sonata_connector.h

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/*
 *  sonata_connector.h
 *
 *  This file is part of NEST.
 *
 *  Copyright (C) 2004 The NEST Initiative
 *
 *  NEST is free software: you can redistribute it and/or modify
 *  it under the terms of the GNU General Public License as published by
 *  the Free Software Foundation, either version 2 of the License, or
 *  (at your option) any later version.
 *
 *  NEST is distributed in the hope that it will be useful,
 *  but WITHOUT ANY WARRANTY; without even the implied warranty of
 *  MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE.  See the
 *  GNU General Public License for more details.
 *
 *  You should have received a copy of the GNU General Public License
 *  along with NEST.  If not, see <http://www.gnu.org/licenses/>.
 *
 */
 
#ifndef SONATA_CONNECTOR_H
#define SONATA_CONNECTOR_H
 
#include "config.h"
 
#ifdef HAVE_HDF5
 
// C++ includes:
#include <map>
#include <string>
#include <vector>
 
// Includes from libnestutil
#include "dict_util.h"
 
// Includes from nestkernel:
#include "conn_parameter.h"
#include "kernel_manager.h"
 
#include "H5Cpp.h"
 
namespace nest
{
 
class SonataConnector
{
public:
  SonataConnector( const Dictionary& graph_specs, const long hyperslab_size );
 
  ~SonataConnector();
 
  void connect();
 
private:
  H5::H5File* open_file_( std::string& fname );
 
  H5::Group* open_group_( const H5::H5File* file, const std::string& grp_name );
 
  H5::Group* open_group_( const H5::Group* group, const std::string& grp_name );
 
  void open_required_dsets_( const H5::Group* pop_grp );
 
  void try_open_edge_group_dsets_( const H5::Group* edge_grp );
 
  void check_dsets_consistency();
 
  void close_dsets_();
 
  void get_attribute_( std::string& attribute_value, const H5::DataSet& dataset, const std::string& attribute_name );
 
 
  void create_edge_type_id_2_syn_spec_( Dictionary edge_dict );
 
 
  void set_synapse_params_( Dictionary syn_dict, size_t synapse_model_id, int type_id );
 
  void get_synapse_params_( size_t snode_id, Node& target, size_t target_thread, RngPtr rng, int edge_type_id );
 
  double get_syn_property_( const Dictionary& syn_spec,
    hsize_t index,
    const bool dataset_exists,
    std::vector< double >& data,
    const std::string& name );
 
  void sequential_chunkwise_connector_();
 
  void connect_chunk_( const hsize_t hyperslab_size, const hsize_t offset );
 
  template < typename T >
  void read_subset_( const H5::DataSet& dataset,
    std::vector< T >& data_buf,
    H5::PredType datatype,
    hsize_t hyperslab_size,
    hsize_t offset );
 
  hsize_t find_edge_groups_( H5::Group* pop_grp, std::vector< std::string >& edge_grp_names );
 
  hsize_t get_nrows_( H5::DataSet dataset );
 
  void reset_params_();
 
  typedef std::map< std::string, std::shared_ptr< ConnParameter > > ConnParameterMap;
 
  std::set< std::string > skip_syn_params_;
 
  Dictionary graph_specs_;
 
  hsize_t hyperslab_size_;
 
  bool weight_dataset_exist_;
 
  bool delay_dataset_exist_;
 
  std::string source_attribute_value_;
 
  std::string target_attribute_value_;
 
  Dictionary cur_edge_params_;
 
  std::map< int, size_t > edge_type_id_2_syn_model_;
 
  std::map< int, ConnParameterMap > edge_type_id_2_syn_spec_;
 
  std::map< int, std::vector< Dictionary > > edge_type_id_2_param_dicts_;
 
  std::string cur_fname_;
  H5::DataSet src_node_id_dset_;
  H5::DataSet tgt_node_id_dset_;
  H5::DataSet edge_type_id_dset_;
  H5::DataSet syn_weight_dset_;
  H5::DataSet delay_dset_;
};
 
 
}  // namespace nest
 
#endif  // ifdef HAVE_HDF5
#endif  /* ifdef SONATA_CONNECTOR_H */