/** * @brief * @param parentId * @return */ virtual int readH5Data(hid_t parentId) { int err = 0; this->Resize(0); IDataArray::Pointer p = H5DataArrayReader::readIDataArray(parentId, GetName()); if (p.get() == NULL) { return -1; } this->NumberOfComponents = p->GetNumberOfComponents(); this->Size = p->GetSize(); this->MaxId = (Size == 0) ? 0 : Size -1; this->Array = reinterpret_cast<T*>(p->GetVoidPointer(0)); p->releaseOwnership(); 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; }