// -----------------------------------------------------------------------------
//
// -----------------------------------------------------------------------------
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");
}
// -----------------------------------------------------------------------------
//
// -----------------------------------------------------------------------------
int VoxelDataContainerWriter::writeFaceData(hid_t dcGid)
{
std::stringstream ss;
int err = 0;
VoxelDataContainer* m = getVoxelDataContainer();
// Write the Voxel Data
err = H5Utilities::createGroupsFromPath(H5_FACE_DATA_GROUP_NAME, dcGid);
if(err < 0)
{
ss.str("");
ss << "Error creating HDF Group " << H5_FACE_DATA_GROUP_NAME << std::endl;
setErrorCondition(-63);
notifyErrorMessage( ss.str(), err);
H5Gclose(dcGid); // Close the Data Container Group
return err;
}
hid_t FaceGroupId = H5Gopen(dcGid, H5_FACE_DATA_GROUP_NAME, H5P_DEFAULT);
if(err < 0)
{
ss.str("");
ss << "Error writing string attribute to HDF Group " << H5_FACE_DATA_GROUP_NAME << std::endl;
setErrorCondition(-64);
notifyErrorMessage( ss.str(), err);
H5Gclose(dcGid); // Close the Data Container Group
return err;
}
NameListType names = m->getFaceArrayNameList();
for (NameListType::iterator iter = names.begin(); iter != names.end(); ++iter)
{
ss.str("");
ss << "Writing Face Data '" << *iter << "' to HDF5 File" << std::endl;
notifyStatusMessage(ss.str());
IDataArray::Pointer array = m->getFaceData(*iter);
err = array->writeH5Data(FaceGroupId);
if(err < 0)
{
ss.str("");
ss << "Error writing array '" << *iter << "' to the HDF5 File";
notifyErrorMessage( ss.str(), err);
setErrorCondition(err);
H5Gclose(FaceGroupId); // Close the Face Group
H5Gclose(dcGid); // Close the Data Container Group
return err;
}
}
H5Gclose(FaceGroupId); // Close the Face Group
return err;
}
// -----------------------------------------------------------------------------
//
// -----------------------------------------------------------------------------
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");
}
// -----------------------------------------------------------------------------
//
// -----------------------------------------------------------------------------
void ConvertData::execute()
{
int err = 0;
std::stringstream ss;
setErrorCondition(err);
VoxelDataContainer* m = getVoxelDataContainer();
if(NULL == m)
{
setErrorCondition(-999);
notifyErrorMessage("The Voxel DataContainer Object was NULL", -999);
return;
}
setErrorCondition(0);
IDataArray::Pointer iArray = m->getCellData(m_SelectedCellArrayName);
bool completed = false;
// UInt8ArrayType* uint8Ptr = UInt8ArrayType::SafePointerDownCast(iArray.get());
// if (uint8Ptr != NULL)
// {
// Detail::ConvertData<UInt8ArrayType>(uint8Ptr, m, m_ScalarType);
// }
CHECK_AND_CONVERT(UInt8ArrayType, m, m_ScalarType, iArray, m_OutputArrayName)
CHECK_AND_CONVERT(Int8ArrayType, m, m_ScalarType, iArray, m_OutputArrayName)
CHECK_AND_CONVERT(UInt16ArrayType, m, m_ScalarType, iArray, m_OutputArrayName)
CHECK_AND_CONVERT(Int16ArrayType, m, m_ScalarType, iArray, m_OutputArrayName)
CHECK_AND_CONVERT(UInt32ArrayType, m, m_ScalarType, iArray, m_OutputArrayName)
CHECK_AND_CONVERT(Int32ArrayType, m, m_ScalarType, iArray, m_OutputArrayName)
CHECK_AND_CONVERT(UInt64ArrayType, m, m_ScalarType, iArray, m_OutputArrayName)
CHECK_AND_CONVERT(Int64ArrayType, m, m_ScalarType, iArray, m_OutputArrayName)
CHECK_AND_CONVERT(FloatArrayType, m, m_ScalarType, iArray, m_OutputArrayName)
CHECK_AND_CONVERT(DoubleArrayType, m, m_ScalarType, iArray, m_OutputArrayName)
/* Let the GUI know we are done with this filter */
notifyStatusMessage("Complete");
}
// -----------------------------------------------------------------------------
//
// -----------------------------------------------------------------------------
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);
}
// -----------------------------------------------------------------------------
//
// -----------------------------------------------------------------------------
void LinkFieldMapToCellArray::execute()
{
VoxelDataContainer* m = getVoxelDataContainer();
if(NULL == m)
{
setErrorCondition(-999);
notifyErrorMessage("The DataContainer Object was NULL", -999);
return;
}
setErrorCondition(0);
int64_t voxels = m->getTotalPoints();
int64_t fields = m->getNumFieldTuples();
dataCheck(false, voxels, fields, m->getNumEnsembleTuples());
if (getErrorCondition() < 0)
{
return;
}
//int err = 0;
std::stringstream ss;
m->clearFieldData();
int maxIndex = 0;
std::vector<bool> active;
for(int64_t i=0;i<voxels;i++)
{
int index = m_SelectedCellData[i];
if((index+1) > maxIndex)
{
active.resize(index+1);
active[index] = true;
maxIndex = index+1;
}
}
BoolArrayType::Pointer m_Active = BoolArrayType::CreateArray(maxIndex, 1, DREAM3D::FieldData::Active);
bool* mActive = m_Active->GetPointer(0);
for(int i=0;i<maxIndex;i++)
{
mActive[i] = active[i];
}
m->addFieldData(DREAM3D::FieldData::Active, m_Active);
notifyStatusMessage("Complete");
}
// -----------------------------------------------------------------------------
//
// -----------------------------------------------------------------------------
int DxReader::readFile()
{
std::stringstream ss;
VoxelDataContainer* m = getVoxelDataContainer();
if (NULL == m)
{
ss.clear();
ss << "DataContainer Pointer was NULL and Must be valid." << __FILE__ << "("<<__LINE__<<")";
addErrorMessage(getHumanLabel(), ss.str(), -5);
setErrorCondition(-5);
return -1;
}
std::string delimeters(", ;\t"); /* delimeters to split the data */
std::vector<std::string> tokens; /* vector to store the split data */
int error, spin; /* dummy variables */
bool finished_header, finished_data;
finished_header = true;
finished_data = false;
size_t index = 0;
size_t totalPoints = m->getTotalPoints();
// Remove the array that we are about to create first as a 'datacheck()' was called from the super class's 'execute'
// method which is performed before this function. This will cause an error -501 because the array with the name
// m_GrainIdsArrayName already exists but of size 1, not the size we are going to read. So we get rid of the array
m->removeCellData(m_GrainIdsArrayName);
// Rerun the data check in order to allocate the array to store the data from the .dx file.
// dataCheck(false, totalPoints, m->getNumFieldTuples(), m->getNumEnsembleTuples());
CREATE_NON_PREREQ_DATA(m, DREAM3D, CellData, GrainIds, ss, int32_t, Int32ArrayType, 0, totalPoints, 1)
if (getErrorCondition() < 0)
{
m_InStream.close();
return -1;
}
for (std::string line; std::getline(m_InStream, line);)
{
// Get the remaining lines of the header and ignore
tokens.clear();
error = 0;
tokenize(line, tokens, delimeters);
size_t total = m->getTotalPoints();
if( index == total || ( finished_header && tokens.size() != 0 && tokens[0] == "attribute") )
{
finished_data = true;
}
// Allocate the DataArray at this point:
if(finished_header && !finished_data)
{
for (size_t in_spins = 0; in_spins < tokens.size(); in_spins++)
{
error += sscanf(tokens[in_spins].c_str(), "%d", &spin);
m_GrainIds[index] = spin;
++index;
}
}
}
if(index != static_cast<size_t>(m->getTotalPoints()))
{
ss.clear();
ss << "ERROR: data size does not match header dimensions" << std::endl;
ss << "\t" << index << "\t" << m->getTotalPoints() << std::endl;
setErrorCondition(-495);
addErrorMessage(getHumanLabel(), ss.str(), getErrorCondition());
m_InStream.close();
return getErrorCondition();
}
tokens.clear();
m_InStream.close();
// Find the unique set of grain ids
// std::set<int32_t> grainIdSet;
// for (int64_t i = 0; i < totalPoints; ++i)
// {
// grainIdSet.insert(m_GrainIds[i]);
// }
// for (std::set<int32_t>::iterator iter = grainIdSet.begin(); iter != grainIdSet.end(); ++iter )
// {
// std::cout << "Grain ID: " << (*iter) << std::endl;
// }
notifyStatusMessage("Complete");
return 0;
}
//-----------------------------------------------------------------------------
//
// -----------------------------------------------------------------------------
int DxReader::readHeader()
{
VoxelDataContainer* m = getVoxelDataContainer();
std::stringstream ss;
int error = 0;
std::string line;
std::string delimeters(", ;\t"); /* delimeters to split the data */
std::vector<std::string> tokens; /* vector to store the split data */
getline(m_InStream, line, '\n');
tokenize(line, tokens, delimeters);
// Process the header information and look for the std::string "counts"
// Then read the data size after that
size_t pos1 = 0;
while (pos1 == 0)
{ // continue until we find the keyword
for (size_t i = 0; i < tokens.size(); i++)
{
if(tokens[i] == "counts")
{
pos1 = i;
}
}
// Read the next line of the header if we did not find the keyword
// in the line
if(pos1 == 0)
{
tokens.clear();
getline(m_InStream, line, '\n');
tokenize(line, tokens, delimeters);
if(tokens.size() == 20)
{
ss.clear();
ss << "ERROR: Unable to read data dimensions from the header" << std::endl;
addErrorMessage(getHumanLabel(), ss.str(), -7);
setErrorCondition(-499);
m_InStream.close();
return -499;
}
}
}
int nx = 0;
int ny = 0;
int nz = 0;
if(pos1 != 0)
{
error = 0;
error += sscanf(tokens[pos1 + 1].c_str(), "%d", &nz);
error += sscanf(tokens[pos1 + 2].c_str(), "%d", &ny);
error += sscanf(tokens[pos1 + 3].c_str(), "%d", &nx);
tokens.clear();
// The dimensions listed in the DX file are always one greater
// than the actual dimensions
nx--;
ny--;
nz--;
}
// std::cout << "INFO: DX data dimensions: " << std::endl;
// std::cout << "nz= " << nz << std::endl;
// std::cout << "ny= " << ny << std::endl;
// std::cout << "nx= " << nx << std::endl;
//The DX file has a unique format of 20 entries on each line. I have
//no idea who initiated this insanity but I am about to perpetuate
//it.
//
//The most simple thing to do is to read the entire dataset into one
//long vector and then read that vector to assign values to the grid
// ADR: 6 Sep 08; time to make the input much more general!
// equivalent to list-direcvted input in Fortran, actually !!
pos1 = 0;
while (pos1 == 0)
{ // continue until we find the keyword
for (size_t i = 0; i < tokens.size(); i++)
{
if(tokens[i] == "items")
{
pos1 = i;
}
}
// Read the next line of the header if we did not find the keyword
// in the line
if(pos1 == 0)
{
tokens.clear();
getline(m_InStream, line, '\n');
tokenize(line, tokens, delimeters);
if(tokens.size() == 20)
{
ss.clear();
ss << "ERROR: Unable to locate the last header line" << std::endl;
addErrorMessage(getHumanLabel(), ss.str(), -8);
setErrorCondition(-496);
m_InStream.close();
return -496;
}
}
} // when we get here, we are looking at data
int points = 0;
if(pos1 != 0)
{
error = 0;
error += sscanf(tokens[pos1 + 1].c_str(), "%d", &points);
tokens.clear();
}
m->setDimensions(nx, ny, nz);
// std::cout << "Compare no. points " << points << " with x*y*z: " << nx * ny * nz << std::endl;
return error;
}
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 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");
}
// -----------------------------------------------------------------------------
//
// -----------------------------------------------------------------------------
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");
}
// -----------------------------------------------------------------------------
//
// -----------------------------------------------------------------------------
void ClearData::dataCheck(bool preflight, size_t voxels, size_t fields, size_t ensembles)
{
setErrorCondition(0);
std::stringstream ss;
VoxelDataContainer* m = getVoxelDataContainer();
if (getXMax() < getXMin())
{
ss.str("");
ss << "X Max (" << getXMax() << ") less than X Min (" << getXMin() << ")";
addErrorMessage(getHumanLabel(), ss.str(), -5555);
setErrorCondition(-5555);
}
if (getYMax() < getYMin())
{
ss.str("");
ss << "Y Max (" << getYMax() << ") less than Y Min (" << getYMin() << ")";
addErrorMessage(getHumanLabel(), ss.str(), -5555);
setErrorCondition(-5555);
}
if (getZMax() < getZMin())
{
ss.str("");
ss << "Z Max (" << getZMax() << ") less than Z Min (" << getZMin() << ")";
addErrorMessage(getHumanLabel(), ss.str(), -5555);
setErrorCondition(-5555);
}
if (getXMin() < 0)
{
ss.str("");
ss << "X Min (" << getXMin() << ") less than 0";
addErrorMessage(getHumanLabel(), ss.str(), -5555);
setErrorCondition(-5555);
}
if (getYMin() < 0)
{
ss.str("");
ss << "Y Min (" << getYMin() << ") less than 0";
addErrorMessage(getHumanLabel(), ss.str(), -5555);
setErrorCondition(-5555);
}
if (getZMin() < 0)
{
ss.str("");
ss <<"Z Min (" << getZMin() << ") less than 0";
addErrorMessage(getHumanLabel(), ss.str(), -5555);
setErrorCondition(-5555);
}
if (getXMax() > (static_cast<int64_t>(m->getXPoints())-1))
{
ss.str("");
ss << "The X Max you entered of " << getXMax() << " is greater than your Max X Point of " << static_cast<int64_t>(m->getXPoints())-1;
addErrorMessage(getHumanLabel(), ss.str(), -5555);
setErrorCondition(-5555);
}
if (getYMax() > (static_cast<int64_t>(m->getYPoints())-1))
{
ss.str("");
ss << "The Y Max you entered of " << getYMax() << " is greater than your Max Y Point of " << static_cast<int64_t>(m->getYPoints())-1;
addErrorMessage(getHumanLabel(), ss.str(), -5555);
setErrorCondition(-5556);
}
if (getZMax() > (static_cast<int64_t>(m->getZPoints())-1))
{
ss.str("");
ss << "The Z Max you entered of " << getZMax() << ") greater than your Max Z Point of " << static_cast<int64_t>(m->getZPoints())-1;
addErrorMessage(getHumanLabel(), ss.str(), -5555);
setErrorCondition(-5557);
}
}
