H5::DataSet CompartmentReportHDF5::_createDataset( const uint32_t gid,
const size_t compCount )
{
LBASSERT( compCount > 0 );
LBASSERT( !_reportName.empty( ));
std::ostringstream neuronName;
neuronName << "a" << gid;
H5::Group neuronGroup = _file.createGroup( neuronName.str().c_str( ));
H5::Group reportGroup = neuronGroup.createGroup( _reportName );
const int dims = 2;
const size_t numSteps = (getEndTime() - getStartTime()) / getTimestep();
const hsize_t mappingDim[dims] = { 1, compCount };
const hsize_t dataDim[dims] = { numSteps, compCount };
LBASSERT( numSteps > 0 );
H5::DataSpace mappingDataspace( dims, mappingDim );
H5::DataSpace dataDataspace( dims, dataDim );
H5::DataSet mappingDataset = reportGroup.createDataSet(
mappingDatasetName, H5::PredType::NATIVE_FLOAT, mappingDataspace );
H5::DataSet dataDataset = reportGroup.createDataSet( dataDatasetName,
H5::PredType::NATIVE_FLOAT, dataDataspace );
_datas[gid] = dataDataset;
_createMappingAttributes( mappingDataset );
_createDataAttributes( dataDataset );
return mappingDataset;
}
/*********************************************************
FunctionName:RecursiveWriteData
FunctionDesc:递归创建Group
InputParam:
OutputParam:
Return:
Author:xiaowei.han
*********************************************************/
void RecursiveWriteData(H5::Group& NodeGroup, Hdf5_Wrapper::LP_HDF5_DATA pData)
{
using namespace H5;
//参数合法性判断
if (nullptr == pData)
{
return;
}
//如果不带子节点
if (pData->SubDataArray.empty())
{
//判断数据类型
boost::scoped_ptr<CAbstractDataTypeHandler> pHandlder(CDataTypeHandlerFactory::CreateDataTypeHandler(pData->Header.eumDataType, pData->Header.nDataByte));
if (pHandlder)
{
pHandlder->WriteDataSet(NodeGroup, pData);
}
}
//如果有子节点
else
{
//创建一个Group
std::string strGroupKeyName = Utility::GB2312ToUTF8(pData->strKeyName);
auto ChildGroupNode = NodeGroup.createGroup(strGroupKeyName);
//插入属性
for (auto& AttributeElement : pData->AttributeArray)
{
boost::scoped_ptr<CAbstractAttrHanlder> p(CreateAttrHandler(AttributeElement.Header.eumDataType, AttributeElement.Header.nDataByte));
if (p)
{
p->WriteAttr(ChildGroupNode, AttributeElement);
}
}
for (auto& SubGroupElement : pData->SubDataArray)
{
RecursiveWriteData(ChildGroupNode, SubGroupElement);
}
}
}
void Bundle2::streamPOI(size_t frame) {
H5::DataSpace scalar;
H5::Group poiGroup = streamFile_->openGroup("/POI");
for(size_t i = poiFirstFrame_; i <= frame; ++i) {
const std::string frameGroupName = boost::str(boost::format("Frame %1$04d") % i);
H5::Group frameGroup = poiGroup.createGroup(frameGroupName);
hsize_t count = poi_[(ptrdiff_t)i - (ptrdiff_t)poiFirstFrame_].size();
H5::Attribute attr = frameGroup.createAttribute("count", H5::PredType::STD_U64LE, scalar);
attr.write(H5::PredType::NATIVE_HSIZE, &count);
attr.close();
for(size_t camera = 0; camera < poi_[(ptrdiff_t)i - (ptrdiff_t)poiFirstFrame_].size(); ++camera)
poi_[(ptrdiff_t)i - (ptrdiff_t)poiFirstFrame_][camera].save(frameGroup, camera);
frameGroup.close();
}
poiGroup.close();
scalar.close();
poi_.erase(poi_.begin(), poi_.begin() + (ptrdiff_t)frame - (ptrdiff_t)poiFirstFrame_ + 1);
poiFirstFrame_ = frame + 1;
}
inline
void vtkStandardMeshRepresenter::Save(const H5::Group& fg) const {
using namespace H5;
statismo::MatrixType vertexMat = statismo::MatrixType::Zero(3,
m_reference->GetNumberOfPoints());
for (unsigned i = 0; i < m_reference->GetNumberOfPoints(); i++) {
PointType pt = m_reference->GetPoint(i);
for (unsigned d = 0; d < 3; d++) {
vertexMat(d, i) = pt[d];
}
}
HDF5Utils::writeMatrix(fg, "./points", vertexMat);
// check the dimensionality of a face (i.e. the number of points it has). We assume that
// all the cells are the same.
unsigned numPointsPerCell = 0;
if (m_reference->GetNumberOfCells() > 0) {
numPointsPerCell = m_reference->GetCell(0)->GetNumberOfPoints();
}
typedef statismo::GenericEigenType<unsigned int>::MatrixType UIntMatrixType;
UIntMatrixType facesMat = UIntMatrixType::Zero(numPointsPerCell,
m_reference->GetNumberOfCells());
for (unsigned i = 0; i < m_reference->GetNumberOfCells(); i++) {
vtkCell* cell = m_reference->GetCell(i);
assert(numPointsPerCell == cell->GetNumberOfPoints());
for (unsigned d = 0; d < numPointsPerCell; d++) {
facesMat(d, i) = cell->GetPointIds()->GetId(d);
}
}
HDF5Utils::writeMatrixOfType<unsigned int>(fg, "./cells", facesMat);
H5::Group pdGroup = fg.createGroup("pointData");
vtkPointData* pd = m_reference->GetPointData();
if (pd != 0 && pd->GetScalars() != 0) {
vtkDataArray* scalars = pd->GetScalars();
WriteDataArray(pdGroup, "scalars", scalars);
}
if (pd != 0 && pd->GetVectors() != 0) {
vtkDataArray* vectors = pd->GetVectors();
WriteDataArray(pdGroup, "vectors", vectors);
}
if (pd != 0 && pd->GetNormals() != 0) {
vtkDataArray* normals = pd->GetNormals();
WriteDataArray(pdGroup, "normals", normals);
}
H5::Group cdGroup = fg.createGroup("cellData");
vtkCellData* cd = m_reference->GetCellData();
if (cd != 0 && cd->GetScalars() != 0) {
vtkDataArray* scalars = cd->GetScalars();
WriteDataArray(cdGroup, "scalars", scalars);
}
if (cd != 0 && cd->GetVectors() != 0) {
vtkDataArray* vectors = cd->GetVectors();
WriteDataArray(cdGroup, "vectors", vectors);
}
if (cd != 0 && cd->GetNormals() != 0) {
vtkDataArray* normals = cd->GetNormals();
WriteDataArray(cdGroup, "normals", normals);
}
}
/**
* \brief Create a subgroup.
* \param key : the name of the subgroup
* \param delete_if_exists : unlink the group if it exists
*/
group create_group(std::string const & key, bool delete_if_exists = true) const {
unlink_key_if_exists(key);
return _g.createGroup(key.c_str());
}
// Bundle management
void Bundle2::save(const boost::filesystem::path& fileName) const {
// Creating HDF5 file
H5::H5File bundleFile(fileName.string(), H5F_ACC_TRUNC);
storeParameters(bundleFile);
H5::DataSpace scalar;
// Saving POI
H5::Group poiGroup = bundleFile.createGroup("/POI");
H5::Attribute attr = poiGroup.createAttribute("count", H5::PredType::STD_U64LE, scalar);
hsize_t count = poi_.size();
attr.write(H5::PredType::NATIVE_HSIZE, &count);
attr.close();
for(size_t frame = 0; frame < poi_.size(); ++frame) {
const std::string frameGroupName = boost::str(boost::format("Frame %1$04d") % frame);
H5::Group frameGroup = poiGroup.createGroup(frameGroupName);
count = poi_[frame].size();
attr = frameGroup.createAttribute("count", H5::PredType::STD_U64LE, scalar);
attr.write(H5::PredType::NATIVE_HSIZE, &count);
attr.close();
for(size_t camera = 0; camera < poi_[frame].size(); ++camera)
poi_[frame][camera].save(frameGroup, camera);
frameGroup.close();
}
poiGroup.close();
// Saving key frames
H5::Group bundleGroup = bundleFile.createGroup("/Bundle");
H5::Group framesGroup = bundleGroup.createGroup("Frames");
count = frames_.size();
attr = framesGroup.createAttribute("count", H5::PredType::STD_U64LE, scalar);
attr.write(H5::PredType::NATIVE_HSIZE, &count);
attr.close();
for(deque<Frame*>::const_iterator it = frames_.begin(); it != frames_.end(); it++) {
(*it)->save(framesGroup);
}
framesGroup.close();
// Saving tracks
const hsize_t chunkDim[] = { 2, 1 };
H5::DSetCreatPropList propList;
propList.setLayout(H5D_CHUNKED);
propList.setChunk(2, chunkDim);
propList.setDeflate(9);
H5::VarLenType tracksDatasetType(&H5::PredType::STD_U64LE);
hsize_t tracksDim[] = { tracks_.size(), 2 };
hsize_t tracksMaxDim[] = { H5S_UNLIMITED, 2 };
H5::DataSpace tracksDataspace(2, tracksDim, tracksMaxDim);
H5::DataSet tracksDataset = bundleGroup.createDataSet("Tracks", tracksDatasetType, tracksDataspace, propList);
for(size_t i = 0; i < tracks_.size(); ++i)
tracks_[i]->save(tracksDataset, i);
tracksDataset.close();
tracksDataspace.close();
tracksDatasetType.close();
propList.close();
bundleGroup.close();
scalar.close();
bundleFile.close();
}
void Bundle2::initFrameStream_() {
H5::DataSpace scalar;
// Creating datasets for each frame
H5::Group bundleGroup = streamFile_->createGroup("/Bundle");
H5::Group framesGroup = bundleGroup.createGroup("Frames");
hsize_t count = frames_.size();
H5::Attribute attr = framesGroup.createAttribute("count", H5::PredType::STD_U64LE, scalar);
attr.write(H5::PredType::NATIVE_HSIZE, &count);
attr.close();
// Defining frame dataset property
hsize_t chunkDim[] = { 1, 2, 10 };
H5::DSetCreatPropList propList;
propList.setLayout(H5D_CHUNKED);
propList.setChunk(3, chunkDim);
propList.setDeflate(9);
// Definig dataset dataspace
hsize_t max_dim[] = { numCameras_, 2, H5S_UNLIMITED };
hsize_t dim[] = { numCameras_, 2, 0 };
H5::DataSpace ds(3, dim, max_dim);
for(deque<Frame*>::const_iterator it = frames_.begin(); it != frames_.end(); it++) {
const std::string datasetName = boost::str(boost::format("Frame %1$04d") % (*it)->number());
// Creating dataset
H5::DataSet frameData = framesGroup.createDataSet(datasetName, H5::PredType::IEEE_F32LE, ds, propList);
// Writing global number
attr = frameData.createAttribute("globalNumber", H5::PredType::STD_U64LE, scalar);
count = (*it)->globalNumber();
attr.write(H5::PredType::NATIVE_HSIZE, &count);
attr.close();
// Clean up!
frameData.close();
}
// Clean up!
ds.close();
propList.close();
// Creating tracks dataset
hsize_t chunkDim2[] = { 2, 10 };
propList = H5::DSetCreatPropList();
propList.setLayout(H5D_CHUNKED);
propList.setChunk(2, chunkDim);
propList.setDeflate(9);
H5::VarLenType tracksDatasetType(&H5::PredType::STD_U64LE);
hsize_t tracksDim[] = { 0, 2 };
hsize_t tracksMaxDim[] = { H5S_UNLIMITED, 2 };
H5::DataSpace tracksDataspace(2, tracksDim, tracksMaxDim);
H5::DataSet tracksDataset = bundleGroup.createDataSet("Tracks", tracksDatasetType, tracksDataspace, propList);
tracksDataset.close();
tracksDataspace.close();
tracksDatasetType.close();
propList.close();
framesGroup.close();
bundleGroup.close();
scalar.close();
}
void Bundle2::saveGeometry(const boost::filesystem::path& fileName) const {
H5::H5File bundleFile;
bundleFile.openFile(fileName.string(), H5F_ACC_RDWR);
H5::Group rootGroup = bundleFile.openGroup("/");
// If the group "Geometry" exists, delete it!
if(checkGeometry_(bundleFile)) {
rootGroup.unlink("Geometry");
}
// Creating group Geometry
H5::Group geometryGroup = rootGroup.createGroup("Geometry");
// Saving poses
const hsize_t posesChunkDim[] = { 3, 12 };
H5::DSetCreatPropList posesPropList;
posesPropList.setLayout(H5D_CHUNKED);
posesPropList.setChunk(2, posesChunkDim);
posesPropList.setDeflate(9);
const hsize_t posesMaxDim[] = { H5S_UNLIMITED, 12 };
const hsize_t posesCurDim[] = { frames_.size(), 12 };
H5::DataSpace posesDS(2, posesCurDim, posesMaxDim);
H5::DataSet posesDataSet = geometryGroup.createDataSet("Poses", H5::PredType::IEEE_F64LE, posesDS, posesPropList);
double* posesData = (double*)malloc(frames_.size()*12*sizeof(double));
size_t i = 0;
for(deque<Frame*>::const_iterator it = frames_.begin(); it != frames_.end(); it++) {
posesData[i*12] = (*it)->pose()->t().x();
posesData[i*12 + 1] = (*it)->pose()->t().y();
posesData[i*12 + 2] = (*it)->pose()->t().z();
core::Matrix<double> R = (*it)->pose()->R();
posesData[i*12 + 3] = R[0][0];
posesData[i*12 + 4] = R[1][0];
posesData[i*12 + 5] = R[2][0];
posesData[i*12 + 6] = R[0][1];
posesData[i*12 + 7] = R[1][1];
posesData[i*12 + 8] = R[2][1];
posesData[i*12 + 9] = R[0][2];
posesData[i*12 + 10] = R[1][2];
posesData[i*12 + 11] = R[2][2];
++i;
}
posesDataSet.write((const void*)posesData, H5::PredType::NATIVE_DOUBLE, H5::DataSpace::ALL, H5::DataSpace::ALL);
free((void*)posesData);
posesDataSet.close();
posesDS.close();
// Saving points
const hsize_t pointsChunkDim[] = {10, 3};
H5::DSetCreatPropList pointsPropList;
pointsPropList.setLayout(H5D_CHUNKED);
pointsPropList.setChunk(2, pointsChunkDim);
pointsPropList.setDeflate(9);
const hsize_t pointsMaxDim[] = { H5S_UNLIMITED, 3 };
const hsize_t pointsCurDim[] = { tracks_.size(), 3 };
H5::DataSpace pointsDS(2, pointsCurDim, pointsMaxDim);
H5::DataSet pointsDataSet = geometryGroup.createDataSet("Points", H5::PredType::IEEE_F64LE, pointsDS, pointsPropList);
double* pointsData = (double*)malloc(tracks_.size()*3*sizeof(double));
i = 0;
for(deque<Track*>::const_iterator it = tracks_.begin(); it != tracks_.end(); it++) {
pointsData[i*3] = (*it)->point()->coords().x();
pointsData[i*3 + 1] = (*it)->point()->coords().y();
pointsData[i*3 + 2] = (*it)->point()->coords().z();
++i;
}
pointsDataSet.write((const void*)pointsData, H5::PredType::NATIVE_DOUBLE, H5::DataSpace::ALL, H5::DataSpace::ALL);
free((void*)pointsData);
pointsDataSet.close();
pointsDS.close();
// Saving inlier information
const hsize_t inliersChunkDim[] = { 3 };
H5::DSetCreatPropList inliersPropList;
inliersPropList.setLayout(H5D_CHUNKED);
inliersPropList.setChunk(1, inliersChunkDim);
inliersPropList.setDeflate(9);
const hsize_t inliersMaxDim[] = { H5S_UNLIMITED };
const hsize_t inliersCurDim[] = { frames_.size() };
H5::DataSpace inliersDS(1, inliersCurDim, inliersMaxDim);
H5::VarLenType inliersType(&H5::PredType::STD_U8LE);
H5::DataSet inliersDataSet = geometryGroup.createDataSet("Inliers", inliersType, inliersDS, inliersPropList);
i = 0;
for(deque<Frame*>::const_iterator it = frames_.begin(); it != frames_.end(); it++) {
hvl_t inliersLine;
size_t inliersLineSize = 0;
for(size_t j = 0; j < (*it)->size(); ++j) {
View& v = (**it)[j];
for(unsigned int cam = 0; cam < v.numCameras(); ++cam) {
if(v.inCamera(cam)) ++inliersLineSize;
}
}
inliersLine.len = inliersLineSize;
inliersLine.p = malloc(inliersLineSize*sizeof(unsigned char));
size_t k = 0;
for(size_t j = 0; j < (*it)->size(); ++j) {
View& v = (**it)[j];
for(unsigned int cam = 0; cam < v.numCameras(); ++cam) {
if(v.inCamera(cam)) {
((unsigned char*)(inliersLine.p))[k] = v.ray(cam).inlier()?1:0;
++k;
}
}
}
const hsize_t dsOffset[] = { i };
const hsize_t dsCount[] = { 1 };
H5::DataSpace inliersCurDS = inliersDataSet.getSpace();
inliersCurDS.selectHyperslab(H5S_SELECT_SET, dsCount, dsOffset);
const hsize_t memDim[] = { 1 };
H5::DataSpace memDS(1, memDim, memDim);
H5::VarLenType memType(&H5::PredType::NATIVE_UCHAR);
inliersDataSet.write((const void*)&inliersLine, memType, memDS, inliersCurDS);
memType.close();
memDS.close();
inliersCurDS.close();
free(inliersLine.p);
++i;
}
inliersDataSet.close();
inliersType.close();
inliersDS.close();
// Saving curves
if(!curves_.empty()) {
const hsize_t chunkDim[] = { 5 };
H5::DSetCreatPropList propList;
propList.setLayout(H5D_CHUNKED);
propList.setChunk(1, chunkDim);
propList.setDeflate(9);
H5::VarLenType curveDatasetType(&H5::PredType::STD_U64LE);
hsize_t curvesDim[] = { curves_.size() };
hsize_t curvesMaxDim[] = { H5S_UNLIMITED };
H5::DataSpace curvesDataspace(1, curvesDim, curvesMaxDim);
H5::DataSet curvesDataset = geometryGroup.createDataSet("Curves", curveDatasetType, curvesDataspace, propList);
for(size_t i = 0; i < curves_.size(); ++i) {
hvl_t curveLine;
curveLine.len = curves_[i].size();
curveLine.p = malloc(curves_[i].size()*sizeof(size_t));
for(size_t j = 0; j < curves_[i].size(); ++j) ((size_t*)(curveLine.p))[j] = curves_[i].track(j);
const hsize_t dsOffset[] = { i };
const hsize_t dsCount[] = { 1 };
H5::DataSpace curDS = curvesDataset.getSpace();
curDS.selectHyperslab(H5S_SELECT_SET, dsCount, dsOffset);
const hsize_t memDim[] = { 1 };
H5::DataSpace memDS(1, memDim, memDim);
H5::VarLenType memType(&H5::PredType::NATIVE_HSIZE);
curvesDataset.write((const void*)&curveLine, memType, memDS, curDS);
memType.close();
memDS.close();
curDS.close();
free(curveLine.p);
}
curvesDataset.close();
curvesDataspace.close();
curveDatasetType.close();
propList.close();
}
geometryGroup.close();
rootGroup.close();
bundleFile.close();
}