int, int>::iterator iter = neighToCount.begin(); iter != neighToCount.end(); ++iter)
    {
      int neigh = iter->first; // get the neighbor grain
      int number = iter->second; // get the number of voxels
      float area = number * m->getXRes() * m->getYRes();

      // Push the neighbor grain id back onto the list so we stay synced up
      neighborlist[i].push_back(neigh);
      neighborsurfacearealist[i].push_back(area);
    }
    m_NumNeighbors[i] = int32_t( neighborlist[i].size() );

    // Set the vector for each list into the NeighborList Object
    NeighborList<int>::SharedVectorType sharedNeiLst(new std::vector<int>);
    sharedNeiLst->assign(neighborlist[i].begin(), neighborlist[i].end());
    m_NeighborList->setList(static_cast<int>(i), sharedNeiLst);

    NeighborList<float>::SharedVectorType sharedSAL(new std::vector<float>);
    sharedSAL->assign(neighborsurfacearealist[i].begin(), neighborsurfacearealist[i].end());
    m_SharedSurfaceAreaList->setList(static_cast<int>(i), sharedSAL);
  }

 notifyStatusMessage("Finding Neighbors Complete");
}