morphology.h

#pragma once

#include <memory>  //std::unique_ptr

#include <highfive/H5Group.hpp>
#include <morphio/properties.h>
#include <morphio/section_iterators.hpp>
#include <morphio/types.h>

namespace morphio {
enum SomaClasses { SOMA_CONTOUR, SOMA_CYLINDER };

using breadth_iterator = breadth_iterator_t<Section, Morphology>;
using depth_iterator = depth_iterator_t<Section, Morphology>;

class Morphology
{
  public:
    virtual ~Morphology();

    Morphology& operator=(const Morphology&);
    Morphology(Morphology&&) noexcept;
    Morphology& operator=(Morphology&&) noexcept;

    explicit Morphology(const std::string& source, unsigned int options = NO_MODIFIER);
    explicit Morphology(const HighFive::Group& group, unsigned int options = NO_MODIFIER);
    explicit Morphology(mut::Morphology);

    Soma soma() const;

    Mitochondria mitochondria() const;

    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