C++ H5File::openGroup方法代码示例

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 Attribute::write(H5::H5File f, const cpath & dataset_root)
{  
  //FIXME we should have a path?
  cpath fullpath = dataset_root / name;
  cpath grouppath = fullpath.parent_path();
    
  if (_link.size())
  {
    if (!h5_obj_exists(f, grouppath))
      h5_create_path_groups(f, grouppath.c_str());
    
    H5::Group g = f.openGroup(grouppath.generic_string().c_str());
    
    if (h5_obj_exists(f, fullpath))
      g.unlink(name.filename().generic_string().c_str());
    
    g.link(H5G_LINK_SOFT, (dataset_root/_link).generic_string().c_str(), name.filename().generic_string().c_str());
  }
  else if (_m.total() == 0) {
    //FIXME remove this (legacy) case
    hsize_t *dim = new hsize_t[size.size()+1];
    for(uint i=0;i<size.size();i++)
      dim[i] = size[i];
    H5::DataSpace space(size.size(), dim);
    H5::Attribute attr;
    H5::Group g;

    delete[] dim;
    
    if (!h5_obj_exists(f, grouppath))
      h5_create_path_groups(f, grouppath);
    
    g = f.openGroup(grouppath.generic_string().c_str());
    
    uint min, max;
    
    H5Pget_attr_phase_change(H5Gget_create_plist(g.getId()), &max, &min);
    
    if (min || max)
      printf("WARNING: could not set dense storage on group, may not be able to write large attributes\n");
    
    //FIXME relative to what?
    if (H5Aexists(g.getId(), name.filename().generic_string().c_str()))
      g.removeAttr(name.filename().generic_string().c_str());
      
    attr = g.createAttribute(name.filename().generic_string().c_str(), toH5DataType(type), space);
        
    attr.write(toH5NativeDataType(type), data);
  }
  else
    Mat_H5AttrWrite(_m, f, fullpath);
}

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, &parameters_.xROI);
	attr.close();

	attr = root.createAttribute("yROI", H5::PredType::STD_U32LE, scalar);
	attr.write(H5::PredType::NATIVE_UINT, &parameters_.yROI);
	attr.close();

	scalar.close();
	root.close();
}

void Attributes::open(H5::H5File &f, const cpath &path)
{
  attrs.resize(0);
  
  H5::Group group = f.openGroup(path.generic_string().c_str());
  
  attributes_append_group(*this, group, path, path);
}

void StateSet::init_from_datafile(std::string filename) {
	// open other file read-only
	H5::H5File otherfile;
	otherfile.openFile(filename, H5F_ACC_RDONLY);
	H5::Group otherroot = otherfile.openGroup("/");
	// check that grid properties match
	int othersx, othersy, otherN;
	double otherdx;
	otherroot.openAttribute("num_states").read(H5::PredType::NATIVE_INT, &otherN);
	otherroot.openAttribute("grid_sizex").read(H5::PredType::NATIVE_INT, &othersx);
	otherroot.openAttribute("grid_sizex").read(H5::PredType::NATIVE_INT, &othersy);
	otherroot.openAttribute("grid_delta").read(H5::PredType::NATIVE_DOUBLE, &otherdx);
	if (static_cast<int>(N) != otherN)
		throw GeneralError("Cannot copy state data from datafile: value for num_states does not match.");
	if (static_cast<int>(datalayout.sizex) != othersx)
		throw GeneralError("Cannot copy state data from datafile: value for grid_sizex does not match.");
	if (static_cast<int>(datalayout.sizey) != othersy)
		throw GeneralError("Cannot copy state data from datafile: value for grid_sizey does not match.");
	if (datalayout.dx != otherdx)
		throw GeneralError("Cannot copy state data from datafile: value for grid_delta does not match.");
	// copy data
	H5::DataSet other_states_data = otherfile.openDataSet("/states");
	other_states_data.read(state_array->get_dataptr(), other_states_data.getArrayType());
}

std::string read_string_attr(H5::H5File &f, const char *parent_group_str, const char *name)
{
  H5::Group group = f.openGroup(parent_group_str);
  return read_string_attr(f, group, name);
}

 /// Takes the "/" group at the top of the file.
 group (H5::H5File f) : _g(f.openGroup("/")) {} // can not fail, right ?

void Bundle2::loadGeometry_(H5::H5File& file) {
	H5::Group geometryGroup = file.openGroup("/Geometry");

	// Loading poses
	H5::DataSet posesDataSet = geometryGroup.openDataSet("Poses");
	double* posesData = (double*)malloc(frames_.size()*12*sizeof(double));
	posesDataSet.read((void*)posesData, H5::PredType::NATIVE_DOUBLE, H5::DataSpace::ALL, H5::DataSpace::ALL);
	posesDataSet.close();

	size_t i = 0;
	for(deque<Frame*>::iterator it = frames_.begin(); it != frames_.end(); ++it) {
		Pose* pose = new Pose;
		pose->sett(core::RealPoint3D<double>(posesData[i*12], posesData[i*12 + 1], posesData[i*12 + 2]));

		core::Matrix<double> R(3, 3);
		R[0][0] = posesData[i*12 + 3]; R[1][0] = posesData[i*12 + 4]; R[2][0] = posesData[i*12 + 5];
		R[0][1] = posesData[i*12 + 6]; R[1][1] = posesData[i*12 + 7]; R[2][1] = posesData[i*12 + 8];
		R[0][2] = posesData[i*12 + 9]; R[1][2] = posesData[i*12 + 10]; R[2][2] = posesData[i*12 + 11];

		pose->setR(R);
		pose->calcEulerAngles();
		pose->setorientationSynchronWithAngles(true);
		pose->setderivationsSynchronWithAngles(false);

		(*it)->setpose(pose);

		++i;
	}
	free((void*)posesData);

	// Loading points
	H5::DataSet pointsDataSet = geometryGroup.openDataSet("Points");
	double* pointsData = (double*)malloc(tracks_.size()*3*sizeof(double));
	pointsDataSet.read((void*)pointsData, H5::PredType::NATIVE_DOUBLE, H5::DataSpace::ALL, H5::DataSpace::ALL);
	pointsDataSet.close();

	i = 0;
	for(deque<Track*>::iterator it = tracks_.begin(); it != tracks_.end(); it++) {
		Point* point = new Point(core::RealPoint3D<double>(pointsData[i*3], pointsData[i*3 + 1], pointsData[i*3 + 2]));
		(*it)->setpoint(point);

		++i;
	}
	free((void*)pointsData);

	// Loading inlier information
	H5::DataSet inliersDataSet = geometryGroup.openDataSet("Inliers");
	hvl_t* inliersData = (hvl_t*)malloc(frames_.size()*sizeof(hvl_t));
	H5::VarLenType memType(&H5::PredType::NATIVE_UCHAR);
	inliersDataSet.read((void*)inliersData, memType, H5::DataSpace::ALL, H5::DataSpace::ALL);
	memType.close();
	inliersDataSet.close();

	i = 0;
	for(deque<Frame*>::iterator it = frames_.begin(); it != frames_.end(); it++) {
		unsigned char* inl = (unsigned char*)(inliersData[i].p);

        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)) {
                    Ray ray;
                    if(inl[k]) ray.setinlier(true);
                    else ray.setinlier(false);

                    v.addRay(cam, ray);
                    ++k;
                }
            }
		}

		++i;
	}

	for(size_t j = 0; j < frames_.size(); ++j) free(inliersData[j].p);
	free((void*)inliersData);

	// Loading curves if they exists
	bool curvesFound = false;
	const hsize_t maxObjs = geometryGroup.getNumObjs();
	for(hsize_t obj = 0; obj < maxObjs; ++obj) {
		string objName = geometryGroup.getObjnameByIdx(obj);
		if(objName == string("Curves")) curvesFound = true;
	}

	if(curvesFound) {
		H5::DataSet curvesDataSet = geometryGroup.openDataSet("Curves");

		hsize_t curvesDim[1];
		H5::DataSpace curvesDS = curvesDataSet.getSpace();
		curvesDS.getSimpleExtentDims(curvesDim);
		curvesDS.close();

		hvl_t* curvesData = (hvl_t*)malloc(curvesDim[0]*sizeof(hvl_t));
		H5::VarLenType memType(&H5::PredType::NATIVE_HSIZE);

		curvesDataSet.read((void*)curvesData, memType, H5::DataSpace::ALL, H5::DataSpace::ALL);

		memType.close();
//.........这里部分代码省略.........

Bundle2::Bundle2(const boost::filesystem::path& fileName, bool loadGeometry):
	version_(BUNDLE_VERSION), poiFirstFrame_(0) {
	// Opening file
	H5::H5File bundleFile;
	bundleFile.openFile(fileName.string(), H5F_ACC_RDONLY);
	loadParameters(bundleFile);

	// Loading POI
	H5::Group poiGroup = bundleFile.openGroup("/POI");

	hsize_t count;
	H5::Attribute attr = poiGroup.openAttribute("count");
	attr.read(H5::PredType::NATIVE_HSIZE, &count);
	attr.close();

	for(size_t frame = 0; frame < count; ++frame) {
		cout.flush();

		const std::string frameGroupName = boost::str(boost::format("Frame %1$04d") % frame);
		H5::Group frameGroup = poiGroup.openGroup(frameGroupName);

		addPOIFrame();
		for(size_t camera = 0; camera < numCameras_; ++camera)
			poi_[poi_.size() - 1][camera].load(frameGroup, camera);

		frameGroup.close();
	}

	poiGroup.close();

	// Loading frames
	H5::Group bundleGroup = bundleFile.openGroup("/Bundle");

	H5::Group framesGroup = bundleGroup.openGroup("Frames");

	attr = framesGroup.openAttribute("count");
	attr.read(H5::PredType::NATIVE_HSIZE, &count);
	attr.close();

	for(size_t frame = 0; frame < count; ++frame) {
		Frame* f = new Frame(framesGroup, frame, numCameras_);
		frames_.push_back(f);
	}

	framesGroup.close();

	// Loading tracks
	H5::DataSet tracksDataset = bundleGroup.openDataSet("Tracks");

	hsize_t tracksDim[2];
	H5::DataSpace tracksDS = tracksDataset.getSpace();
	tracksDS.getSimpleExtentDims(tracksDim);
	tracksDS.close();

	for(size_t i = 0; i < tracksDim[0]; ++i) {
		size_t j = addTrack();
		tracks_[j]->load(tracksDataset, frames_, i);
	}

	tracksDataset.close();

	bundleGroup.close();

	if(loadGeometry && checkGeometry_(bundleFile)) loadGeometry_(bundleFile);

	bundleFile.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;
//.........这里部分代码省略.........