void CropVolumePipeline::execute()
{
    VoxelDataContainer* m = getVoxelDataContainer();
  float m_MisorientationTolerance = 5.0f;
  float m_AlignMisorientationTolerance = 5.0f;
  float m_Zres = 4.0f;
  int m_MinAllowedGrainSize = 10;
  int m_MinNumNeighbors = 1;
  int m_PhaseNumberMinSize = 1;
  int m_NumIterations_Erode = 3;
  int NUM_OF_CROPS = getNumLinesinFile(m_InputFile);

  std::vector<int> m_Xmin(NUM_OF_CROPS+1, 0);
  std::vector<int> m_Ymin(NUM_OF_CROPS+1, 0);
  std::vector<int> m_Zmin(NUM_OF_CROPS+1, 0);
  std::vector<int> m_Xmax(NUM_OF_CROPS+1, 0);
  std::vector<int> m_Ymax(NUM_OF_CROPS+1, 0);
  std::vector<int> m_Zmax(NUM_OF_CROPS+1, 0);

  get_max_and_min_xyz_for_crop(m_Xmax, m_Ymax, m_Zmax, m_Xmin, m_Ymin, m_Zmin);

  /*  int m_Zmin = 1 ;
  int m_Xmax = 495;
  int m_Ymax = 355;
  int m_Zmax = 163;*/

for (DimType i = 1; i < NUM_OF_CROPS+1; i++)
{


      // Create our Pipeline object
      FilterPipeline::Pointer pipeline = FilterPipeline::New();




     // updateProgressAndMessage(("Loading Slices"), 10);
      ReadH5Ebsd::Pointer read_h5ebsd = ReadH5Ebsd::New();

      read_h5ebsd->setH5EbsdFile(getH5EbsdFile());
      //read_h5ebsd->setRefFrameZDir(Ebsd::LowtoHigh);
      read_h5ebsd->setZStartIndex(getZStartIndex());
      read_h5ebsd->setZEndIndex(getZEndIndex());
      read_h5ebsd->setPTypes(getPhaseTypes());
      read_h5ebsd->setQualityMetricFilters(getQualityMetricFilters());
      read_h5ebsd->setVoxelDataContainer(m);
      read_h5ebsd->execute();
      pipeline->pushBack(read_h5ebsd);



      ConvertEulerAngles::Pointer convert_euler = ConvertEulerAngles::New();
      convert_euler->setConversionType(DREAM3D::EulerAngleConversionType::DegreesToRadians);
      convert_euler->setVoxelDataContainer(m);
      convert_euler->execute();
      pipeline->pushBack(convert_euler);


      AlignSectionsMisorientation::Pointer align_sections = AlignSectionsMisorientation::New();
      align_sections->setMisorientationTolerance(m_AlignMisorientationTolerance);
      align_sections->setVoxelDataContainer(m);
      align_sections->execute();
      pipeline->pushBack(align_sections);

      CropVolume::Pointer crop_volume = CropVolume::New();
      crop_volume->setXMin(m_Xmin[i]);
      crop_volume->setYMin(m_Ymin[i]);
      crop_volume->setZMin(m_Zmin[i]);
      crop_volume->setXMax(m_Xmax[i]);
      crop_volume->setYMax(m_Ymax[i]);
      crop_volume->setZMax(m_Zmax[i]);
      crop_volume->setRenumberGrains(false);
      crop_volume->setVoxelDataContainer(m);
      crop_volume->execute();
      pipeline->pushBack(crop_volume);

      RegularizeZSpacing::Pointer regularize_z = RegularizeZSpacing::New();
      regularize_z->setInputFile(getZ_spacingfile());
      regularize_z->setZRes(m_Zres);
      regularize_z->setVoxelDataContainer(m);
      regularize_z->execute();
      pipeline->pushBack(regularize_z);

      EBSDSegmentGrains::Pointer ebsdsegment_grains = EBSDSegmentGrains::New();
      ebsdsegment_grains->setMisorientationTolerance(m_MisorientationTolerance);
      ebsdsegment_grains->setVoxelDataContainer(m);
      ebsdsegment_grains->execute();
      pipeline->pushBack(ebsdsegment_grains);

      OpenCloseBadData::Pointer erode_dilate = OpenCloseBadData::New();
      erode_dilate->setDirection(1); // 1 is erode.
      erode_dilate->setNumIterations(m_NumIterations_Erode);
      erode_dilate->setVoxelDataContainer(m);
      erode_dilate->execute();
      pipeline->pushBack(erode_dilate);

      FindNeighbors::Pointer find_neighbors = FindNeighbors::New();
      find_neighbors->setVoxelDataContainer(m);
      find_neighbors->execute();
      pipeline->pushBack(find_neighbors);


      PerPhaseMinSize::Pointer min_size = PerPhaseMinSize::New();
      min_size->setMinAllowedGrainSize(m_MinAllowedGrainSize);
      min_size->setPhaseNumber(m_PhaseNumberMinSize);
      min_size->setVoxelDataContainer(m);
      min_size->execute();
      pipeline->pushBack(min_size);

      MinNeighbors::Pointer min_neighbors = MinNeighbors::New();
      min_neighbors->setMinNumNeighbors(m_MinNumNeighbors);
      min_neighbors->setVoxelDataContainer(m);
      min_neighbors->execute();
      pipeline->pushBack(min_neighbors);

      FindSizes::Pointer find_sizes = FindSizes::New();
      //find_sizes->setDistributionType(DREAM3D::DistributionType::Beta);
      find_sizes->setVoxelDataContainer(m);
      find_sizes->execute();
      pipeline->pushBack(find_sizes);


      FindShapes::Pointer find_shapes = FindShapes::New();
      //find_shapes->setDistributionType(DREAM3D::DistributionType::Beta);
      find_shapes->setVoxelDataContainer(m);
      find_shapes->execute();
      pipeline->pushBack(find_shapes);



      FieldDataCSVWriter::Pointer field_data_write_csv = FieldDataCSVWriter::New();
      std::string field_csv =  "D:/IN100_run1/DREAM3D_files/crop_line_"+ convertIntToString(i) +".csv";
      field_data_write_csv->setFieldDataFile(field_csv);
      field_data_write_csv->setVoxelDataContainer(m);
      field_data_write_csv->execute();
      pipeline->pushBack(field_data_write_csv);



      bool m_WriteVtkFile = true ;
      bool m_WriteBinaryVTKFiles= true ;
      bool m_WriteGrainID= true;
      bool m_WritePhaseId= true ;
      bool m_WriteIPFColor= true ;
      bool m_WriteGoodVoxels= true ;
      bool m_WriteGrainSizes = true ;
      bool m_WriteBandContrasts = true ;

      VtkRectilinearGridWriter::Pointer vtkWriter = VtkRectilinearGridWriter::New();

      if(m_WriteVtkFile)
      {
        std::string vtk_file = "D:/IN100_run1/DREAM3D_files/crop_line_" + convertIntToString(i) + ".vtk";
        vtkWriter->setOutputFile(vtk_file);
        vtkWriter->setWriteGrainIds(m_WriteGrainID);
        vtkWriter->setWritePhaseIds(m_WritePhaseId);
        vtkWriter->setWriteBandContrasts(m_WriteBandContrasts);
        vtkWriter->setWriteGoodVoxels(m_WriteGoodVoxels);
        vtkWriter->setWriteIPFColors(m_WriteIPFColor);
        vtkWriter->setWriteBinaryFile(m_WriteBinaryVTKFiles);
        vtkWriter->setWriteBinaryFile(m_WriteGrainSizes);
        vtkWriter->setVoxelDataContainer(m);
        vtkWriter->execute();
        pipeline->pushBack(vtkWriter);
      }

      DataContainerWriter::Pointer writer = DataContainerWriter::New();
      std::string dream_3d_file = "D:/IN100_run1/DREAM3D_files/crop_line_" + convertIntToString(i) + ".dream3d";
      writer->setOutputFile(dream_3d_file);
      writer->setVoxelDataContainer(m);
      pipeline->pushBack(writer);
      writer->execute();



    //  std::cout << "********* RUNNING PIPELINE **********************" << std::endl;
    // // pipeline->run();
      pipeline->clear();


      //delete [] m;
      m->clearCellData();
      m->clearEnsembleData();
      m->clearFieldData();



}
}
Example #2
0
// -----------------------------------------------------------------------------
//
// -----------------------------------------------------------------------------
void TestSyntheticBuilder()
{

  MXADir::mkdir(m_OutputDirectory, true);

  Observer* observer = new Observer;


  int err = 0;

  // Create our Pipeline object
  FilterPipeline::Pointer pipeline = FilterPipeline::New();
  VoxelDataContainer::Pointer m = VoxelDataContainer::New();
  pipeline->setVoxelDataContainer(m);

    ShapeTypeArrayType::Pointer m_ShapeTypes = ShapeTypeArrayType::CreateArray(4, DREAM3D::EnsembleData::ShapeTypes);
    m_ShapeTypes->SetValue(0, DREAM3D::ShapeType::UnknownShapeType);
    m_ShapeTypes->SetValue(1, DREAM3D::ShapeType::EllipsoidShape);
    m_ShapeTypes->SetValue(2, DREAM3D::ShapeType::EllipsoidShape);
    m_ShapeTypes->SetValue(3, DREAM3D::ShapeType::EllipsoidShape);

    InitializeSyntheticVolume::Pointer init_volume = InitializeSyntheticVolume::New();
    init_volume->setShapeTypes(m_ShapeTypes);
    init_volume->setInputFile(getH5StatsFile());
    init_volume->setXVoxels(m_XPoints);
    init_volume->setYVoxels(m_YPoints);
    init_volume->setZVoxels(m_ZPoints);
    init_volume->setXRes(m_XResolution);
    init_volume->setYRes(m_YResolution);
    init_volume->setZRes(m_ZResolution);
	pipeline->pushBack(init_volume);

    PackPrimaryPhases::Pointer pack_grains = PackPrimaryPhases::New();
    pack_grains->setPeriodicBoundaries(m_PeriodicBoundary);
    pack_grains->setNeighborhoodErrorWeight(m_NeighborhoodErrorWeight);
#if PACK_GRAINS_ERROR_TXT_OUT
    MAKE_OUTPUT_FILE_PATH( errorFile, DREAM3D::SyntheticBuilder::ErrorFile)
    pack_grains->setErrorOutputFile(errorFile);
#endif
#if PACK_GRAINS_VTK_FILE_OUT
    MAKE_OUTPUT_FILE_PATH( vtkFile, DREAM3D::SyntheticBuilder::VtkFile)
    pack_grains->setVtkOutputFile(vtkFile);
#endif
    pipeline->pushBack(pack_grains);

    AdjustVolume::Pointer adjust_grains = AdjustVolume::New();
    pipeline->pushBack(adjust_grains);

    InsertPrecipitatePhases::Pointer place_precipitates = InsertPrecipitatePhases::New();
    place_precipitates->setPeriodicBoundaries(m_PeriodicBoundary);
    pipeline->pushBack(place_precipitates);

  MatchCrystallography::Pointer match_crystallography = MatchCrystallography::New();
//  pipeline->pushBack(match_crystallography);

  FieldDataCSVWriter::Pointer write_fielddata = FieldDataCSVWriter::New();
  write_fielddata->setFieldDataFile(UnitTest::SyntheticBuilderTest::CsvFile);
  pipeline->pushBack(write_fielddata);

  DataContainerWriter::Pointer writer = DataContainerWriter::New();
  writer->setOutputFile(UnitTest::SyntheticBuilderTest::OutputFile);
  pipeline->pushBack(writer);

  bool m_WriteVtkFile(true);
  bool m_WriteBinaryVTKFiles(true);
  bool m_WritePhaseId(true);
  bool m_WriteIPFColor(false);

  if(m_WriteVtkFile)
  {
    VtkRectilinearGridWriter::Pointer vtkWriter = VtkRectilinearGridWriter::New();
    vtkWriter->setOutputFile(UnitTest::SyntheticBuilderTest::VtkOutputFile);
    vtkWriter->setWriteGrainIds(true);
    vtkWriter->setWritePhaseIds(m_WritePhaseId);
   // vtkWriter->setWriteGoodVoxels(m_WriteGoodVoxels);
    vtkWriter->setWriteIPFColors(m_WriteIPFColor);
    vtkWriter->setWriteBinaryFile(m_WriteBinaryVTKFiles);
    pipeline->pushBack(vtkWriter);
  }

  std::cout << "********* RUNNING PIPELINE **********************" << std::endl;

  m = VoxelDataContainer::New();

  pipeline->setVoxelDataContainer(m);
  pipeline->run();
  err = pipeline->getErrorCondition();
  DREAM3D_REQUIRE_EQUAL(err, 0);

  DREAM3D_REQUIRE_EQUAL(false, pipeline->empty());

  pipeline->clear();
  DREAM3D_REQUIRE_EQUAL(0, pipeline->size());
  DREAM3D_REQUIRE_EQUAL(true, pipeline->empty());

  delete observer;
}