// -----------------------------------------------------------------------------
//
// -----------------------------------------------------------------------------
int AttributeMatrix::writeAttributeArraysToHDF5(hid_t parentId)
{
int err;
for(QMap<QString, IDataArray::Pointer>::iterator iter = m_AttributeArrays.begin(); iter != m_AttributeArrays.end(); ++iter)
{
IDataArray::Pointer d = iter.value();
err = d->writeH5Data(parentId, m_TupleDims);
if(err < 0)
{
return err;
}
}
return 0;
}
// -----------------------------------------------------------------------------
//
// -----------------------------------------------------------------------------
int VoxelDataContainerWriter::writeEnsembleData(hid_t dcGid)
{
std::stringstream ss;
int err = 0;
VoxelDataContainer* m = getVoxelDataContainer();
// Write the Ensemble data
err = H5Utilities::createGroupsFromPath(H5_ENSEMBLE_DATA_GROUP_NAME, dcGid);
if(err < 0)
{
ss.str("");
ss << "Error creating HDF Group " << H5_ENSEMBLE_DATA_GROUP_NAME << std::endl;
setErrorCondition(-66);
notifyErrorMessage( ss.str(), err);
H5Gclose(dcGid); // Close the Data Container Group
return err;
}
err = H5Lite::writeStringAttribute(dcGid, H5_ENSEMBLE_DATA_GROUP_NAME, H5_NAME, H5_ENSEMBLE_DATA_DEFAULT);
hid_t ensembleGid = H5Gopen(dcGid, H5_ENSEMBLE_DATA_GROUP_NAME, H5P_DEFAULT);
if(err < 0)
{
ss.str("");
ss << "Error opening ensemble Group " << H5_ENSEMBLE_DATA_GROUP_NAME << std::endl;
setErrorCondition(-67);
notifyErrorMessage( ss.str(), err);
H5Gclose(dcGid); // Close the Data Container Group
return err;
}
NameListType names = m->getEnsembleArrayNameList();
for (NameListType::iterator iter = names.begin(); iter != names.end(); ++iter)
{
IDataArray::Pointer array = m->getEnsembleData(*iter);
err = array->writeH5Data(ensembleGid);
if(err < 0)
{
ss.str("");
ss << "Error writing Ensemble array '" << *iter << "' to the HDF5 File";
notifyErrorMessage( ss.str(), err);
setErrorCondition(err);
H5Gclose(ensembleGid); // Close the Cell Group
H5Gclose(dcGid); // Close the Data Container Group
return err;
}
}
H5Gclose(ensembleGid);
return err;
}
// -----------------------------------------------------------------------------
//
// -----------------------------------------------------------------------------
int VoxelDataContainerWriter::writeFaceData(hid_t dcGid)
{
std::stringstream ss;
int err = 0;
VoxelDataContainer* m = getVoxelDataContainer();
// Write the Voxel Data
err = H5Utilities::createGroupsFromPath(H5_FACE_DATA_GROUP_NAME, dcGid);
if(err < 0)
{
ss.str("");
ss << "Error creating HDF Group " << H5_FACE_DATA_GROUP_NAME << std::endl;
setErrorCondition(-63);
notifyErrorMessage( ss.str(), err);
H5Gclose(dcGid); // Close the Data Container Group
return err;
}
hid_t FaceGroupId = H5Gopen(dcGid, H5_FACE_DATA_GROUP_NAME, H5P_DEFAULT);
if(err < 0)
{
ss.str("");
ss << "Error writing string attribute to HDF Group " << H5_FACE_DATA_GROUP_NAME << std::endl;
setErrorCondition(-64);
notifyErrorMessage( ss.str(), err);
H5Gclose(dcGid); // Close the Data Container Group
return err;
}
NameListType names = m->getFaceArrayNameList();
for (NameListType::iterator iter = names.begin(); iter != names.end(); ++iter)
{
ss.str("");
ss << "Writing Face Data '" << *iter << "' to HDF5 File" << std::endl;
notifyStatusMessage(ss.str());
IDataArray::Pointer array = m->getFaceData(*iter);
err = array->writeH5Data(FaceGroupId);
if(err < 0)
{
ss.str("");
ss << "Error writing array '" << *iter << "' to the HDF5 File";
notifyErrorMessage( ss.str(), err);
setErrorCondition(err);
H5Gclose(FaceGroupId); // Close the Face Group
H5Gclose(dcGid); // Close the Data Container Group
return err;
}
}
H5Gclose(FaceGroupId); // Close the Face Group
return err;
}
// -----------------------------------------------------------------------------
//
// -----------------------------------------------------------------------------
int VoxelDataContainerWriter::writeFieldData(hid_t dcGid)
{
std::stringstream ss;
int err = 0;
VoxelDataContainer* m = getVoxelDataContainer();
#if WRITE_FIELD_XDMF
// Get the name of the .dream3d file that we are writing to:
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);
std::string xdmfGroupPath = std::string(":/") + VoxelDataContainer::ClassName() + std::string("/") + H5_FIELD_DATA_GROUP_NAME;
#endif
int64_t volDims[3] = { 0,0,0 };
// Write the Field Data
err = H5Utilities::createGroupsFromPath(H5_FIELD_DATA_GROUP_NAME, dcGid);
if(err < 0)
{
std::cout << "Error creating HDF Group " << H5_FIELD_DATA_GROUP_NAME << std::endl;
return err;
}
err = H5Lite::writeStringAttribute(dcGid, H5_FIELD_DATA_GROUP_NAME, H5_NAME, H5_FIELD_DATA_DEFAULT);
if(err < 0)
{
return err;
}
hid_t fieldGroupId = H5Gopen(dcGid, H5_FIELD_DATA_GROUP_NAME, H5P_DEFAULT);
if(err < 0)
{
ss.str("");
ss << "Error opening field Group " << H5_FIELD_DATA_GROUP_NAME << std::endl;
setErrorCondition(-65);
notifyErrorMessage( ss.str(), err);
H5Gclose(dcGid); // Close the Data Container Group
return err;
}
size_t total = 0;
typedef std::vector<IDataArray*> VectorOfIDataArrays_t;
VectorOfIDataArrays_t neighborListArrays;
NameListType names = m->getFieldArrayNameList();
if (names.size() > 0)
{
IDataArray::Pointer array = m->getFieldData(names.front());
total = array->GetSize();
volDims[0] = total;
volDims[1] = 1;
volDims[2] = 1;
#if WRITE_FIELD_XDMF
ss.str("");
ss << "Field Data (" << total << ")";
writeFieldXdmfGridHeader(total, ss.str());
#endif
}
// Now loop over all the field data and write it out, possibly wrapping it with XDMF code also.
for (NameListType::iterator iter = names.begin(); iter != names.end(); ++iter)
{
IDataArray::Pointer array = m->getFieldData(*iter);
if (array->getTypeAsString().compare(NeighborList<int>::ClassName()) == 0)
{
neighborListArrays.push_back(array.get());
}
else if (NULL != array.get())
{
err = array->writeH5Data(fieldGroupId);
if(err < 0)
{
ss.str("");
ss << "Error writing field array '" << (*iter).c_str() << "' to the HDF5 File";
notifyErrorMessage( ss.str(), err);
setErrorCondition(err);
H5Gclose(fieldGroupId); // Close the Cell Group
H5Gclose(dcGid); // Close the Data Container Group
return err;
}
#if WRITE_FIELD_XDMF
array->writeXdmfAttribute( *m_XdmfPtr, volDims, hdfFileName, xdmfGroupPath, " (Field)");
#endif
}
}
#if WRITE_FIELD_XDMF
if (names.size() > 0)
{
writeXdmfGridFooter("Field Data");
}
#endif
// Write the NeighborLists onto their own grid
// We need to determine how many total elements we are going to end up with and group the arrays by
// those totals so we can minimize the number of grids
typedef std::map<size_t, VectorOfIDataArrays_t> SizeToIDataArrays_t;
SizeToIDataArrays_t sizeToDataArrays;
for(VectorOfIDataArrays_t::iterator iter = neighborListArrays.begin(); iter < neighborListArrays.end(); ++iter)
{
IDataArray* array = (*iter);
sizeToDataArrays[array->GetSize()].push_back(array);
}
// Now loop over each pair in the map creating a section in the XDMF and also writing the data to the HDF5 file
for(SizeToIDataArrays_t::iterator pair = sizeToDataArrays.begin(); pair != sizeToDataArrays.end(); ++pair)
{
total = (*pair).first;
VectorOfIDataArrays_t& arrays = (*pair).second;
volDims[0] = total;
volDims[1] = 1;
volDims[2] = 1;
#if WRITE_FIELD_XDMF
ss.str("");
ss << "Neighbor Data (" << total << ")";
writeFieldXdmfGridHeader(total, ss.str());
#endif
for(VectorOfIDataArrays_t::iterator iter = arrays.begin(); iter < arrays.end(); ++iter)
{
err = (*iter)->writeH5Data(fieldGroupId);
if(err < 0)
{
ss.str("");
ss << "Error writing neighbor list field array '" << (*iter)->GetName() << "' to the HDF5 File";
notifyErrorMessage( ss.str(), err);
setErrorCondition(err);
H5Gclose(fieldGroupId); // Close the Cell Group
H5Gclose(dcGid); // Close the Data Container Group
return err;
}
#if WRITE_FIELD_XDMF
(*iter)->writeXdmfAttribute( *m_XdmfPtr, volDims, hdfFileName, xdmfGroupPath, " (Neighbor Data)");
#endif
}
#if WRITE_FIELD_XDMF
writeXdmfGridFooter(ss.str());
#endif
}
H5Gclose(fieldGroupId);
return err;
}
// -----------------------------------------------------------------------------
//
// -----------------------------------------------------------------------------
int VoxelDataContainerWriter::writeCellData(hid_t dcGid)
{
std::stringstream ss;
int err = 0;
VoxelDataContainer* m = getVoxelDataContainer();
int64_t volDims[3] =
{ m->getXPoints(), m->getYPoints(), m->getZPoints() };
float spacing[3] =
{ m->getXRes(), m->getYRes(), m->getZRes() };
float origin[3] =
{ 0.0f, 0.0f, 0.0f };
m->getOrigin(origin);
writeCellXdmfGridHeader(origin, spacing, volDims);
// Get the name of the .dream3d file that we are writing to:
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);
std::string xdmfGroupPath = std::string(":/") + VoxelDataContainer::ClassName() + std::string("/") + H5_CELL_DATA_GROUP_NAME;
// Write the Voxel Data
err = H5Utilities::createGroupsFromPath(H5_CELL_DATA_GROUP_NAME, dcGid);
if(err < 0)
{
ss.str("");
ss << "Error creating HDF Group " << H5_CELL_DATA_GROUP_NAME << std::endl;
setErrorCondition(-63);
notifyErrorMessage(ss.str(), err);
H5Gclose(dcGid); // Close the Data Container Group
return err;
}
hid_t cellGroupId = H5Gopen(dcGid, H5_CELL_DATA_GROUP_NAME, H5P_DEFAULT);
if(err < 0)
{
ss.str("");
ss << "Error writing string attribute to HDF Group " << H5_CELL_DATA_GROUP_NAME << std::endl;
setErrorCondition(-64);
notifyErrorMessage(ss.str(), err);
H5Gclose(dcGid); // Close the Data Container Group
return err;
}
NameListType names = m->getCellArrayNameList();
for (NameListType::iterator iter = names.begin(); iter != names.end(); ++iter)
{
ss.str("");
ss << "Writing Cell Data '" << *iter << "' to HDF5 File" << std::endl;
notifyStatusMessage(ss.str());
IDataArray::Pointer array = m->getCellData(*iter);
err = array->writeH5Data(cellGroupId);
if(err < 0)
{
ss.str("");
ss << "Error writing array '" << *iter << "' to the HDF5 File";
notifyErrorMessage(ss.str(), err);
setErrorCondition(err);
H5Gclose(cellGroupId); // Close the Cell Group
H5Gclose(dcGid); // Close the Data Container Group
return err;
}
array->writeXdmfAttribute( *m_XdmfPtr, volDims, hdfFileName, xdmfGroupPath, " (Cell)");
}
H5Gclose(cellGroupId); // Close the Cell Group
writeXdmfGridFooter("Cell Data");
return err;
}