// -----------------------------------------------------------------------------
//
// -----------------------------------------------------------------------------
void VoxelDataContainer::addVertexData(const std::string &name, IDataArray::Pointer data)
{
if (data->GetName().compare(name) != 0)
{
std::cout << "Adding Vertex array with different array name than key name" << std::endl;
std::cout << "Key name: " << name << std::endl;
std::cout << "Array Name:" << data->GetName() << std::endl;
data->SetName(name);
}
m_VertexData[name] = data;
m_NumVertexTuples = data->GetNumberOfTuples();
}
// -----------------------------------------------------------------------------
//
// -----------------------------------------------------------------------------
void SurfaceMeshDataContainer::addEnsembleData(const std::string &name, IDataArray::Pointer data)
{
if (data->GetName().compare(name) != 0)
{
std::cout << "Adding Ensemble array with different array name than key name" << std::endl;
std::cout << "Key name: " << name << std::endl;
std::cout << "Array Name:" << data->GetName() << std::endl;
data->SetName(name);
}
m_EnsembleData[name] = data;
m_NumEnsembleTuples = data->GetNumberOfTuples();
}
// -----------------------------------------------------------------------------
//
// -----------------------------------------------------------------------------
void FieldDataCSVWriter::execute()
{
int err = 0;
setErrorCondition(err);
VoxelDataContainer* m = getVoxelDataContainer();
if(NULL == m)
{
setErrorCondition(-999);
notifyErrorMessage("The DataContainer Object was NULL", -999);
return;
}
// 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_FieldDataFile);
if(!MXADir::mkdir(parentPath, true))
{
std::stringstream ss;
ss << "Error creating parent path '" << parentPath << "'";
notifyErrorMessage(ss.str(), -1);
setErrorCondition(-1);
return;
}
std::string filename = getFieldDataFile();
std::ofstream outFile;
outFile.open(filename.c_str(), std::ios_base::binary);
char space = DREAM3D::GrainData::Delimiter;
// Write the total number of grains
outFile << m->getNumFieldTuples()-1 << std::endl;
// Get all the names of the arrays from the Data Container
std::list<std::string> headers = m->getFieldArrayNameList();
std::vector<IDataArray::Pointer> data;
//For checking if an array is a neighborlist
NeighborList<int>::Pointer neighborlistPtr = NeighborList<int>::New();
// Print the GrainIds Header before the rest of the headers
outFile << DREAM3D::GrainData::GrainID;
// Loop throught the list and print the rest of the headers, ignoring those we don't want
for(std::list<std::string>::iterator iter = headers.begin(); iter != headers.end(); ++iter)
{
// Only get the array if the name does NOT match those listed
IDataArray::Pointer p = m->getFieldData(*iter);
if(p->getNameOfClass().compare(neighborlistPtr->getNameOfClass()) != 0)
{
if (p->GetNumberOfComponents() == 1) {
outFile << space << (*iter);
}
else // There are more than a single component so we need to add multiple header values
{
for(int k = 0; k < p->GetNumberOfComponents(); ++k)
{
outFile << space << (*iter) << "_" << k;
}
}
// Get the IDataArray from the DataContainer
data.push_back(p);
}
}
outFile << std::endl;
// Get the number of tuples in the arrays
size_t numTuples = data[0]->GetNumberOfTuples();
std::stringstream ss;
float threshold = 0.0f;
// Skip the first grain
for(size_t i = 1; i < numTuples; ++i)
{
if (((float)i / numTuples) * 100.0f > threshold) {
ss.str("");
ss << "Writing Field Data - " << ((float)i / numTuples) * 100 << "% Complete";
notifyStatusMessage(ss.str());
threshold = threshold + 5.0f;
if (threshold < ((float)i / numTuples) * 100.0f) {
threshold = ((float)i / numTuples) * 100.0f;
}
}
// Print the grain id
outFile << i;
// Print a row of data
for( std::vector<IDataArray::Pointer>::iterator p = data.begin(); p != data.end(); ++p)
{
outFile << space;
(*p)->printTuple(outFile, i, space);
}
outFile << std::endl;
}
if(m_WriteNeighborListData == true)
{
// Print the GrainIds Header before the rest of the headers
// Loop throught the list and print the rest of the headers, ignoring those we don't want
for(std::list<std::string>::iterator iter = headers.begin(); iter != headers.end(); ++iter)
{
// Only get the array if the name does NOT match those listed
IDataArray::Pointer p = m->getFieldData(*iter);
if(p->getNameOfClass().compare(neighborlistPtr->getNameOfClass()) == 0)
{
outFile << DREAM3D::GrainData::GrainID << space << DREAM3D::GrainData::NumNeighbors << space << (*iter) << std::endl;
size_t numTuples = p->GetNumberOfTuples();
// float threshold = 0.0f;
// Skip the first grain
for(size_t i = 1; i < numTuples; ++i)
{
// Print the grain id
outFile << i;
// Print a row of data
outFile << space;
p->printTuple(outFile, i, space);
outFile << std::endl;
}
}
}
}
outFile.close();
// If there is an error set this to something negative and also set a message
notifyStatusMessage("FieldDataCSVWriter Completed");
}
// -----------------------------------------------------------------------------
//
// -----------------------------------------------------------------------------
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");
}
// -----------------------------------------------------------------------------
//
// -----------------------------------------------------------------------------
IDataArray::Pointer H5DataArrayReader::readStringDataArray(hid_t gid, const std::string &name, bool preflightOnly)
{
herr_t err = -1;
herr_t retErr = 1;
hid_t typeId = -1;
H5T_class_t attr_type;
size_t attr_size;
std::string res;
std::vector<hsize_t> dims; //Reusable for the loop
IDataArray::Pointer ptr = IDataArray::NullPointer();
//std::cout << "Reading Attribute " << *iter << std::endl;
typeId = H5Lite::getDatasetType(gid, name);
if (typeId < 0)
{
return ptr;
}
err = H5Lite::getDatasetInfo(gid, name, dims, attr_type, attr_size);
if(err < 0)
{
std::cout << "Error in getAttributeInfo method in readUserMetaData." << std::endl;
}
else
{
std::string classType;
err = H5Lite::readStringAttribute(gid, name, DREAM3D::HDF5::ObjectType, classType);
if (err < 0)
{
return ptr;
}
int numComp = 1;
err = H5Lite::readScalarAttribute(gid, name, DREAM3D::HDF5::NumComponents, numComp);
if (err < 0)
{
numComp = 1;
}
if(H5Tequal(typeId, H5T_STD_U8BE) || H5Tequal(typeId, H5T_STD_U8LE)
|| H5Tequal(typeId, H5T_STD_I8BE) || H5Tequal(typeId, H5T_STD_I8LE) )
{
if (preflightOnly == false) {
IDataArray::Pointer bufferPtr = Detail::readH5Dataset<char>(gid, name, dims);
const char* buf = reinterpret_cast<char*>(bufferPtr->GetVoidPointer(0));
// count the number of 0x00 characters which are the 'null termination' of each string
size_t size = bufferPtr->GetNumberOfTuples();
size_t count = 0;
for(size_t i = 0; i < size; ++i)
{
if(buf[i] == 0)
{
++count;
}
}
ptr = StringDataArray::CreateArray(count, name);
StringDataArray* strArray = StringDataArray::SafePointerDownCast(ptr.get());
size_t start = 0;
size_t index = 0;
for(size_t i = 0; i < size; ++i)
{
if(buf[i] == 0)
{
std::string str( &(buf[start]) );
strArray->SetValue(index, str);
++index;
start = i + 1;
}
}
}
else // We are preflighting only so just create a StringDataArray of lenght 1
{
ptr = StringDataArray::CreateArray(1, name);
}
}
}
CloseH5T(typeId, err, retErr);
return ptr;
}
// -----------------------------------------------------------------------------
//
// -----------------------------------------------------------------------------
std::string SurfaceMeshDataContainerWriter::writeXdmfAttributeDataHelper(int numComp, const std::string &attrType,
const std::string &groupName,
IDataArray::Pointer array,
const std::string ¢ering,
int precision, const std::string &xdmfTypeName)
{
std::stringstream out;
std::stringstream dimStr;
std::stringstream dimStr1;
std::stringstream dimStr1half;
std::stringstream dimStr2;
std::stringstream dimStr2half;
if((numComp%2) == 1)
{
out << " <Attribute Name=\"" << array->GetName() << "\" ";
out << "AttributeType=\"" << attrType << "\" ";
dimStr << array->GetNumberOfTuples() << " " << array->GetNumberOfComponents();
out << "Center=\"" << centering << "\">" << std::endl;
// Open the <DataItem> Tag
out << " <DataItem Format=\"HDF\" Dimensions=\"" << dimStr.str() << "\" ";
out << "NumberType=\"" << xdmfTypeName << "\" " << "Precision=\"" << precision << "\" >" << std::endl;
ssize_t nameSize = H5Fget_name(m_HdfFileId, NULL, 0) + 1;
std::vector<char> nameBuffer(nameSize, 0);
nameSize = H5Fget_name(m_HdfFileId, &(nameBuffer.front()), nameSize);
std::string hdfFileName(&(nameBuffer.front()), nameSize);
hdfFileName = MXAFileInfo::filename(hdfFileName);
out << " " << hdfFileName << ":/SurfaceMeshDataContainer/" << groupName << "/" << array->GetName() << std::endl;
out << " </DataItem>" << std::endl;
out << " </Attribute>" << std::endl << std::endl;
}
else
{
//First Slab
out << " <Attribute Name=\"" << array->GetName() << " (Field 0)\" ";
out << "AttributeType=\"" << attrType << "\" ";
dimStr1 << array->GetNumberOfTuples() << " " << array->GetNumberOfComponents();
dimStr1half << array->GetNumberOfTuples() << " " << (array->GetNumberOfComponents()/2);
out << "Center=\"" << centering << "\">" << std::endl;
// Open the <DataItem> Tag
out << " <DataItem ItemType=\"HyperSlab\" Dimensions=\"" << dimStr1half.str() << "\" ";
out << "Type=\"HyperSlab\" " << "Name=\"" << array->GetName() << " (Field 0)\" >" << std::endl;
out << " <DataItem Dimensions=\"3 2\" " << "Format=\"XML\" >" << std::endl;
out << " 0 0" << std::endl;
out << " 1 1" << std::endl;
out << " " << dimStr1half.str() << " </DataItem>" << std::endl;
out << std::endl;
out << " <DataItem Format=\"HDF\" Dimensions=\"" << dimStr1.str() << "\" " << "NumberType=\"" << xdmfTypeName << "\" " << "Precision=\"" << precision << "\" >" << std::endl;
ssize_t nameSize = H5Fget_name(m_HdfFileId, NULL, 0) + 1;
std::vector<char> nameBuffer(nameSize, 0);
nameSize = H5Fget_name(m_HdfFileId, &(nameBuffer.front()), nameSize);
std::string hdfFileName(&(nameBuffer.front()), nameSize);
hdfFileName = MXAFileInfo::filename(hdfFileName);
out << " " << hdfFileName << ":/SurfaceMeshDataContainer/" << groupName << "/" << array->GetName() << std::endl;
out << " </DataItem>" << std::endl;
out << " </DataItem>" << std::endl;
out << " </Attribute>" << std::endl << std::endl;
//Second Slab
out << " <Attribute Name=\"" << array->GetName() << " (Field 1)\" ";
out << "AttributeType=\"" << attrType << "\" ";
dimStr2 << array->GetNumberOfTuples() << " " << array->GetNumberOfComponents();
dimStr2half << array->GetNumberOfTuples() << " " << (array->GetNumberOfComponents()/2);
out << "Center=\"" << centering << "\">" << std::endl;
// Open the <DataItem> Tag
out << " <DataItem ItemType=\"HyperSlab\" Dimensions=\"" << dimStr2half.str() << "\" ";
out << "Type=\"HyperSlab\" " << "Name=\"" << array->GetName() << " (Field 1)\" >" << std::endl;
out << " <DataItem Dimensions=\"3 2\" " << "Format=\"XML\" >" << std::endl;
out << " 0 " << (array->GetNumberOfComponents()/2) << std::endl;
out << " 1 1" << std::endl;
out << " " << dimStr2half.str() << " </DataItem>" << std::endl;
out << std::endl;
out << " <DataItem Format=\"HDF\" Dimensions=\"" << dimStr2.str() << "\" " << "NumberType=\"" << xdmfTypeName << "\" " << "Precision=\"" << precision << "\" >" << std::endl;
ssize_t nameSize2 = H5Fget_name(m_HdfFileId, NULL, 0) + 1;
std::vector<char> nameBuffer2(nameSize2, 0);
nameSize2 = H5Fget_name(m_HdfFileId, &(nameBuffer2.front()), nameSize2);
std::string hdfFileName2(&(nameBuffer2.front()), nameSize2);
hdfFileName2 = MXAFileInfo::filename(hdfFileName2);
out << " " << hdfFileName2 << ":/SurfaceMeshDataContainer/" << groupName << "/" << array->GetName() << std::endl;
out << " </DataItem>" << std::endl;
out << " </DataItem>" << std::endl;
out << " </Attribute>" << std::endl << std::endl;
}
return out.str();
}