morphology.h

/* Copyright (c) 2013-2023, EPFL/Blue Brain Project
 *
 * SPDX-License-Identifier: Apache-2.0
 */
#pragma once
 
#include <highfive/H5Group.hpp>
 
#include <morphio/properties.h>
#include <morphio/section_iterators.hpp>
#include <morphio/types.h>
#include <morphio/warning_handling.h>  // WarningHandler
 
namespace morphio {
 
using breadth_iterator = breadth_iterator_t<Section, Morphology>;
using depth_iterator = depth_iterator_t<Section, Morphology>;
 
class Morphology
{
  public:
    virtual ~Morphology() = default;
 
    Morphology(const Morphology&) noexcept = default;
    Morphology& operator=(const Morphology&) noexcept = default;
    Morphology(Morphology&&) noexcept = default;
    Morphology& operator=(Morphology&&) noexcept = default;
 
    explicit Morphology(const std::string& path,
                        unsigned int options = NO_MODIFIER,
                        std::shared_ptr<WarningHandler> = nullptr);
 
 
    explicit Morphology(const HighFive::Group& group,
                        unsigned int options = NO_MODIFIER,
                        std::shared_ptr<WarningHandler> = nullptr);
 
    explicit Morphology(const mut::Morphology&);
 
    explicit Morphology(const std::string& contents,
                        const std::string& extension,
                        unsigned int options = NO_MODIFIER,
                        std::shared_ptr<WarningHandler> = nullptr);
 
    Soma soma() const;
 
    Mitochondria mitochondria() const;
 
    EndoplasmicReticulum endoplasmicReticulum() const;
 
    const std::vector<Property::Annotation>& annotations() const;
 
    const std::vector<Property::Marker>& markers() const;
 
    std::vector<Section> rootSections() const;
 
    std::vector<Section> sections() const;
 
    Section section(uint32_t id) const;
 
    const Points& points() const noexcept;
 
    std::vector<uint32_t> sectionOffsets() const;
 
    const std::vector<morphio::floatType>& diameters() const;
 
    const std::vector<morphio::floatType>& perimeters() const;
 
    const std::vector<SectionType>& sectionTypes() const;
 
    const std::map<int, std::vector<unsigned int>>& connectivity() const;
 
    depth_iterator depth_begin() const;
    depth_iterator depth_end() const;
 
    breadth_iterator breadth_begin() const;
    breadth_iterator breadth_end() const;
 
    const SomaType& somaType() const;
 
    const CellFamily& cellFamily() const;
 
    const MorphologyVersion& version() const;
 
  protected:
    friend class mut::Morphology;
    Morphology(const Property::Properties& properties, unsigned int options);
 
    std::shared_ptr<Property::Properties> properties_;
 
    template <typename Property>
    const std::vector<typename Property::Type>& get() const;
};
}  // namespace morphio