// -----------------------------------------------------------------------------
//
// -----------------------------------------------------------------------------
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 ChangeResolution::execute()
{
int err = 0;
setErrorCondition(err);
DREAM3D_RANDOMNG_NEW()
VoxelDataContainer* m = getVoxelDataContainer();
if(NULL == m)
{
setErrorCondition(-999);
notifyErrorMessage("The DataContainer Object was NULL", -999);
return;
}
setErrorCondition(0);
if (getErrorCondition() < 0)
{
return;
}
if(m->getXRes() == m_Resolution.x
&& m->getYRes() == m_Resolution.y
&& m->getZRes() == m_Resolution.z)
{
return;
}
size_t dims[3];
m->getDimensions(dims);
float sizex = (dims[0])*m->getXRes();
float sizey = (dims[1])*m->getYRes();
float sizez = (dims[2])*m->getZRes();
int m_XP = int(sizex / m_Resolution.x);
int m_YP = int(sizey / m_Resolution.y);
int m_ZP = int(sizez / m_Resolution.z);
int64_t totalPoints = m_XP*m_YP*m_ZP;
float x, y, z;
int col, row, plane;
int index;
int index_old;
std::vector<size_t> newindicies;
newindicies.resize(totalPoints);
for (int i = 0; i < m_ZP; i++)
{
std::stringstream ss;
ss << "Changing Resolution - " << ((float)i/m->getZPoints())*100 << " Percent Complete";
notifyStatusMessage(ss.str());
for (int j = 0; j < m_YP; j++)
{
for (int k = 0; k < m_XP; k++)
{
x = (k * m_Resolution.x);
y = (j * m_Resolution.y);
z = (i * m_Resolution.z);
col = int(x / m->getXRes());
row = int(y / m->getYRes());
plane = int(z / m->getZRes());
index_old = (plane * m->getXPoints() * m->getYPoints()) + (row * m->getXPoints()) + col;
index = (i * m_XP * m_YP) + (j * m_XP) + k;
newindicies[index] = index_old;
}
}
}
std::list<std::string> voxelArrayNames = m->getCellArrayNameList();
for (std::list<std::string>::iterator iter = voxelArrayNames.begin(); iter != voxelArrayNames.end(); ++iter)
{
std::string name = *iter;
IDataArray::Pointer p = m->getCellData(*iter);
// Make a copy of the 'p' array that has the same name. When placed into
// the data container this will over write the current array with
// the same name. At least in theory
IDataArray::Pointer data = p->createNewArray(p->GetNumberOfTuples(), p->GetNumberOfComponents(), p->GetName());
data->Resize(totalPoints);
void* source = NULL;
void* destination = NULL;
size_t newIndicies_I = 0;
int nComp = data->GetNumberOfComponents();
for (size_t i = 0; i < static_cast<size_t>(totalPoints); i++)
{
newIndicies_I = newindicies[i];
source = p->GetVoidPointer((nComp * newIndicies_I));
destination = data->GetVoidPointer((data->GetNumberOfComponents() * i));
::memcpy(destination, source, p->GetTypeSize() * data->GetNumberOfComponents());
}
m->addCellData(*iter, data);
}
m->setResolution(m_Resolution.x, m_Resolution.y, m_Resolution.z);
m->setDimensions(m_XP, m_YP, m_ZP);
notifyStatusMessage("Complete");
}
// -----------------------------------------------------------------------------
//
// -----------------------------------------------------------------------------
void RawBinaryReader::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);
// Get the total size of the array from the options
size_t voxels = m_Dimensions.x * m_Dimensions.y * m_Dimensions.z;
if (m_OverRideOriginResolution == true)
{
m->setOrigin(m_Origin.x, m_Origin.y, m_Origin.z);
m->setResolution(m_Resolution.x, m_Resolution.y, m_Resolution.z);
}
m->setDimensions(m_Dimensions.x, m_Dimensions.y, m_Dimensions.z);
array = IDataArray::NullPointer();
if (m_ScalarType == Detail::Int8)
{
Int8ArrayType::Pointer p = Int8ArrayType::CreateArray(voxels, m_NumberOfComponents, m_OutputArrayName);
err = ReadBinaryFile<int8_t>(p, m_InputFile, m_SkipHeaderBytes);
if (err >= 0 ) { SWAP_ARRAY(p)
array = p;}
}
else if (m_ScalarType == Detail::UInt8)
{
UInt8ArrayType::Pointer p = UInt8ArrayType::CreateArray(voxels, m_NumberOfComponents, m_OutputArrayName);
err = ReadBinaryFile<uint8_t>(p, m_InputFile, m_SkipHeaderBytes);
if (err >= 0 ) { SWAP_ARRAY(p)
array = p;}
}
else if (m_ScalarType == Detail::Int16)
{
Int16ArrayType::Pointer p = Int16ArrayType::CreateArray(voxels, m_NumberOfComponents, m_OutputArrayName);
err = ReadBinaryFile<int16_t>(p, m_InputFile, m_SkipHeaderBytes);
if (err >= 0 ) { SWAP_ARRAY(p)
array = p;}
}
else if (m_ScalarType == Detail::UInt16)
{
UInt16ArrayType::Pointer p = UInt16ArrayType::CreateArray(voxels, m_NumberOfComponents, m_OutputArrayName);
err = ReadBinaryFile<uint16_t>(p, m_InputFile, m_SkipHeaderBytes);
if (err >= 0 ) { SWAP_ARRAY(p)
array = p;}
}
else if (m_ScalarType == Detail::Int32)
{
Int32ArrayType::Pointer p = Int32ArrayType::CreateArray(voxels, m_NumberOfComponents, m_OutputArrayName);
err = ReadBinaryFile<int32_t>(p, m_InputFile, m_SkipHeaderBytes);
if (err >= 0 ) { SWAP_ARRAY(p)
array = p;}
}
else if (m_ScalarType == Detail::UInt32)
{
UInt32ArrayType::Pointer p = UInt32ArrayType::CreateArray(voxels, m_NumberOfComponents, m_OutputArrayName);
err = ReadBinaryFile<uint32_t>(p, m_InputFile, m_SkipHeaderBytes);
if (err >= 0 ) { SWAP_ARRAY(p)
array = p;}
}
else if (m_ScalarType == Detail::Int64)
{
Int64ArrayType::Pointer p = Int64ArrayType::CreateArray(voxels, m_NumberOfComponents, m_OutputArrayName);
err = ReadBinaryFile<int64_t>(p, m_InputFile, m_SkipHeaderBytes);
if (err >= 0 ) { SWAP_ARRAY(p)
array = p;}
}
else if (m_ScalarType == Detail::UInt64)
{
UInt64ArrayType::Pointer p = UInt64ArrayType::CreateArray(voxels, m_NumberOfComponents, m_OutputArrayName);
err = ReadBinaryFile<uint64_t>(p, m_InputFile, m_SkipHeaderBytes);
if (err >= 0 ) { SWAP_ARRAY(p)
array = p;}
}
else if (m_ScalarType == Detail::Float)
{
FloatArrayType::Pointer p = FloatArrayType::CreateArray(voxels, m_NumberOfComponents, m_OutputArrayName);
err = ReadBinaryFile<float>(p, m_InputFile, m_SkipHeaderBytes);
if (err >= 0 ) { SWAP_ARRAY(p)
array = p;}
}
else if (m_ScalarType == Detail::Double)
{
DoubleArrayType::Pointer p = DoubleArrayType::CreateArray(voxels, m_NumberOfComponents, m_OutputArrayName);
err = ReadBinaryFile<double>(p, m_InputFile, m_SkipHeaderBytes);
if (err >= 0 ) { SWAP_ARRAY(p)
array = p;}
}
if (NULL != array.get())
{
m->addCellData(array->GetName(), array);
}
else if(err == RBR_FILE_NOT_OPEN )
{
setErrorCondition(RBR_FILE_NOT_OPEN);
notifyErrorMessage("RawBinaryReader was unable to open the specified file.", getErrorCondition());
}
else if (err == RBR_FILE_TOO_SMALL)
{
setErrorCondition(RBR_FILE_TOO_SMALL);
notifyErrorMessage("The file size is smaller than the allocated size.", getErrorCondition());
}
else if (err == RBR_FILE_TOO_BIG)
{
notifyWarningMessage("The file size is larger than the allocated size.", RBR_FILE_TOO_BIG);
}
else if(err == RBR_READ_EOF)
{
setErrorCondition(RBR_READ_EOF);
notifyErrorMessage("RawBinaryReader read past the end of the specified file.", getErrorCondition());
}
/* Let the GUI know we are done with this filter */
notifyStatusMessage("Complete");
}
// -----------------------------------------------------------------------------
//
// -----------------------------------------------------------------------------
void RawBinaryReader::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());
}
if(m_OutputArrayName.empty() == true)
{
ss.str("");
ss << "The Output Array Name is blank (empty) and a value must be filled in for the pipeline to complete.";
setErrorCondition(-398);
addErrorMessage(getHumanLabel(), ss.str(), getErrorCondition());
}
if (m_NumberOfComponents < 1)
{
ss.str("");
ss << "The number of components must be larger than Zero";
setErrorCondition(-391);
addErrorMessage(getHumanLabel(), ss.str(), getErrorCondition());
}
if (m_Dimensionality < 1)
{
ss.str("");
ss << "The dimensionality must be larger than Zero";
setErrorCondition(-389);
addErrorMessage(getHumanLabel(), ss.str(), getErrorCondition());
}
if ( m_Dimensions.x == 0 || m_Dimensions.y == 0 || m_Dimensions.z == 0)
{
ss.str("");
ss << "One of the dimensions has a size less than or Equal to Zero (0). The minimum size must be greater than One (1).";
setErrorCondition(-390);
addErrorMessage(getHumanLabel(), ss.str(), getErrorCondition());
}
if (true == preflight)
{
size_t allocatedBytes = 0;
IDataArray::Pointer p = IDataArray::NullPointer();
if (m_ScalarType == Detail::Int8)
{
p = Int8ArrayType::CreateArray(voxels, m_NumberOfComponents, m_OutputArrayName);
allocatedBytes = sizeof(int8_t) * m_NumberOfComponents * m_Dimensions.x * m_Dimensions.y * m_Dimensions.z;
}
else if (m_ScalarType == Detail::UInt8)
{
p = UInt8ArrayType::CreateArray(voxels, m_NumberOfComponents, m_OutputArrayName);
allocatedBytes = sizeof(uint8_t) * m_NumberOfComponents * m_Dimensions.x * m_Dimensions.y * m_Dimensions.z;
}
else if (m_ScalarType == Detail::Int16)
{
p = Int16ArrayType::CreateArray(voxels, m_NumberOfComponents, m_OutputArrayName);
allocatedBytes = sizeof(int16_t) * m_NumberOfComponents * m_Dimensions.x * m_Dimensions.y * m_Dimensions.z;
}
else if (m_ScalarType == Detail::UInt16)
{
p = UInt16ArrayType::CreateArray(voxels, m_NumberOfComponents, m_OutputArrayName);
allocatedBytes = sizeof(uint16_t) * m_NumberOfComponents * m_Dimensions.x * m_Dimensions.y * m_Dimensions.z;
}
else if (m_ScalarType == Detail::Int32)
{
p = Int32ArrayType::CreateArray(voxels, m_NumberOfComponents, m_OutputArrayName);
allocatedBytes = sizeof(int32_t) * m_NumberOfComponents * m_Dimensions.x * m_Dimensions.y * m_Dimensions.z;
}
else if (m_ScalarType == Detail::UInt32)
{
p = UInt32ArrayType::CreateArray(voxels, m_NumberOfComponents, m_OutputArrayName);
allocatedBytes = sizeof(uint32_t) * m_NumberOfComponents * m_Dimensions.x * m_Dimensions.y * m_Dimensions.z;
}
else if (m_ScalarType == Detail::Int64)
{
p = Int64ArrayType::CreateArray(voxels, m_NumberOfComponents, m_OutputArrayName);
allocatedBytes = sizeof(int64_t) * m_NumberOfComponents * m_Dimensions.x * m_Dimensions.y * m_Dimensions.z;
}
else if (m_ScalarType == Detail::UInt64)
{
p = UInt64ArrayType::CreateArray(voxels, m_NumberOfComponents, m_OutputArrayName);
allocatedBytes = sizeof(uint64_t) * m_NumberOfComponents * m_Dimensions.x * m_Dimensions.y * m_Dimensions.z;
}
else if (m_ScalarType == Detail::Float)
{
p = FloatArrayType::CreateArray(voxels, m_NumberOfComponents, m_OutputArrayName);
allocatedBytes = sizeof(float) * m_NumberOfComponents * m_Dimensions.x * m_Dimensions.y * m_Dimensions.z;
}
else if (m_ScalarType == Detail::Double)
{
p = DoubleArrayType::CreateArray(voxels, m_NumberOfComponents, m_OutputArrayName);
allocatedBytes = sizeof(double) * m_NumberOfComponents * m_Dimensions.x * m_Dimensions.y * m_Dimensions.z;
}
// Sanity Check Allocated Bytes versus size of file
uint64_t fileSize = MXAFileInfo::fileSize(m_InputFile);
int check = SanityCheckFileSizeVersusAllocatedSize(allocatedBytes, fileSize, m_SkipHeaderBytes);
if (check == -1)
{
ss.str("");
ss << "The file size is " << fileSize << " but the number of bytes needed to fill the array is " << allocatedBytes << ". This condition would cause an error reading the input file.";
ss << " Please adjust the input parameters to match the size of the file or select a different data file.";
setErrorCondition(RBR_FILE_TOO_SMALL);
addErrorMessage(getHumanLabel(), ss.str(), getErrorCondition());
}
else if (check == 1)
{
ss.str("");
ss << "The file size is " << fileSize << " but the number of bytes needed to fill the array is " << allocatedBytes << " which is less than the size of the file.";
ss << " DREAM3D will read only the first part of the file into the array.";
addWarningMessage(getHumanLabel(), ss.str(), RBR_FILE_TOO_BIG);
}
m->addCellData(p->GetName(), p);
m->setDimensions(m_Dimensions.x, m_Dimensions.y, m_Dimensions.z);
m->setResolution(m_Resolution.x, m_Resolution.y, m_Resolution.z);
m->setOrigin(m_Origin.x, m_Origin.y, m_Origin.z);
}
}
// -----------------------------------------------------------------------------
//
// -----------------------------------------------------------------------------
void ReadH5Ebsd::copyTSLArrays(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_CellPhasesArrayName) != m_SelectedVoxelCellArrays.end() )
{
phasePtr = reinterpret_cast<int*>(ebsdReader->getPointerByName(Ebsd::Ang::PhaseData));
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(m_CellEulerAnglesArrayName) != m_SelectedVoxelCellArrays.end() )
{
f1 = reinterpret_cast<float*>(ebsdReader->getPointerByName(Ebsd::Ang::Phi1));
f2 = reinterpret_cast<float*>(ebsdReader->getPointerByName(Ebsd::Ang::Phi));
f3 = reinterpret_cast<float*>(ebsdReader->getPointerByName(Ebsd::Ang::Phi2));
fArray = FloatArrayType::CreateArray(totalPoints, 3, DREAM3D::CellData::EulerAngles);
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(Ebsd::Ang::ImageQuality) != m_SelectedVoxelCellArrays.end() )
{
f1 = reinterpret_cast<float*>(ebsdReader->getPointerByName(Ebsd::Ang::ImageQuality));
fArray = FloatArrayType::CreateArray(totalPoints, Ebsd::Ang::ImageQuality);
::memcpy(fArray->GetPointer(0), f1, sizeof(float) * totalPoints);
m->addCellData(Ebsd::Ang::ImageQuality, fArray);
}
if (m_SelectedVoxelCellArrays.find(Ebsd::Ang::ConfidenceIndex) != m_SelectedVoxelCellArrays.end() )
{
f1 = reinterpret_cast<float*>(ebsdReader->getPointerByName(Ebsd::Ang::ConfidenceIndex));
fArray = FloatArrayType::CreateArray(totalPoints, Ebsd::Ang::ConfidenceIndex);
::memcpy(fArray->GetPointer(0), f1, sizeof(float) * totalPoints);
m->addCellData(Ebsd::Ang::ConfidenceIndex, fArray);
}
if (m_SelectedVoxelCellArrays.find(Ebsd::Ang::SEMSignal) != m_SelectedVoxelCellArrays.end() )
{
f1 = reinterpret_cast<float*>(ebsdReader->getPointerByName(Ebsd::Ang::SEMSignal));
fArray = FloatArrayType::CreateArray(totalPoints, Ebsd::Ang::SEMSignal);
::memcpy(fArray->GetPointer(0), f1, sizeof(float) * totalPoints);
m->addCellData(Ebsd::Ang::SEMSignal, fArray);
}
if (m_SelectedVoxelCellArrays.find(Ebsd::Ang::Fit) != m_SelectedVoxelCellArrays.end() )
{
f1 = reinterpret_cast<float*>(ebsdReader->getPointerByName(Ebsd::Ang::Fit));
fArray = FloatArrayType::CreateArray(totalPoints, Ebsd::Ang::Fit);
::memcpy(fArray->GetPointer(0), f1, sizeof(float) * totalPoints);
m->addCellData(Ebsd::Ang::Fit, fArray);
}
}
// -----------------------------------------------------------------------------
//
// -----------------------------------------------------------------------------
void ReadH5Ebsd::dataCheck(bool preflight, size_t voxels, size_t fields, size_t ensembles)
{
setErrorCondition(0);
std::stringstream ss;
VoxelDataContainer* m = getVoxelDataContainer();
if (NULL == m)
{
ss.str("");
ss << getHumanLabel() << "The VoxelDataContainer was NULL and this is NOT allowed. There is an error in the programming. Please contact the developers";
setErrorCondition(-1);
addErrorMessage(getHumanLabel(), ss.str(), -1);
return;
}
if (m_InputFile.empty() == true && m_Manufacturer == Ebsd::UnknownManufacturer)
{
ss.str("");
ss << getHumanLabel() << ": Either the H5Ebsd file must exist or the Manufacturer must be set";
setErrorCondition(-1);
addErrorMessage(getHumanLabel(), ss.str(), -1);
}
else if (MXAFileInfo::exists(m_InputFile) == false)
{
ss << "The input file does not exist.";
setErrorCondition(-388);
addErrorMessage(getHumanLabel(), ss.str(), getErrorCondition());
}
else if (m_InputFile.empty() == false)
{
H5EbsdVolumeInfo::Pointer reader = H5EbsdVolumeInfo::New();
reader->setFileName(m_InputFile);
int err = reader->readVolumeInfo();
if (err < 0)
{
ss << getHumanLabel() << ": Error reading VolumeInfo from H5Ebsd File";
setErrorCondition(-1);
addErrorMessage(getHumanLabel(), ss.str(), -1);
return;
}
std::string manufacturer = reader->getManufacturer();
if(manufacturer.compare(Ebsd::Ang::Manufacturer) == 0)
{
m_Manufacturer = Ebsd::TSL;
}
else if(manufacturer.compare(Ebsd::Ctf::Manufacturer) == 0)
{
m_Manufacturer = Ebsd::HKL;
}
else if(manufacturer.compare(Ebsd::Mic::Manufacturer) == 0)
{
m_Manufacturer = Ebsd::HEDM;
}
else
{
ss << getHumanLabel() << ": Original Data source could not be determined. It should be TSL, HKL or HEDM";
setErrorCondition(-1);
addErrorMessage(getHumanLabel(), ss.str(), -1);
return;
}
int64_t dims[3];
float res[3];
reader->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);
m->setOrigin(0.0f, 0.0f, 0.0f);
}
H5EbsdVolumeReader::Pointer reader;
std::vector<std::string> names;
if (m_Manufacturer == Ebsd::TSL)
{
AngFields fields;
reader = H5AngVolumeReader::New();
names = fields.getFilterFields<std::vector<std::string> > ();
}
else if (m_Manufacturer == Ebsd::HKL)
{
CtfFields fields;
reader = H5CtfVolumeReader::New();
names = fields.getFilterFields<std::vector<std::string> > ();
}
else if (m_Manufacturer == Ebsd::HEDM)
{
MicFields fields;
reader = H5MicVolumeReader::New();
names = fields.getFilterFields<std::vector<std::string> > ();
}
else
{
ss << getHumanLabel() << ": Original Data source could not be determined. It should be TSL or HKL";
setErrorCondition(-1);
addErrorMessage(getHumanLabel(), ss.str(), -1);
return;
}
for (size_t i = 0; i < names.size(); ++i)
{
if (reader->getPointerType(names[i]) == Ebsd::Int32)
{
Int32ArrayType::Pointer array = Int32ArrayType::CreateArray(voxels, names[i]);
m->addCellData(names[i], array);
}
else if (reader->getPointerType(names[i]) == Ebsd::Float)
{
FloatArrayType::Pointer array = FloatArrayType::CreateArray(voxels, names[i]);
m->addCellData(names[i], array);
}
}
CREATE_NON_PREREQ_DATA(m, DREAM3D, CellData, CellEulerAngles, ss, float, FloatArrayType, 0, voxels, 3)
CREATE_NON_PREREQ_DATA(m, DREAM3D, CellData, CellPhases, ss, int32_t, Int32ArrayType, 0, voxels, 1)
typedef DataArray<unsigned int> XTalStructArrayType;
CREATE_NON_PREREQ_DATA(m, DREAM3D, EnsembleData, CrystalStructures, ss, unsigned int, XTalStructArrayType, Ebsd::CrystalStructure::UnknownCrystalStructure, ensembles, 1)
CREATE_NON_PREREQ_DATA(m, DREAM3D, EnsembleData, LatticeConstants, ss, float, FloatArrayType, 0.0, ensembles, 6)
StringDataArray::Pointer materialNames = StringDataArray::CreateArray(1, DREAM3D::EnsembleData::MaterialName);
m->addEnsembleData( DREAM3D::EnsembleData::MaterialName, materialNames);
ADD_HELP_INDEX_ENTRY(EnsembleData, MaterialName, XTalStructArrayType, 1);
}
// -----------------------------------------------------------------------------
//
// -----------------------------------------------------------------------------
void ConvertData::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)
{
ss.str("");
ss << "The Input Voxel Cell Array Name is blank (empty) and a value must be filled in for the pipeline to complete.";
setErrorCondition(-397);
addErrorMessage(getHumanLabel(), ss.str(), getErrorCondition());
}
if(m_OutputArrayName.empty() == true)
{
ss.str("");
ss << "The Output Array Name is blank (empty) and a value must be filled in for the pipeline to complete.";
setErrorCondition(-398);
addErrorMessage(getHumanLabel(), ss.str(), getErrorCondition());
}
int numberOfComponents = 0;
IDataArray::Pointer iArray = m->getCellData(m_SelectedCellArrayName);
if (NULL != iArray)
{
numberOfComponents = iArray->GetNumberOfComponents();
}
if (true == preflight)
{
IDataArray::Pointer p = IDataArray::NullPointer();
if (m_ScalarType == Detail::Int8)
{
p = Int8ArrayType::CreateArray(voxels, numberOfComponents, m_OutputArrayName);
}
else if (m_ScalarType == Detail::UInt8)
{
p = UInt8ArrayType::CreateArray(voxels, numberOfComponents, m_OutputArrayName);
}
else if (m_ScalarType == Detail::Int16)
{
p = Int16ArrayType::CreateArray(voxels, numberOfComponents, m_OutputArrayName);
}
else if (m_ScalarType == Detail::UInt16)
{
p = UInt16ArrayType::CreateArray(voxels, numberOfComponents, m_OutputArrayName);
}
else if (m_ScalarType == Detail::Int32)
{
p = Int32ArrayType::CreateArray(voxels, numberOfComponents, m_OutputArrayName);
}
else if (m_ScalarType == Detail::UInt32)
{
p = UInt32ArrayType::CreateArray(voxels, numberOfComponents, m_OutputArrayName);
}
else if (m_ScalarType == Detail::Int64)
{
p = Int64ArrayType::CreateArray(voxels, numberOfComponents, m_OutputArrayName);
}
else if (m_ScalarType == Detail::UInt64)
{
p = UInt64ArrayType::CreateArray(voxels, numberOfComponents, m_OutputArrayName);
}
else if (m_ScalarType == Detail::Float)
{
p = FloatArrayType::CreateArray(voxels, numberOfComponents, m_OutputArrayName);
}
else if (m_ScalarType == Detail::Double)
{
p = DoubleArrayType::CreateArray(voxels, numberOfComponents, m_OutputArrayName);
}
m->addCellData(p->GetName(), p);
}
}