Program Listing for File population.h

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/*************************************************************************
 * 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 <memory>  // std::shared_ptr, std::unique_ptr
#include <set>
#include <string>
#include <utility>  // std::move
#include <vector>


namespace bbp {
namespace sonata {

//--------------------------------------------------------------------------------------------------

class SONATA_API Selection
{
  public:
    using Value = uint64_t;
    using Values = std::vector<Value>;
    using Range = std::pair<Value, Value>;
    using Ranges = std::vector<Range>;

    explicit Selection(Ranges&& ranges);
    explicit Selection(const Ranges& ranges);

    template <typename Iterator>
    static Selection fromValues(Iterator first, Iterator last);
    static Selection fromValues(const Values& values);

    const Ranges& ranges() const;

    Values flatten() const;

    size_t flatSize() const;

    bool empty() const;

  private:
    const Ranges ranges_;
};

bool SONATA_API operator==(const Selection&, const Selection&);
bool SONATA_API operator!=(const Selection&, const Selection&);

Selection SONATA_API operator&(const Selection&, const Selection&);
Selection SONATA_API operator|(const Selection&, const Selection&);

template <typename Iterator>
Selection Selection::fromValues(Iterator first, Iterator last) {
    Selection::Ranges ranges;

    Selection::Range range{0, 0};
    while (first != last) {
        const auto v = *first;
        if (v == range.second) {
            ++range.second;
        } else {
            if (range.first < range.second) {
                ranges.push_back(range);
            }
            range.first = v;
            range.second = v + 1;
        }
        ++first;
    }

    if (range.first < range.second) {
        ranges.push_back(range);
    }

    return Selection(std::move(ranges));
}

//--------------------------------------------------------------------------------------------------

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;

  protected:
    Population(const std::string& h5FilePath,
               const std::string& csvFilePath,
               const std::string& name,
               const std::string& prefix);

    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, const std::string& csvFilePath = "");

    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