7 #include <highfive/H5Group.hpp>
9 #include <morphio/properties.h>
10 #include <morphio/section_iterators.hpp>
11 #include <morphio/types.h>
12 #include <morphio/warning_handling.h>
17 using breadth_iterator = breadth_iterator_t<Section, Morphology>;
19 using depth_iterator = depth_iterator_t<Section, Morphology>;
49 std::shared_ptr<WarningHandler> =
nullptr);
53 explicit Morphology(
const HighFive::Group& group,
55 std::shared_ptr<WarningHandler> =
nullptr);
61 explicit Morphology(
const std::string& contents,
62 const std::string& extension,
64 std::shared_ptr<WarningHandler> =
nullptr);
76 const std::vector<Property::Annotation>&
annotations()
const;
79 const std::vector<Property::Marker>&
markers()
const;
92 std::vector<Section>
sections()
const;
105 const Points&
points()
const noexcept;
123 const std::vector<morphio::floatType>&
diameters()
const;
126 const std::vector<morphio::floatType>&
perimeters()
const;
136 const std::map<int, std::vector<unsigned int>>&
connectivity()
const;
164 const MorphologyVersion&
version()
const;
170 std::shared_ptr<Property::Properties> properties_;
172 template <
typename Property>
173 const std::vector<typename Property::Type>& get()
const;
Definition: properties.h:209
SomaType
Definition: enums.h:59
const CellFamily & cellFamily() const
Definition: section_iterators.hpp:82
std::vector< uint32_t > sectionOffsets() const
@ NO_MODIFIER
Read morphology as is without any modification.
Definition: enums.h:18
const Points & points() const noexcept
breadth_iterator breadth_begin() const
const std::vector< Property::Marker > & markers() const
const std::vector< morphio::floatType > & diameters() const
Definition: morphology.h:26
depth_iterator depth_end() const
const std::map< int, std::vector< unsigned int > > & connectivity() const
const std::vector< morphio::floatType > & perimeters() const
depth_iterator depth_begin() const
const MorphologyVersion & version() const
Mitochondria mitochondria() const
std::vector< Section > sections() const
const SomaType & somaType() const
CellFamily
Definition: enums.h:52
std::vector< Section > rootSections() const
const std::vector< SectionType > & sectionTypes() const
const std::vector< Property::Annotation > & annotations() const
Definition: mitochondria.h:22
Definition: section_iterators.hpp:53
Definition: morphology.h:32
Definition: endoplasmic_reticulum.h:22
EndoplasmicReticulum endoplasmicReticulum() const
breadth_iterator breadth_end() const
Section section(uint32_t id) const