// -----------------------------------------------------------------------------
//
// -----------------------------------------------------------------------------
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 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 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 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 AvizoRectilinearCoordinateWriter::execute()
{
int err = 0;
setErrorCondition(err);
VoxelDataContainer* m = getVoxelDataContainer();
if(NULL == m)
{
setErrorCondition(-999);
notifyErrorMessage("The DataContainer Object was NULL", -999);
return;
}
setErrorCondition(0);
// Make sure any directory path is also available as the user may have just typed
// in a path without actually creating the full path
std::string parentPath = MXAFileInfo::parentPath(m_OutputFile);
if(!MXADir::mkdir(parentPath, true))
{
std::stringstream ss;
ss << "Error creating parent path '" << parentPath << "'";
notifyErrorMessage(ss.str(), -1);
setErrorCondition(-1);
return;
}
int64_t totalPoints = m->getTotalPoints();
size_t totalFields = m->getNumFieldTuples();
size_t totalEnsembleTuples = m->getNumEnsembleTuples();
dataCheck(false, totalPoints, totalFields, totalEnsembleTuples);
MXAFileWriter64 writer(m_OutputFile);
if(false == writer.initWriter())
{
std::stringstream ss;
ss << "Error opening file '" << parentPath << "'";
notifyErrorMessage(ss.str(), -1);
setErrorCondition(-1);
return;
}
std::string header = generateHeader();
writer.writeString(header);
err = writeData(writer);
/* Let the GUI know we are done with this filter */
notifyStatusMessage("Complete");
}
// -----------------------------------------------------------------------------
//
// -----------------------------------------------------------------------------
void 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");
}
// -----------------------------------------------------------------------------
//
// -----------------------------------------------------------------------------
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 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 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");
}
// -----------------------------------------------------------------------------
//
// -----------------------------------------------------------------------------
void FindAxisODF::execute()
{
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;
}
StatsDataArray& statsDataArray = *m_StatsDataArray;
typedef DataArray<unsigned int> XTalType;
XTalType* crystruct = XTalType::SafeObjectDownCast<IDataArray*, XTalType*>(m->getEnsembleData(DREAM3D::EnsembleData::CrystalStructures).get());
float r1, r2, r3;
int bin;
std::vector<FloatArrayType::Pointer> axisodf;
std::vector<float> totalaxes;
size_t numXTals = crystruct->GetNumberOfTuples();
axisodf.resize(numXTals);
totalaxes.resize(numXTals);
for (size_t i = 1; i < numXTals; i++)
{
totalaxes[i] = 0.0;
axisodf[i] = FloatArrayType::CreateArray((36 * 36 * 36), DREAM3D::HDF5::AxisOrientation);
for (int j = 0; j < (36 * 36 * 36); j++)
{
axisodf[i]->SetValue(j, 0.0);
}
}
size_t numgrains = m->getNumFieldTuples();
for (size_t i = 0; i < numgrains; i++)
{
if(m_SurfaceFields[i] == false)
{
totalaxes[m_FieldPhases[i]]++;
}
}
for (size_t i = 1; i < numgrains; i++)
{
float ea1 = m_AxisEulerAngles[3 * i];
float ea2 = m_AxisEulerAngles[3 * i + 1];
float ea3 = m_AxisEulerAngles[3 * i + 2];
if(m_SurfaceFields[i] == 0)
{
OrientationMath::EulerToRod( ea1, ea2, ea3, r1, r2, r3);
m_OrientationOps[Ebsd::CrystalStructure::OrthoRhombic]->getODFFZRod(r1, r2, r3);
bin = m_OrientationOps[Ebsd::CrystalStructure::OrthoRhombic]->getOdfBin(r1, r2, r3);
axisodf[m_FieldPhases[i]]->SetValue(bin, (axisodf[m_FieldPhases[i]]->GetValue(bin) + static_cast<float>((1.0 / totalaxes[m_FieldPhases[i]]))));
}
}
// int err;
for (size_t i = 1; i < numXTals; i++)
{
if(m_PhaseTypes[i] == DREAM3D::PhaseType::PrimaryPhase)
{
PrimaryStatsData* pp = PrimaryStatsData::SafePointerDownCast(statsDataArray[i].get());
pp->setAxisOrientation(axisodf[i]);
}
if(m_PhaseTypes[i] == DREAM3D::PhaseType::PrecipitatePhase)
{
PrecipitateStatsData* pp = PrecipitateStatsData::SafePointerDownCast(statsDataArray[i].get());
pp->setAxisOrientation(axisodf[i]);
}
if(m_PhaseTypes[i] == DREAM3D::PhaseType::TransformationPhase)
{
TransformationStatsData* tp = TransformationStatsData::SafePointerDownCast(statsDataArray[i].get());
tp->setAxisOrientation(axisodf[i]);
}
}
notifyStatusMessage("Completed");
}
// -----------------------------------------------------------------------------
//
// -----------------------------------------------------------------------------
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");
}
// -----------------------------------------------------------------------------
//
// -----------------------------------------------------------------------------
void MultiThresholdCells::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);
int64_t nPoints = m->getTotalPoints();
dataCheck(false, m->getTotalPoints(), m->getNumFieldTuples(), m->getNumEnsembleTuples());
if (getErrorCondition() < 0)
{
return;
}
/* Place all your code to execute your filter here. */
IDataArray::Pointer outputArrayPtr = m->getCellData(m_OutputArrayName);
BoolArrayType* outputArray = BoolArrayType::SafeObjectDownCast<IDataArray*, BoolArrayType*>(outputArrayPtr.get());
if (NULL == outputArray)
{
setErrorCondition(-11002);
notifyErrorMessage("Could not properly cast the output array to a BoolArrayType", getErrorCondition());
return;
}
m_Output = outputArray->GetPointer(0);
// Prime our output array with the result of the first comparison
{
ComparisonInput_t& comp_0 = m_ComparisonInputs[0];
ThresholdFilterHelper filter(static_cast<DREAM3D::Comparison::Enumeration>(comp_0.compOperator),
comp_0.compValue,
outputArray);
err = filter.execute(m->getCellData(comp_0.arrayName).get(), outputArrayPtr.get());
if (err < 0)
{
setErrorCondition(-13001);
notifyErrorMessage("Error Executing threshold filter on first array", getErrorCondition());
return;
}
}
for(size_t i = 1; i < m_ComparisonInputs.size(); ++i)
{
BoolArrayType::Pointer currentArrayPtr = BoolArrayType::CreateArray(m->getTotalPoints(), "TEMP");
currentArrayPtr->initializeWithZeros();
bool* currentArray = currentArrayPtr->GetPointer(0);
ComparisonInput_t& compRef = m_ComparisonInputs[i];
ThresholdFilterHelper filter(static_cast<DREAM3D::Comparison::Enumeration>(compRef.compOperator),
compRef.compValue,
currentArrayPtr.get());
err = filter.execute(m->getCellData(compRef.arrayName).get(), currentArrayPtr.get());
if (err < 0)
{
setErrorCondition(-13002);
notifyErrorMessage("Error Executing threshold filter on array", getErrorCondition());
return;
}
for (int64_t p = 0; p < nPoints; ++p)
{
if(m_Output[p] == false || currentArray[p] == false)
{
m_Output[p] = false;
}
}
}
/* Let the GUI know we are done with this filter */
notifyStatusMessage("Complete");
}
// -----------------------------------------------------------------------------
//
// -----------------------------------------------------------------------------
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");
}
// -----------------------------------------------------------------------------
//
// -----------------------------------------------------------------------------
void ReadH5Ebsd::execute()
{
std::stringstream ss;
VoxelDataContainer* m = getVoxelDataContainer();
if(NULL == m)
{
setErrorCondition(-1);
ss << " DataContainer was NULL";
addErrorMessage(getHumanLabel(), ss.str(), -1);
return;
}
int err = 0;
setErrorCondition(err);
std::string manufacturer;
// Get the Size and Resolution of the Volume
{
H5EbsdVolumeInfo::Pointer volumeInfoReader = H5EbsdVolumeInfo::New();
volumeInfoReader->setFileName(m_InputFile);
err = volumeInfoReader->readVolumeInfo();
setErrorCondition(err);
int64_t dims[3];
float res[3];
volumeInfoReader->getDimsAndResolution(dims[0], dims[1], dims[2], res[0], res[1], res[2]);
/* Sanity check what we are trying to load to make sure it can fit in our address space.
* Note that this does not guarantee the user has enough left, just that the
* size of the volume can fit in the address space of the program
*/
#if (CMP_SIZEOF_SSIZE_T==4)
int64_t max = std::numeric_limits<size_t>::max();
#else
int64_t max = std::numeric_limits<int64_t>::max();
#endif
if(dims[0] * dims[1] * dims[2] > max)
{
err = -1;
std::stringstream s;
s << "The total number of elements '" << (dims[0] * dims[1] * dims[2]) << "' is greater than this program can hold. Try the 64 bit version.";
setErrorCondition(err);
addErrorMessage(getHumanLabel(), s.str(), -1);
return;
}
if(dims[0] > max || dims[1] > max || dims[2] > max)
{
err = -1;
std::stringstream s;
s << "One of the dimensions is greater than the max index for this sysem. Try the 64 bit version.";
s << " dim[0]=" << dims[0] << " dim[1]=" << dims[1] << " dim[2]=" << dims[2];
setErrorCondition(err);
addErrorMessage(getHumanLabel(), s.str(), -1);
return;
}
/* ************ End Sanity Check *************************** */
size_t dcDims[3] =
{ dims[0], dims[1], dims[2] };
m->setDimensions(dcDims);
m->setResolution(res);
//Now Calculate our "subvolume" of slices, ie, those start and end values that the user selected from the GUI
dcDims[2] = m_ZEndIndex - m_ZStartIndex + 1;
m->setDimensions(dcDims);
manufacturer = volumeInfoReader->getManufacturer();
m_RefFrameZDir = volumeInfoReader->getStackingOrder();
m_SampleTransformationAngle = volumeInfoReader->getSampleTransformationAngle();
m_SampleTransformationAxis = volumeInfoReader->getSampleTransformationAxis();
m_EulerTransformationAngle = volumeInfoReader->getEulerTransformationAngle();
m_EulerTransformationAxis = volumeInfoReader->getEulerTransformationAxis();
volumeInfoReader = H5EbsdVolumeInfo::NullPointer();
}
H5EbsdVolumeReader::Pointer ebsdReader;
if(manufacturer.compare(Ebsd::Ang::Manufacturer) == 0)
{
ebsdReader = initTSLEbsdVolumeReader();
}
else if(manufacturer.compare(Ebsd::Ctf::Manufacturer) == 0)
{
ebsdReader = initHKLEbsdVolumeReader();
}
else if(manufacturer.compare(Ebsd::Mic::Manufacturer) == 0)
{
ebsdReader = initHEDMEbsdVolumeReader();
}
else
{
setErrorCondition(-1);
std::string msg("Could not determine or match a supported manufacturer from the data file.");
msg = msg.append("Supported manufacturer codes are: ").append(Ebsd::Ctf::Manufacturer);
msg = msg.append(", ").append(Ebsd::Ang::Manufacturer).append(" and ").append(Ebsd::Mic::Manufacturer);
addErrorMessage(getHumanLabel(), msg, -1);
return;
}
// Sanity Check the Error Condition or the state of the EBSD Reader Object.
if(getErrorCondition() < 0 || NULL == ebsdReader.get())
{
return;
}
// Initialize all the arrays with some default values
int64_t totalPoints = m->getTotalPoints();
ss.str("");
ss << " - Initializing " << totalPoints << " voxels";
notifyStatusMessage(ss.str());
ss.str("");
ss << " - Reading Ebsd Data from file";
notifyStatusMessage(ss.str());
ebsdReader->setSliceStart(m_ZStartIndex);
ebsdReader->setSliceEnd(m_ZEndIndex);
ebsdReader->readAllArrays(false);
ebsdReader->setArraysToRead(m_SelectedVoxelCellArrays);
err = ebsdReader->loadData(m->getXPoints(), m->getYPoints(), m->getZPoints(), m_RefFrameZDir);
if(err < 0)
{
setErrorCondition(err);
PipelineMessage em (getHumanLabel(), "Error Loading Data from Ebsd Data file.", -1);
addErrorMessage(em);
return;
}
typedef DataArray<unsigned int> XTalStructArrayType;
GET_PREREQ_DATA(m, DREAM3D, EnsembleData, CrystalStructures, ss, -304, unsigned int, XTalStructArrayType, m->getNumEnsembleTuples(), 1)
GET_PREREQ_DATA(m, DREAM3D, EnsembleData, LatticeConstants, ss, -305, float, FloatArrayType, m->getNumEnsembleTuples(), 6)
// Copy the data from the pointers embedded in the reader object into our data container (Cell array).
if(manufacturer.compare(Ebsd::Ang::Manufacturer) == 0)
{
copyTSLArrays(ebsdReader.get());
}
else if(manufacturer.compare(Ebsd::Ctf::Manufacturer) == 0)
{
copyHKLArrays(ebsdReader.get());
}
else if(manufacturer.compare(Ebsd::Mic::Manufacturer) == 0)
{
copyHEDMArrays(ebsdReader.get());
}
else
{
std::string msg("Could not determine or match a supported manufacturer from the data file.");
msg = msg.append("Supported manufacturer codes are: ").append(Ebsd::Ctf::Manufacturer);
msg = msg.append(" and ").append(Ebsd::Ang::Manufacturer);
addErrorMessage(getHumanLabel(), msg, -10001);
return;
}
if(m_UseTransformations == true)
{
if(m_EulerTransformationAngle > 0)
{
FloatVec3Widget_t eulerAxis;
eulerAxis.x = m_EulerTransformationAxis[0];
eulerAxis.y = m_EulerTransformationAxis[1];
eulerAxis.z = m_EulerTransformationAxis[2];
RotateEulerRefFrame::Pointer rot_Euler = RotateEulerRefFrame::New();
rot_Euler->setObservers(this->getObservers());
rot_Euler->setVoxelDataContainer(getVoxelDataContainer());
rot_Euler->setRotationAngle(m_EulerTransformationAngle);
rot_Euler->setRotationAxis(eulerAxis);
rot_Euler->execute();
}
if(m_SampleTransformationAngle > 0)
{
FloatVec3Widget_t sampleAxis;
sampleAxis.x = m_SampleTransformationAxis[0];
sampleAxis.y = m_SampleTransformationAxis[1];
sampleAxis.z = m_SampleTransformationAxis[2];
RotateSampleRefFrame::Pointer rot_Sample = RotateSampleRefFrame::New();
rot_Sample->setObservers(this->getObservers());
rot_Sample->setVoxelDataContainer(getVoxelDataContainer());
rot_Sample->setRotationAngle(m_SampleTransformationAngle);
rot_Sample->setRotationAxis(sampleAxis);
rot_Sample->setsliceBySlice(true);
rot_Sample->execute();
}
}
// If there is an error set this to something negative and also set a message
ss.str("");
ss << getHumanLabel() << " Completed";
notifyStatusMessage(ss.str());
}
// -----------------------------------------------------------------------------
//
// -----------------------------------------------------------------------------
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");
}
// -----------------------------------------------------------------------------
//
// -----------------------------------------------------------------------------
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");
}
// -----------------------------------------------------------------------------
//
// -----------------------------------------------------------------------------
void DecimateSolidMesh::execute()
{
setErrorCondition(0);
VoxelDataContainer* m = getVoxelDataContainer();
SolidMeshDataContainer* sm = getSolidMeshDataContainer();
int64_t totalPoints = m->getTotalPoints();
size_t totalFields = m->getNumFieldTuples();
size_t totalEnsembles = m->getNumEnsembleTuples();
dataCheck(false, totalPoints, totalFields, totalEnsembles);
if (getErrorCondition() < 0)
{
return;
}
StructArray<Node>& nodes = *(sm->getNodes());
StructArray<Tetrahedron>& tetrahedrons = *(sm->getTetrahedrons());
int numNodes = nodes.GetNumberOfTuples();
int numTets = tetrahedrons.GetNumberOfTuples();
int gnum;
size_t nodeId1, nodeId2, nodeId3, nodeId4;
//Locate Boundary Nodes
nodeGrainIds.resize(numNodes,-1);
nodeEuclideanDistances.resize(numNodes,-1);
for(int k = 0; k < numTets; k++)
{
gnum = tetrahedrons[k].nSpin;
// float x = nodes[k].coord[0];
nodeId1 = tetrahedrons[k].node_id[0];
nodeId2 = tetrahedrons[k].node_id[1];
nodeId3 = tetrahedrons[k].node_id[2];
nodeId4 = tetrahedrons[k].node_id[3];
if(nodeGrainIds[nodeId1] == -1 || nodeGrainIds[nodeId1] == gnum) nodeGrainIds[nodeId1] = gnum;
else
{
nodeGrainIds[nodeId1] = -1000;
nodeEuclideanDistances[nodeId1] = 0;
}
if(nodeGrainIds[nodeId2] == -1 || nodeGrainIds[nodeId2] == gnum) nodeGrainIds[nodeId2] = gnum;
else
{
nodeGrainIds[nodeId2] = -1000;
nodeEuclideanDistances[nodeId2] = 0;
}
if(nodeGrainIds[nodeId3] == -1 || nodeGrainIds[nodeId3] == gnum) nodeGrainIds[nodeId3] = gnum;
else
{
nodeGrainIds[nodeId3] = -1000;
nodeEuclideanDistances[nodeId3] = 0;
}
if(nodeGrainIds[nodeId4] == -1 || nodeGrainIds[nodeId4] == gnum) nodeGrainIds[nodeId4] = gnum;
else
{
nodeGrainIds[nodeId4] = -1000;
nodeEuclideanDistances[nodeId4] = 0;
}
}
nodeGrainIds.clear();
//Determine Node Euclidean Distance Map
tetDone.resize(numTets,false);
int tetsLeft = 1;
int ED1, ED2, ED3, ED4;
int currentED = 0;
int maxGlobalED = 0;
while(tetsLeft > 0)
{
tetsLeft = 0;
currentED++;
for(int k = 0; k < numTets; k++)
{
if(tetDone[k] == false)
{
nodeId1 = tetrahedrons[k].node_id[0];
nodeId2 = tetrahedrons[k].node_id[1];
nodeId3 = tetrahedrons[k].node_id[2];
nodeId4 = tetrahedrons[k].node_id[3];
ED1 = nodeEuclideanDistances[nodeId1];
ED2 = nodeEuclideanDistances[nodeId2];
ED3 = nodeEuclideanDistances[nodeId3];
ED4 = nodeEuclideanDistances[nodeId4];
if(ED1 == -1 || ED2 == -1 || ED3 == -1 || ED4 == -1) tetsLeft++;
if(ED1 == (currentED-1) || ED2 == (currentED-1) || ED3 == (currentED-1) || ED4 == (currentED-1))
{
if(ED1 == -1) nodeEuclideanDistances[nodeId1] = currentED;
if(ED2 == -1) nodeEuclideanDistances[nodeId2] = currentED;
if(ED3 == -1) nodeEuclideanDistances[nodeId3] = currentED;
if(ED4 == -1) nodeEuclideanDistances[nodeId4] = currentED;
tetDone[k] = true;
}
}
}
maxGlobalED = currentED;
}
tetDone.clear();
//Decimate Mesh
// ED1, ED2, ED3, ED4;
int removeED = maxGlobalED;
// int secondLargestED = 0;
int point;
int otherPoint;
while(numTets > m_GoalElementNumber && removeED > 1)
{
for(int k = 0; k < numTets; k++)
{
nodeId1 = tetrahedrons[k].node_id[0];
nodeId2 = tetrahedrons[k].node_id[1];
nodeId3 = tetrahedrons[k].node_id[2];
nodeId4 = tetrahedrons[k].node_id[3];
ED1 = nodeEuclideanDistances[nodeId1];
ED2 = nodeEuclideanDistances[nodeId2];
ED3 = nodeEuclideanDistances[nodeId3];
ED4 = nodeEuclideanDistances[nodeId4];
if(ED1 >= removeED)
{
point = nodeId1;
// secondLargestED = ED2;
otherPoint = nodeId2;
// if(ED3 > secondLargestED) secondLargestED = ED3, otherPoint = nodeId3;
// if(ED4 > secondLargestED) secondLargestED = ED4, otherPoint = nodeId4;
k = updateNodesandTets(k, point, otherPoint);
}
else if(ED2 >= removeED)
{
point = nodeId2;
// secondLargestED = ED1;
otherPoint = nodeId3;
// if(ED3 > secondLargestED) secondLargestED = ED3, otherPoint = nodeId3;
// if(ED4 > secondLargestED) secondLargestED = ED4, otherPoint = nodeId4;
k = updateNodesandTets(k, point, otherPoint);
}
else if(ED3 >= removeED)
{
point = nodeId3;
// secondLargestED = ED1;
otherPoint = nodeId4;
// if(ED2 > secondLargestED) secondLargestED = ED2, otherPoint = nodeId2;
// if(ED4 > secondLargestED) secondLargestED = ED4, otherPoint = nodeId4;
k = updateNodesandTets(k, point, otherPoint);
}
else if(ED4 >= removeED)
{
point = nodeId4;
// secondLargestED = ED1;
otherPoint = nodeId1;
// if(ED2 > secondLargestED) secondLargestED = ED2, otherPoint = nodeId2;
// if(ED3 > secondLargestED) secondLargestED = ED3, otherPoint = nodeId3;
k = updateNodesandTets(k, point, otherPoint);
}
numTets = tetrahedrons.GetNumberOfTuples();
StructArray<Node>& nodes = *(sm->getNodes());
StructArray<Tetrahedron>& tetrahedrons = *(sm->getTetrahedrons());
numNodes = nodes.GetNumberOfTuples();
numTets = tetrahedrons.GetNumberOfTuples();
}
removeED = removeED-1;
}
notifyStatusMessage("Complete");
}