C++ h5::H5File类代码示例

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;
}

arma::Mat<uint16_t> readLUT(const std::string& path)
{
    H5::H5File file (path.c_str(), H5F_ACC_RDONLY);
    H5::DataSet ds = file.openDataSet("LUT");

    H5::DataSpace filespace = ds.getSpace();
    int ndims = filespace.getSimpleExtentNdims();
    assert(ndims == 2);
    hsize_t dims[2] = {1, 1};
    filespace.getSimpleExtentDims(dims);

    H5::DataSpace memspace (ndims, dims);

    arma::Mat<uint16_t> res (dims[0], dims[1]);

    ds.read(res.memptr(), H5::PredType::NATIVE_UINT16, memspace, filespace);

    filespace.close();
    memspace.close();
    ds.close();
    file.close();

    // NOTE: Armadillo stores data in column-major order, while HDF5 uses
    // row-major ordering. Above, we read the data directly from HDF5 into
    // the arma matrix, so it was implicitly transposed. The next function
    // fixes this problem.
    arma::inplace_trans(res);
    return res;
}

void get_input_pixels(std::string fname, std::vector<std::string> &pix_name) {
	H5::H5File *file = H5Utils::openFile(fname, H5Utils::READ);
	
	file->iterateElems("/photometry/", NULL, fetch_pixel_name, reinterpret_cast<void*>(&pix_name));
	
	delete file;
}

H5::DataSet CompartmentReportHDF5::_openDataset( const H5::H5File& file,
                                                 const uint32_t cellID )
{
    std::stringstream cellName;
    cellName << "a" << cellID;
    const std::string datasetName = "/" + cellName.str() + "/" + _reportName +
                                    "/" + dataDatasetName;
    H5::DataSet dataset;
    H5E_BEGIN_TRY
        dataset = file.openDataSet( datasetName );
    H5E_END_TRY
    if( !dataset.getId() )
    {
        LBTHROW(
            std::runtime_error( "ReportReaderHDF5: "
                              "Dataset " + datasetName + " not found "
                              "in file: " + file.getFileName( )));
    }

    if( dataset.getSpace().getSimpleExtentNdims() != 2 )
    {
        LBTHROW(
            std::runtime_error("Compartment_Report_HDF5_File_Reader: "
                             "Error, not 2 dimensional array on " +
                             datasetName));
    }

    return dataset;
}

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);
}

bool hdfutil::HasDataSet (const H5::H5File & h5file, const std::string & name) {
    hid_t loc_id = h5file.getLocId();
#if H5_VERS_MINOR >= 8
    hid_t dataset_id = H5Dopen1( loc_id, name.c_str());
#else
    hid_t dataset_id = H5Dopen( loc_id, name.c_str());
#endif
   if(dataset_id < 0)
      return false;

   H5Dclose(dataset_id);
   return true;
}

void pyne::Material::from_hdf5(std::string filename, std::string datapath, int row, int protocol)
{
  // Turn off annoying HDF5 errors
  H5::Exception::dontPrint();

  // Check that the file is there
  if (!pyne::file_exists(filename))
    throw pyne::FileNotFound(filename);

  // Check to see if the file is in HDF5 format.
  bool isH5 = H5::H5File::isHdf5(filename);
  if (!isH5)
    throw h5wrap::FileNotHDF5(filename);

  // Open the database
  H5::H5File db (filename, H5F_ACC_RDONLY);

  bool datapath_exists = h5wrap::path_exists(&db, datapath);
  if (!datapath_exists)
    throw h5wrap::PathNotFound(filename, datapath);

  // Clear current content
  comp.clear();

  // Load via various protocols
  if (protocol == 0)
    _load_comp_protocol0(&db, datapath, row);
  else if (protocol == 1)
    _load_comp_protocol1(&db, datapath, row);
  else
    throw pyne::MaterialProtocolError();

  // Close the database
  db.close();

  // Renomalize the composition, just to be safe.
  norm_comp();
};

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());
}

    bool readDataset1D(const H5::H5File &file, const std::string &name, std::vector<_Tp> &data)
    {
        H5::DataSet dataset = file.openDataSet(name);
        H5::DataSpace dataspace = dataset.getSpace();
        hsize_t dims_out[1];
        int rank = dataspace.getSimpleExtentDims( dims_out, NULL);

        int _type;
        bool read = getNodeType(dataset,  _type);
        read &= (_type == StorageNode::SEQ);
        read &= (rank  == 1);

        if (!read)
            return read;
        data.resize(dims_out[0]);
        dataset.read(data.data(), dataset.getDataType());
        return true;
    }

void pyne::Material::write_hdf5(std::string filename, std::string datapath, std::string nucpath, float row, int chunksize)
{
  // Turn off annoying HDF5 errors
  H5::Exception::dontPrint();

  // Create new/open datafile.
  H5::H5File db;
  if (pyne::file_exists(filename))
  {
    bool isH5 = H5::H5File::isHdf5(filename);
    if (!isH5)
      throw h5wrap::FileNotHDF5(filename);
    db = H5::H5File(filename, H5F_ACC_RDWR);
  }
  else
    db = H5::H5File(filename, H5F_ACC_TRUNC);

  //
  // Read in nuclist if available, write it out if not
  //
  bool nucpath_exists = h5wrap::path_exists(&db, nucpath);
  std::vector<int> nuclides;
  int nuc_size;
  hsize_t nuc_dims[1];
  
  if (nucpath_exists)
  {
    nuclides = h5wrap::h5_array_to_cpp_vector_1d<int>(&db, nucpath, H5::PredType::NATIVE_INT);
    nuc_size = nuclides.size();
    nuc_dims[0] = nuc_size;
  }
  else
  {
    nuclides = std::vector<int>();
    for (pyne::comp_iter i = comp.begin(); i != comp.end(); i++)
      nuclides.push_back(i->first);
    nuc_size = nuclides.size();

    // Create the data if it doesn't exist
    int nuc_data [nuc_size];
    for (int n = 0; n != nuc_size; n++)
      nuc_data[n] = nuclides[n];
    nuc_dims[0] = nuc_size;
    H5::DataSpace nuc_space(1, nuc_dims);
    H5::DataSet nuc_set = db.createDataSet(nucpath, H5::PredType::NATIVE_INT, nuc_space);
    nuc_set.write(nuc_data, H5::PredType::NATIVE_INT);
    db.flush(H5F_SCOPE_GLOBAL);
  };



  //
  // Write out to the file
  //
  H5::DataSet data_set;
  H5::DataSpace data_space, data_hyperslab;
  int data_rank = 1;
  hsize_t data_dims[1] = {1};
  hsize_t data_max_dims[1] = {H5S_UNLIMITED};
  hsize_t data_offset[1] = {0};

  size_t material_struct_size = sizeof(pyne::material_struct) + sizeof(double)*(nuc_size);
  H5::CompType data_desc(material_struct_size);
  H5::ArrayType comp_values_array_type (H5::PredType::NATIVE_DOUBLE, 1, nuc_dims);

  // make the data table type
  data_desc.insertMember("name", HOFFSET(pyne::material_struct, name), H5::StrType(0, 20));
  data_desc.insertMember("mass", HOFFSET(pyne::material_struct, mass), H5::PredType::NATIVE_DOUBLE);
  data_desc.insertMember("atoms_per_mol", HOFFSET(pyne::material_struct, atoms_per_mol), H5::PredType::NATIVE_DOUBLE);
  data_desc.insertMember("comp", HOFFSET(pyne::material_struct, comp), comp_values_array_type);

  // make the data array, have to over-allocate
  material_struct * mat_data  = (material_struct *) malloc(material_struct_size);
  int name_len = name.length();
  for (int i=0; i < 20; i++)
  {
    if (i < name_len)
      (*mat_data).name[i] = name[i];
    else
      (*mat_data).name[i] = NULL;
  };
  (*mat_data).mass = mass;
  (*mat_data).atoms_per_mol = atoms_per_mol;
  for (int n = 0; n != nuc_size; n++)
  {
    if (0 < comp.count(nuclides[n]))
      (*mat_data).comp[n] = comp[nuclides[n]];
    else
      (*mat_data).comp[n] = 0.0;
  };

  // get / make the data set
  bool datapath_exists = h5wrap::path_exists(&db, datapath);
  if (datapath_exists)
  {
    data_set = db.openDataSet(datapath);
    data_space = data_set.getSpace();
    data_rank = data_space.getSimpleExtentDims(data_dims, data_max_dims);

    // Determine the row size.
//.........这里部分代码省略.........

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);
}

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.........

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