population.h

/*************************************************************************
 * Copyright (C) 2018-2020 Blue Brain Project
 *
 * This file is part of 'libsonata', distributed under the terms
 * of the GNU Lesser General Public License version 3.
 *
 * See top-level COPYING.LESSER and COPYING files for details.
 *************************************************************************/
 
#pragma once
 
#include "common.h"
 
#include <cstdint>
#include <functional>
#include <memory>  // std::shared_ptr, std::unique_ptr
#include <set>
#include <string>
#include <utility>  // std::move
#include <vector>
 
#include <bbp/sonata/hdf5_reader.h>
#include <bbp/sonata/selection.h>
 
namespace bbp {
namespace sonata {
 
class SONATA_API Population
{
  public:
    std::string name() const;
 
    uint64_t size() const;
 
    Selection selectAll() const;
 
    const std::set<std::string>& attributeNames() const;
 
    const std::set<std::string>& enumerationNames() const;
 
    template <typename T>
    std::vector<T> getAttribute(const std::string& name, const Selection& selection) const;
 
    template <typename T>
    std::vector<T> getAttribute(const std::string& name,
                                const Selection& selection,
                                const T& defaultValue) const;
 
    template <typename T>
    std::vector<T> getEnumeration(const std::string& name, const Selection& selection) const;
 
    std::vector<std::string> enumerationValues(const std::string& name) const;
 
    std::string _attributeDataType(const std::string& name,
                                   bool translate_enumeration = false) const;
 
    const std::set<std::string>& dynamicsAttributeNames() const;
 
    template <typename T>
    std::vector<T> getDynamicsAttribute(const std::string& name, const Selection& selection) const;
 
    template <typename T>
    std::vector<T> getDynamicsAttribute(const std::string& name,
                                        const Selection& selection,
                                        const T& defaultValue) const;
 
    std::string _dynamicsAttributeDataType(const std::string& name) const;
 
    template <typename T>
    Selection filterAttribute(const std::string& name, std::function<bool(const T)> pred) const;
 
  protected:
    Population(const std::string& h5FilePath,
               const std::string& csvFilePath,
               const std::string& name,
               const std::string& prefix,
               const Hdf5Reader& hdf5_reader);
 
    Population(const Population&) = delete;
 
    Population(Population&&) noexcept;
 
    virtual ~Population() noexcept;
 
    struct Impl;
    std::unique_ptr<Impl> impl_;
};
 
template <>
std::vector<std::string> Population::getAttribute<std::string>(const std::string& name,
                                                               const Selection& selection) const;
 
//--------------------------------------------------------------------------------------------------
 
template <typename Population>
class SONATA_API PopulationStorage
{
  public:
    PopulationStorage(const std::string& h5FilePath);
    PopulationStorage(const std::string& h5FilePath, const std::string& csvFilePath);
    PopulationStorage(const std::string& h5FilePath, const Hdf5Reader& hdf5_reader);
    PopulationStorage(const std::string& h5FilePath,
                      const std::string& csvFilePath,
                      const Hdf5Reader& hdf5_reader);
 
    PopulationStorage(const PopulationStorage&) = delete;
 
    PopulationStorage(PopulationStorage&&) noexcept;
 
    ~PopulationStorage() noexcept;
 
    std::set<std::string> populationNames() const;
 
    std::shared_ptr<Population> openPopulation(const std::string& name) const;
 
  protected:
    struct Impl;
    std::unique_ptr<Impl> impl_;
};
 
//--------------------------------------------------------------------------------------------------
 
}  // namespace sonata
}  // namespace bbp