// -----------------------------------------------------------------------------
//
// -----------------------------------------------------------------------------
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 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);
}
//-----------------------------------------------------------------------------
//
// -----------------------------------------------------------------------------
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 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::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 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 ImportR3DStack::execute()
{
int err = 0;
setErrorCondition(err);
dataCheck(false,1,1,1);
if (getErrorCondition() < 0) { notifyErrorMessage("There is a problem with the data check", getErrorCondition()); }
VoxelDataContainer* m = getVoxelDataContainer();
if(NULL == m)
{
setErrorCondition(-999);
notifyErrorMessage("The DataContainer Object was NULL", -999);
return;
}
setErrorCondition(0);
std::stringstream ss;
m->setResolution(m_Resolution.x, m_Resolution.y, m_Resolution.z);
m->setOrigin(m_Origin.x, m_Origin.y, m_Origin.z);
int x = 0;
int y = 0;
readXYSize(x, y);
if (x < 1 || y < 1)
{
setErrorCondition(-1000);
notifyErrorMessage("At least one dimension is less than 1", getErrorCondition());
}
size_t numSlices = m_ZEndIndex - m_ZStartIndex + 1;
size_t totalVoxels = numSlices * x * y;
// Create a new array, eventually substituting this into the DataContainer later on.
Int32ArrayType::Pointer grainIdsPtr = Int32ArrayType::CreateArray(totalVoxels, 1, DREAM3D::CellData::GrainIds);
grainIdsPtr->initializeWithZeros();
m_GrainIds = grainIdsPtr->GetPointer(0); // Get the pointer to the front of the array
int32_t* currentPositionPtr = m_GrainIds;
bool ok = false;
int pixelBytes = 0;
int totalPixels = 0;
int height = 0;
int width = 0;
size_t index = 0;
int64_t z = m_ZStartIndex;
m->setDimensions(x,y,numSlices);
for (std::vector<std::string>::iterator filepath = m_R3DFileList.begin(); filepath != m_R3DFileList.end(); ++filepath)
{
QString R3DFName = QString::fromStdString(*filepath);
ss.str("");
ss << "Importing file " << R3DFName.toStdString();
notifyStatusMessage(ss.str());
QByteArray buf;
QFile in(R3DFName);
if (!in.open(QIODevice::ReadOnly | QIODevice::Text))
{
QString msg = QString("R3D file could not be opened: ") + R3DFName;
setErrorCondition(-14000);
notifyErrorMessage(msg.toStdString(), getErrorCondition());
}
buf = in.readLine(); // Read first line which is the x and y sizes
QList<QByteArray> tokens = buf.split(',');
width = tokens.at(0).toInt();
height = tokens.at(1).toInt();
int32_t value = 0;
for(qint32 i = 0; i < height; ++i)
{
buf = in.readLine();
tokens = buf.split(',');
if (tokens.size() != width+2)
{
notifyStatusMessage("A file did not have the correct width partilcuar line");
break;
}
for(int j = 1; j < width+1; j++)
{
currentPositionPtr[index] = tokens[j].toInt(&ok, 10);
++index;
if (!ok)
{
setErrorCondition(-2004);
notifyErrorMessage("Width dimension entry was not an integer", getErrorCondition());
break;
}
}
if (in.atEnd() == true && i < height - 2)
{
notifyStatusMessage("A file did not have the correct height");
break;
}
}
++z;
if(getCancel() == true)
{
notifyStatusMessage("Conversion was Canceled");
return;
}
}
// OVer write any GrainIds array that is already in the DataContainer
getVoxelDataContainer()->addCellData(DREAM3D::CellData::GrainIds, grainIdsPtr);
/* Let the GUI know we are done with this filter */
notifyStatusMessage("Complete");
}
