void HDF5IO::saveStdVector(const std::string& GroupName, const std::string& Name,
const std::vector<std::complex<double> >& V)
{
try{
H5::CompType ComplexDataType = openCompType("complex");
hsize_t Dim[1] = {hsize_t(V.size())};
H5::DataSpace dataspace(1,Dim);
H5::Group FG = getGroup( GroupName.c_str() );
try{
H5::Exception::dontPrint();
H5::DataSet dataset = FG.openDataSet(Name.c_str());
dataset.write(V.data(), ComplexDataType, dataspace);
} catch( const H5::GroupIException not_found_error ){
H5::DataSet dataset = FG.createDataSet(Name.c_str(), ComplexDataType,
dataspace);
dataset.write(V.data(), ComplexDataType);
} catch( const H5::FileIException error){
error.printError();
} catch( const H5::DataSetIException error){
error.printError();
}
FG.close();
} catch( const H5::Exception err ){
err.printError();
RUNTIME_ERROR("HDF5IO::saveComplexStdVector. ");
}
}
void Bundle2::storeParameters(H5::H5File& file) const {
H5::Group root = file.openGroup("/");
H5::DataSpace scalar;
H5::Attribute attr = root.createAttribute("version", H5::PredType::STD_U32LE, scalar);
attr.write(H5::PredType::NATIVE_UINT, &version_);
attr.close();
unsigned char r2 = parameters_.reduce2?1:0;
attr = root.createAttribute("reduce2", H5::PredType::STD_U8LE, scalar);
attr.write(H5::PredType::NATIVE_UCHAR, &r2);
attr.close();
attr = root.createAttribute("xROI", H5::PredType::STD_U32LE, scalar);
attr.write(H5::PredType::NATIVE_UINT, ¶meters_.xROI);
attr.close();
attr = root.createAttribute("yROI", H5::PredType::STD_U32LE, scalar);
attr.write(H5::PredType::NATIVE_UINT, ¶meters_.yROI);
attr.close();
scalar.close();
root.close();
}
int Channel::read_state_from_hdf5(H5::H5File & H5StateFile, const string & rootStr){
clear_data();
// read waveform data
waveform_ = h5array2vector<float>(&H5StateFile, rootStr + "/waveformLib", H5::PredType::NATIVE_INT16);
// load state information
H5::Group tmpGroup = H5StateFile.openGroup(rootStr);
offset_ = h5element2element<float>("offset",&tmpGroup, H5::PredType::NATIVE_FLOAT);
scale_ = h5element2element<float>("scale",&tmpGroup, H5::PredType::NATIVE_FLOAT);
enabled_ = h5element2element<bool>("enabled",&tmpGroup, H5::PredType::NATIVE_UINT);
trigDelay_ = h5element2element<int>("trigDelay",&tmpGroup, H5::PredType::NATIVE_INT);
//Load the linklist data
//First figure our how many banks there are from the attribute
tmpGroup = H5StateFile.openGroup(rootStr + "/linkListData");
USHORT numBanks;
numBanks = h5element2element<USHORT>("numBanks",&tmpGroup, H5::PredType::NATIVE_UINT16);
tmpGroup.close();
std::ostringstream tmpStream;
//Now loop over the number of banks found and add the bank
for (USHORT bankct=0; bankct<numBanks; bankct++){
LLBank bank;
tmpStream.str(rootStr);
tmpStream << "/linkListData/bank" << bankct+1;
FILE_LOG(logDEBUG) << "Reading State Bank: " << bankct+1 << " from hdf5";
bank.read_state_from_hdf5( H5StateFile, tmpStream.str());
// banks_.push_back(bank);
}
return 0;
}
void HDF5IO::saveMatrix(const std::string& GroupName, const std::string& Name,
const ComplexMatrixType& M)
{
try{
H5::CompType ComplexDataType = this->openCompType("complex");
hsize_t Dims[2] = {hsize_t(M.rows()),hsize_t(M.cols())};
H5::DataSpace dataspace(2,Dims);
H5::Group FG = getGroup( GroupName );
try{
H5::Exception::dontPrint();
H5::DataSet dset = FG.openDataSet(Name.c_str());
// dset.extend( Dims );not working
dset.write(M.data(), ComplexDataType);
} catch ( const H5::GroupIException not_found_error ){
H5::DataSet dset = FG.createDataSet(Name.c_str(), ComplexDataType, dataspace);
dset.write(M.data(), ComplexDataType);
} catch ( const H5::DataSetIException error ){
error.printError();
RUNTIME_ERROR("HDF5IO::saveComplexMatrix at ");
}
FG.close();
} catch( const H5::Exception error ){
error.printError();
RUNTIME_ERROR("HDF5IO::saveComplexMatrix at ");
}
}
// Stream saving mode
void Bundle2::openSaveStream(const boost::filesystem::path& fileName) {
// Open file for streaming
streamFile_ = new H5::H5File(fileName.string(), H5F_ACC_TRUNC);
storeParameters(*streamFile_);
// Creating basic file structure
H5::Group group = streamFile_->createGroup("/POI");
group.close();
initFrameStream_();
initGeometryStream_();
}
int HDF5IO::loadInt(const std::string& GroupName, const std::string& Name)
{
try{
H5::Group FG = getGroup( GroupName );
H5::DataSet DataSet = FG.openDataSet( Name.c_str());
int x;
DataSet.read(&x,H5::PredType::NATIVE_INT);
FG.close();
return x;
}catch( H5::GroupIException not_found_error ){
RUNTIME_ERROR("No dataset found in loadInt. ");
}
}
size_t HDF5IO::loadUlong(const std::string& GroupName, const std::string& Name)
{
try{
H5::Group FG = getGroup( GroupName );
H5::DataSet DataSet = FG.openDataSet( Name.c_str() );
size_t x;
DataSet.read(&x, H5::PredType::NATIVE_ULONG);
return x;
FG.close();
}catch( H5::GroupIException not_found_error ){
INFO("In Group - " << GroupName << ", and Name is " << Name);
RUNTIME_ERROR("No dataset found in loadUlong. ");
}
}
bool Bundle2::checkGeometry_(H5::H5File& file) const {
bool found = false;
H5::Group root = file.openGroup("/");
const hsize_t maxObjs = root.getNumObjs();
for(hsize_t obj = 0; obj < maxObjs; ++obj) {
string objName = root.getObjnameByIdx(obj);
if(objName == string("Geometry")) found = true;
}
root.close();
return found;
}
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;
}
void HDF5IO::saveNumber(const std::string& GroupName, const std::string& Name,
unsigned long x)
{
H5::Group FG = getGroup( GroupName );
try{
H5::Exception::dontPrint();
H5::DataSet dataset = FG.openDataSet( Name.c_str() );
dataset.write(&x, H5::PredType::NATIVE_ULONG);
} catch ( const H5::GroupIException not_found_error ){
H5::DataSet dataset = FG.createDataSet( Name.c_str(), H5::PredType::NATIVE_ULONG, H5::DataSpace());
dataset.write(&x, H5::PredType::NATIVE_ULONG);
}
FG.close();
}
ComplexType HDF5IO::loadComplex(const std::string& GroupName, const std::string& Name)
{
try{
H5::CompType ComplexDataType = this->openCompType("complex");
H5::Group FG = getGroup( GroupName );
H5::DataSet DataSet = FG.openDataSet(Name.c_str());
ComplexType C;
RealType RealImag[2];
DataSet.read(RealImag, ComplexDataType);
FG.close();
return ComplexType(RealImag[0],RealImag[1]);
}catch( H5::GroupIException not_found_error ){
RUNTIME_ERROR("No dataset found in loadComplex. ");
}
}
void HDF5IO::loadStdVector(const std::string& GroupName, const std::string& Name,
std::vector<RealType>& V)
{
try{
H5::Group FG = getGroup( GroupName );
H5::DataSet DataSet = FG.openDataSet(Name.c_str());
H5::DataSpace DataSpace = DataSet.getSpace();
if(DataSpace.getSimpleExtentNdims() != 1)
throw(H5::DataSpaceIException("HDF5IO::loadRealVector()","Unexpected multidimentional dataspace."));
V.resize(DataSpace.getSimpleExtentNpoints());
DataSet.read(V.data(),H5::PredType::NATIVE_DOUBLE);
FG.close();
} catch( const H5::Exception err ){
RUNTIME_ERROR("HDF5IO::loadRealStdVector");
}
}
void HDF5IO::loadVector(const std::string& GroupName, const std::string& Name,
RealVectorType& V)
{
H5::Group FG = getGroup( GroupName );
H5::DataSet DataSet = FG.openDataSet(Name.c_str());
H5::DataSpace DataSpace = DataSet.getSpace();
if(DataSpace.getSimpleExtentNdims() != 1)
throw(H5::DataSpaceIException("HDF5IO::loadRealVector()",
"Unexpected multidimentional dataspace."));
V.resize(DataSpace.getSimpleExtentNpoints());
try{
DataSet.read(V.data(),H5::PredType::NATIVE_DOUBLE);
}catch( H5::GroupIException not_found_error ){
RUNTIME_ERROR("No dataset found in loadRealVector. ");
}
FG.close();
}
void Bundle2::closeSaveStream() {
H5::DataSpace scalar;
// Saving remaining POI information
H5::Group poiGroup = streamFile_->openGroup("/POI");
H5::Attribute attr = poiGroup.createAttribute("count", H5::PredType::STD_U64LE, scalar);
hsize_t count = poiFirstFrame_;
attr.write(H5::PredType::NATIVE_HSIZE, &count);
attr.close();
poiGroup.close();
scalar.close();
// Closing HDF5 file
streamFile_->close();
delete streamFile_;
streamFile_ = NULL;
}
void HDF5IO::saveNumber(const std::string& GroupName, const std::string& Name,
ComplexType C)
{
H5::CompType ComplexDataType = openCompType("complex");
H5::Group FG = getGroup( GroupName );
try{
H5::Exception::dontPrint();
H5::DataSet dataset = FG.openDataSet(Name.c_str());
RealType RealImag[2] = {real(C),imag(C)};
dataset.write(RealImag, ComplexDataType);
} catch ( const H5::GroupIException not_found_error ){
H5::DataSet dataset = FG.createDataSet(Name.c_str(), ComplexDataType, H5::DataSpace());
RealType RealImag[2] = {real(C),imag(C)};
dataset.write(RealImag, ComplexDataType);
}
FG.close();
}
void HDF5IO::loadStdVector(const std::string& GroupName, const std::string& Name,
std::vector<ComplexType>& V)
{
try{
H5::CompType ComplexDataType = this->openCompType("complex");
H5::Group FG = getGroup( GroupName );
H5::DataSet DataSet = FG.openDataSet(Name.c_str());
H5::DataSpace DataSpace = DataSet.getSpace();
if(DataSpace.getSimpleExtentNdims() != 1)
throw(H5::DataSpaceIException("HDF5IO::loadComplexVector()","Unexpected multidimentional dataspace."));
V.resize(DataSpace.getSimpleExtentNpoints());
DataSet.read(V.data(),ComplexDataType);
FG.close();
} catch( const H5::Exception err ){
RUNTIME_ERROR("HDF5IO::loadComplexStdVector");
}
}
/* only for Eigen3 matrix/vector */
void HDF5IO::saveVector(const std::string& GroupName,
const std::string& Name, const RealVectorType& V)
{
hsize_t Dim[1] = {hsize_t(V.size())};
H5::DataSpace dspace(1,Dim);
H5::Group FG = getGroup( GroupName );
try{
H5::Exception::dontPrint();
H5::DataSet DataSet = FG.openDataSet(Name.c_str());
DataSet.write(V.data(),H5::PredType::NATIVE_DOUBLE, dspace);
} catch ( const H5::GroupIException not_found_error ){
H5::DataSet DataSet = FG.createDataSet(Name.c_str(),
H5::PredType::NATIVE_DOUBLE,dspace);
DataSet.write(V.data(),H5::PredType::NATIVE_DOUBLE);
}
FG.close();
}
void HDF5IO::loadMatrix(const std::string& GroupName, const std::string& Name,
ComplexMatrixType& M)
{
try{
H5::CompType ComplexDataType = this->openCompType("complex");
H5::Group FG = getGroup( GroupName );
H5::DataSet DataSet = FG.openDataSet(Name.c_str());
H5::DataSpace DataSpace = DataSet.getSpace();
if(DataSpace.getSimpleExtentNdims() != 2)
throw(H5::DataSpaceIException("HDF5IO::loadMatrix()","A dataspace must be precisely two-dimensional."));
hsize_t Dims[2];
DataSpace.getSimpleExtentDims(Dims);
M.resize(Dims[0],Dims[1]);
DataSet.read(M.data(), ComplexDataType);
FG.close();
} catch( const H5::Exception err ){
RUNTIME_ERROR("HDF5IO::loadComplexMatrix at ");
}
}
void HDF5IO::saveMatrix(const std::string& GroupName, const std::string& Name,
const RealMatrixType& M)
{
try{
hsize_t Dims[2] = {hsize_t(M.rows()),hsize_t(M.cols())};
H5::DataSpace dataspace(2,Dims);
H5::Group FG = getGroup( GroupName );
try{
H5::Exception::dontPrint();
H5::DataSet DataSet = FG.openDataSet(Name.c_str());
DataSet.write(M.data(),H5::PredType::NATIVE_DOUBLE,dataspace);
} catch ( const H5::GroupIException not_found_error ){
H5::DataSet DataSet = FG.createDataSet(Name.c_str(),H5::PredType::NATIVE_DOUBLE,dataspace);
DataSet.write(M.data(),H5::PredType::NATIVE_DOUBLE);
}
FG.close();
} catch( const H5::Exception err ){
RUNTIME_ERROR("HDF5IO::saveRealMatrix");
}
}
void HDF5IO::saveStdVector(const std::string& GroupName, const std::string& Name,
const std::vector<double>& V)
{
try{
hsize_t Dim[1] = {hsize_t(V.size())};
H5::DataSpace dataspace(1,Dim);
H5::Group FG = getGroup( GroupName );
try{
H5::Exception::dontPrint();
H5::DataSet dataset = FG.openDataSet(Name.c_str());
dataset.write(V.data(),H5::PredType::NATIVE_DOUBLE, dataspace);
} catch ( const H5::GroupIException not_found_error ){
H5::DataSet dataset = FG.createDataSet(Name.c_str(),
H5::PredType::NATIVE_DOUBLE,dataspace);
dataset.write(V.data(),H5::PredType::NATIVE_DOUBLE);
}
FG.close();
} catch( const H5::Exception err ){
RUNTIME_ERROR("HDF5IO::saveRealStdVector");
}
}
int APSRack::save_bulk_state_file(string & stateFile){
if (stateFile.length() == 0) {
stateFile += "cache_APSRack.h5";
}
FILE_LOG(logDEBUG) << "Writing Bulk State File " << stateFile;
H5::H5File H5StateFile(stateFile, H5F_ACC_TRUNC);
// loop through available APS Units and save state
for(unsigned int apsct = 0; apsct < APSs_.size(); apsct++) {
string rootStr = "/";
rootStr += APSs_[apsct].deviceSerial_ ;
FILE_LOG(logDEBUG) << "Creating Group: " << rootStr;
H5::Group tmpGroup = H5StateFile.createGroup(rootStr);
tmpGroup.close();
APSs_[apsct].write_state_to_hdf5(H5StateFile, rootStr);
}
//Close the file
H5StateFile.close();
return 0;
}
void Bundle2::loadParameters(H5::H5File& file) {
H5::Group root = file.openGroup("/");
// Checking version
unsigned int fileVersion;
H5::Attribute attr = root.openAttribute("version");
attr.read(H5::PredType::NATIVE_UINT, &fileVersion);
attr.close();
if(fileVersion != version_) throw std::runtime_error("Incompatible bundle version!");
// Reading number of cameras
hsize_t count;
H5::Group frame0Group = root.openGroup("POI/Frame 0000");
attr = frame0Group.openAttribute("count");
attr.read(H5::PredType::NATIVE_HSIZE, &count);
attr.close();
frame0Group.close();
numCameras_ = count;
// Reading parameters
unsigned char r2;
attr = root.openAttribute("reduce2");
attr.read(H5::PredType::NATIVE_UCHAR, &r2);
attr.close();
parameters_.reduce2 = (r2 == 1);
attr = root.openAttribute("xROI");
attr.read(H5::PredType::NATIVE_UINT, ¶meters_.xROI);
attr.close();
attr = root.openAttribute("yROI");
attr.read(H5::PredType::NATIVE_UINT, ¶meters_.yROI);
attr.close();
root.close();
}
int Channel::write_state_to_hdf5(H5::H5File & H5StateFile, const string & rootStr){
// write waveform data
FILE_LOG(logDEBUG) << "Writing Waveform: " << rootStr + "/waveformLib";
vector2h5array<float>(waveform_, &H5StateFile, rootStr + "/waveformLib", rootStr + "/waveformLib", H5::PredType::NATIVE_FLOAT);
// add channel state information to root group
H5::Group tmpGroup = H5StateFile.openGroup(rootStr);
element2h5attribute<float>("offset", offset_, &tmpGroup, H5::PredType::NATIVE_FLOAT);
element2h5attribute<float>("scale", scale_, &tmpGroup, H5::PredType::NATIVE_FLOAT);
element2h5attribute<bool>("enabled", enabled_, &tmpGroup, H5::PredType::NATIVE_UINT);
element2h5attribute<int>("trigDelay", trigDelay_, &tmpGroup, H5::PredType::NATIVE_INT);
tmpGroup.close();
//Save the linklist data
// save number of banks to rootStr + /linkListData attribute "numBanks"
// USHORT numBanks;
// numBanks = banks_.size();//get number of banks from channel
//
// // set attribute
// FILE_LOG(logDEBUG) << "Creating Group: " << rootStr + "/linkListData";
// tmpGroup = H5StateFile.createGroup(rootStr + "/linkListData");
// element2h5attribute<USHORT>("numBanks", numBanks, &tmpGroup,H5::PredType::NATIVE_UINT16);
// tmpGroup.close();
//
// std::ostringstream tmpStream;
// //Now loop over the number of banks found and add the bank
// for (USHORT bankct=0; bankct<numBanks; bankct++) {
// tmpStream.str("");
// tmpStream << rootStr << "/linkListData/bank" << bankct+1 ;
// FILE_LOG(logDEBUG) << "Writing State Bank: " << bankct+1 << " from hdf5";
// banks_[bankct].write_state_to_hdf5(H5StateFile, tmpStream.str() );
// }
return 0;
}
void HDF5IO::saveVector(const std::string& GroupName,
const std::string& Name, const ComplexVectorType& V)
{
try{
H5::CompType ComplexDataType = this->openCompType("complex");
hsize_t Dim[1] = {hsize_t(V.size())};
H5::DataSpace dspace(1,Dim);
H5::Group FG = getGroup( GroupName );
try{
H5::Exception::dontPrint();
H5::DataSet DataSet = FG.openDataSet(Name.c_str());
DataSet.write(V.data(), ComplexDataType, dspace);
} catch ( const H5::GroupIException not_found_error ){
H5::DataSet DataSet = FG.createDataSet(Name.c_str(), ComplexDataType,
dspace);
DataSet.write(V.data(), ComplexDataType);
}
FG.close();
} catch ( const H5::DataSetIException error ){
error.printError();
RUNTIME_ERROR("HDF5IO::saveComplexVector at ");
}
}
PcaModel PcaModel::loadStatismoModel(path h5file, PcaModel::ModelType modelType)
{
logging::Logger logger = Loggers->getLogger("shapemodels");
PcaModel model;
// Load the shape or color model from the .h5 file
string h5GroupType;
if (modelType == ModelType::SHAPE) {
h5GroupType = "shape";
} else if (modelType == ModelType::COLOR) {
h5GroupType = "color";
}
H5::H5File h5Model;
try {
h5Model = H5::H5File(h5file.string(), H5F_ACC_RDONLY);
}
catch (H5::Exception& e) {
string errorMessage = "Could not open HDF5 file: " + string(e.getCDetailMsg());
logger.error(errorMessage);
throw errorMessage;
}
// Load either the shape or texture mean
string h5Group = "/" + h5GroupType + "/model";
H5::Group modelReconstructive = h5Model.openGroup(h5Group);
// Read the mean
H5::DataSet dsMean = modelReconstructive.openDataSet("./mean");
hsize_t dims[2];
dsMean.getSpace().getSimpleExtentDims(dims, NULL); // dsMean.getSpace() leaks memory... maybe a hdf5 bug, maybe vlenReclaim(...) could be a fix. No idea.
//H5::DataSpace dsp = dsMean.getSpace();
//dsp.close();
Loggers->getLogger("shapemodels").debug("Dimensions of the model mean: " + lexical_cast<string>(dims[0]));
model.mean = Mat(1, dims[0], CV_32FC1); // Use a row-vector, because of faster memory access and I'm not sure the memory block is allocated contiguously if we have multiple rows.
dsMean.read(model.mean.ptr<float>(0), H5::PredType::NATIVE_FLOAT);
model.mean = model.mean.t(); // Transpose it to a col-vector
dsMean.close();
// Read the eigenvalues
dsMean = modelReconstructive.openDataSet("./pcaVariance");
dsMean.getSpace().getSimpleExtentDims(dims, NULL);
Loggers->getLogger("shapemodels").debug("Dimensions of the pcaVariance: " + lexical_cast<string>(dims[0]));
model.eigenvalues = Mat(1, dims[0], CV_32FC1);
dsMean.read(model.eigenvalues.ptr<float>(0), H5::PredType::NATIVE_FLOAT);
model.eigenvalues = model.eigenvalues.t();
dsMean.close();
// Read the PCA basis matrix
dsMean = modelReconstructive.openDataSet("./pcaBasis");
dsMean.getSpace().getSimpleExtentDims(dims, NULL);
Loggers->getLogger("shapemodels").debug("Dimensions of the PCA basis matrix: " + lexical_cast<string>(dims[0]) + ", " + lexical_cast<string>(dims[1]));
model.pcaBasis = Mat(dims[0], dims[1], CV_32FC1);
dsMean.read(model.pcaBasis.ptr<float>(0), H5::PredType::NATIVE_FLOAT);
dsMean.close();
modelReconstructive.close(); // close the model-group
// Read the noise variance (not implemented)
/*dsMean = modelReconstructive.openDataSet("./noiseVariance");
float noiseVariance = 10.0f;
dsMean.read(&noiseVariance, H5::PredType::NATIVE_FLOAT);
dsMean.close(); */
// Read the triangle-list
string representerGroupName = "/" + h5GroupType + "/representer";
H5::Group representerGroup = h5Model.openGroup(representerGroupName);
dsMean = representerGroup.openDataSet("./reference-mesh/triangle-list");
dsMean.getSpace().getSimpleExtentDims(dims, NULL);
Loggers->getLogger("shapemodels").debug("Dimensions of the triangle-list: " + lexical_cast<string>(dims[0]) + ", " + lexical_cast<string>(dims[1]));
Mat triangles(dims[0], dims[1], CV_32SC1);
dsMean.read(triangles.ptr<int>(0), H5::PredType::NATIVE_INT32);
dsMean.close();
representerGroup.close();
model.triangleList.resize(triangles.rows);
for (unsigned int i = 0; i < model.triangleList.size(); ++i) {
model.triangleList[i][0] = triangles.at<int>(i, 0);
model.triangleList[i][1] = triangles.at<int>(i, 1);
model.triangleList[i][2] = triangles.at<int>(i, 2);
}
// Load the landmarks mappings:
// load the reference-mesh
representerGroup = h5Model.openGroup(representerGroupName);
dsMean = representerGroup.openDataSet("./reference-mesh/vertex-coordinates");
dsMean.getSpace().getSimpleExtentDims(dims, NULL);
Loggers->getLogger("shapemodels").debug("Dimensions of the reference-mesh vertex-coordinates matrix: " + lexical_cast<string>(dims[0]) + ", " + lexical_cast<string>(dims[1]));
Mat referenceMesh(dims[0], dims[1], CV_32FC1);
dsMean.read(referenceMesh.ptr<float>(0), H5::PredType::NATIVE_FLOAT);
dsMean.close();
representerGroup.close();
// convert to 3 vectors with the x, y and z coordinates for easy searching
vector<float> refx(referenceMesh.col(0).clone());
vector<float> refy(referenceMesh.col(1).clone());
vector<float> refz(referenceMesh.col(2).clone());
// load the landmarks info (mapping name <-> reference (x, y, z)-coords)
H5::Group landmarksGroup = h5Model.openGroup("/metadata/landmarks");
dsMean = landmarksGroup.openDataSet("./text");
H5std_string outputString;
Loggers->getLogger("shapemodels").debug("Reading landmark information from the model.");
dsMean.read(outputString, dsMean.getStrType());
dsMean.close();
landmarksGroup.close();
vector<string> landmarkLines;
boost::split(landmarkLines, outputString, boost::is_any_of("\n"), boost::token_compress_on);
for (const auto& l : landmarkLines) {
if (l == "") {
continue;
}
vector<string> line;
boost::split(line, l, boost::is_any_of(" "), boost::token_compress_on);
string name = line[0];
int visibility = lexical_cast<int>(line[1]);
float x = lexical_cast<float>(line[2]);
float y = lexical_cast<float>(line[3]);
float z = lexical_cast<float>(line[4]);
// Find the x, y and z values in the reference
const auto ivx = std::find(begin(refx), end(refx), x);
const auto ivy = std::find(begin(refy), end(refy), y);
const auto ivz = std::find(begin(refz), end(refz), z);
// TODO Check for .end()!
const auto vertexIdX = std::distance(begin(refx), ivx);
const auto vertexIdY = std::distance(begin(refy), ivy);
const auto vertexIdZ = std::distance(begin(refz), ivz);
// assert vx=vy=vz
// Hmm this is not perfect. If there's another vertex where 1 or 2 coords are the same, it fails.
// We should do the search differently: Find _all_ the vertices that are equal, then take the one that has the right x, y and z.
model.landmarkVertexMap.insert(make_pair(name, vertexIdX));
}
h5Model.close();
return model;
}
inline
vtkPolyData* vtkStandardMeshRepresenter::LoadRef(const H5::Group& fg) const {
statismo::MatrixType vertexMat;
HDF5Utils::readMatrix(fg, "./points", vertexMat);
typedef statismo::GenericEigenType<unsigned int>::MatrixType UIntMatrixType;
UIntMatrixType cellsMat;
HDF5Utils::readMatrixOfType<unsigned int>(fg, "./cells", cellsMat);
// create the reference from this information
vtkPolyData* ref = vtkPolyData::New();
unsigned nVertices = vertexMat.cols();
unsigned nCells = cellsMat.cols();
vtkFloatArray* pcoords = vtkFloatArray::New();
pcoords->SetNumberOfComponents(3);
pcoords->SetNumberOfTuples(nVertices);
for (unsigned i = 0; i < nVertices; i++) {
pcoords->SetTuple3(i, vertexMat(0, i), vertexMat(1, i),
vertexMat(2, i));
}
vtkPoints* points = vtkPoints::New();
points->SetData(pcoords);
ref->SetPoints(points);
vtkCellArray* cell = vtkCellArray::New();
unsigned cellDim = cellsMat.rows();
for (unsigned i = 0; i < nCells; i++) {
cell->InsertNextCell(cellDim);
for (unsigned d = 0; d < cellDim; d++) {
cell->InsertCellPoint(cellsMat(d, i));
}
}
if (cellDim == 2) {
ref->SetLines(cell);
} else {
ref->SetPolys(cell);
}
// read the point and cell data
assert(ref->GetPointData() != 0);
if (HDF5Utils::existsObjectWithName(fg, "pointData")) {
H5::Group pdGroup = fg.openGroup("./pointData");
if (HDF5Utils::existsObjectWithName(pdGroup, "scalars")) {
ref->GetPointData()->SetScalars(GetAsDataArray(pdGroup, "scalars"));
}
if (HDF5Utils::existsObjectWithName(pdGroup, "vectors")) {
ref->GetPointData()->SetVectors(GetAsDataArray(pdGroup, "vectors"));
}
if (HDF5Utils::existsObjectWithName(pdGroup, "normals")) {
ref->GetPointData()->SetNormals(GetAsDataArray(pdGroup, "normals"));
}
pdGroup.close();
}
if (HDF5Utils::existsObjectWithName(fg, "cellData")) {
H5::Group cdGroup = fg.openGroup("./cellData");
assert(ref->GetCellData() != 0);
if (HDF5Utils::existsObjectWithName(cdGroup, "scalars")) {
ref->GetPointData()->SetScalars(GetAsDataArray(cdGroup, "scalars"));
}
if (HDF5Utils::existsObjectWithName(cdGroup, "vectors")) {
ref->GetPointData()->SetVectors(GetAsDataArray(cdGroup, "vectors"));
}
if (HDF5Utils::existsObjectWithName(cdGroup, "normals")) {
ref->GetPointData()->SetNormals(GetAsDataArray(cdGroup, "normals"));
}
cdGroup.close();
}
return ref;
}
void ossim_hdf5::iterateGroupForDatasetNames( H5::H5File* file,
const std::string& groupName,
std::vector<std::string>& datasetNames,
ossim_uint32& recursedCount )
{
if ( file && groupName.size() )
{
++recursedCount;
// std::cout << "iterateGroup: " << groupName << std::endl;
H5::Group* group = new H5::Group( file->openGroup(groupName) );
const hsize_t OBJ_COUNT = group->getNumObjs();
for ( hsize_t i = 0; i < OBJ_COUNT; ++i )
{
std::string objName = group->getObjnameByIdx(i);
if ( objName.size() )
{
char separator = '/';
std::string combinedName;
combine( groupName, objName, separator, combinedName );
H5G_obj_t objType = group->getObjTypeByIdx(i);
#if 0
std::cout << "combinedName: " << combinedName
<< "\ngetObjnameByIdx[" << i << "]: " << objName
<< "\ngetObjTypeByIdx[" << i << "]: " << objType
<< std::endl;
#endif
if ( objType == H5G_GROUP )
{
// Recursive call:
if ( recursedCount < ossim_hdf5::MAX_RECURSION_LEVEL )
{
ossim_hdf5::iterateGroupForDatasetNames(
file, combinedName, datasetNames, recursedCount );
}
else
{
ossimNotify(ossimNotifyLevel_WARN)
<< "ossim_hdf5::iterateGroupForDatasetNames WARNING!"
<< "\nMax iterations reached!" << std::endl;
}
}
else if ( objType == H5G_DATASET )
{
datasetNames.push_back( combinedName );
}
else
{
ossimNotify(ossimNotifyLevel_WARN)
<< "ossim_hdf5::iterateGroupForDatasetNames WARNING!"
<< "\nUnhandled object type: " << objType << std::endl;
}
}
}
group->close();
delete group;
group = 0;
--recursedCount;
} // Matches: if ( file )
} // End: void ossim_hdf5::iterateGroupForDatasetNames
void ossim_hdf5::printIterative( H5::H5File* file,
const std::string& groupName,
const std::string& prefix,
ossim_uint32& recursedCount,
std::ostream& out )
{
if ( file && groupName.size() )
{
++recursedCount;
H5::Group* group = new H5::Group( file->openGroup(groupName) );
// Print attributes:
const ossim_uint32 ATTRS_COUNT = group->getNumAttrs();
for ( ossim_uint32 aIdx = 0; aIdx < ATTRS_COUNT; ++aIdx )
{
H5::Attribute attr( group->openAttribute( aIdx ) );
ossim_hdf5::printAttribute( attr, prefix, out );
attr.close();
}
const hsize_t OBJ_COUNT = group->getNumObjs();
for ( hsize_t i = 0; i < OBJ_COUNT; ++i )
{
std::string objName = group->getObjnameByIdx(i);
if ( objName.size() )
{
char separator = '/';
std::string combinedName;
combine( groupName, objName, separator, combinedName );
separator = '.';
std::string combinedPrefix;
combine( prefix, objName, separator, combinedPrefix );
H5G_obj_t objType = group->getObjTypeByIdx(i);
#if 0
std::cout << "combinedName: " << combinedName
<< "\ncombinedPrefix: " << combinedPrefix
<< "\ngetObjnameByIdx[" << i << "]: " << objName
<< "\ngetObjTypeByIdx[" << i << "]: " << objType
<< std::endl;
#endif
if ( objType == H5G_GROUP )
{
// Recursive call:
if ( recursedCount < ossim_hdf5::MAX_RECURSION_LEVEL )
{
ossim_hdf5::printIterative(
file, combinedName, combinedPrefix, recursedCount, out );
}
else
{
ossimNotify(ossimNotifyLevel_WARN)
<< "ossim_hdf5::printIterative WARNING!"
<< "\nMax iterations reached!" << std::endl;
}
}
else if ( objType == H5G_DATASET )
{
printObject( file, combinedName, combinedPrefix, out );
}
else
{
ossimNotify(ossimNotifyLevel_WARN)
<< "ossim_hdf5::printIterative WARNING!"
<< "\nUnhandled object type: " << objType << std::endl;
}
}
}
group->close();
delete group;
group = 0;
--recursedCount;
} // Matches: if ( file )
} // End: void ossim_hdf5::printIterative method.
void Bundle2::initGeometryStream_() {
// Creating group Geometry
H5::Group geometryGroup = streamFile_->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();
// Creating points dataset
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[] = { 0, 3 };
H5::DataSpace pointsDS(2, pointsCurDim, pointsMaxDim);
H5::DataSet pointsDataSet = geometryGroup.createDataSet("Points", H5::PredType::IEEE_F64LE, pointsDS, pointsPropList);
pointsDataSet.close();
pointsDS.close();
// Creating inliers dataset
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);
inliersDataSet.close();
inliersType.close();
inliersDS.close();
// Creating curve dataset
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[] = { 0 };
hsize_t curvesMaxDim[] = { H5S_UNLIMITED };
H5::DataSpace curvesDataspace(1, curvesDim, curvesMaxDim);
H5::DataSet curvesDataset = geometryGroup.createDataSet("Curves", curveDatasetType, curvesDataspace, propList);
curvesDataset.close();
curvesDataspace.close();
curveDatasetType.close();
propList.close();
geometryGroup.close();
}
// 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();
}