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();
}
}
// -----------------------------------------------------------------------------
//
// -----------------------------------------------------------------------------
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;
}