#include <morphology.h>

Inheritance diagram for morphio::mut::Morphology:

Public Member Functions
	Morphology (std::shared_ptr< WarningHandler > warning_handler=nullptr)

	Morphology (const std::string &uri, unsigned int options=NO_MODIFIER, std::shared_ptr< WarningHandler > warning_handler=nullptr)

	Morphology (const HighFive::Group &group, unsigned int options=NO_MODIFIER, std::shared_ptr< WarningHandler > warning_handler=nullptr)
	Build a mutable Morphology from an HighFive::Group.

	Morphology (const mut::Morphology &morphology, unsigned int options=NO_MODIFIER, std::shared_ptr< WarningHandler > warning_handler=nullptr)
	Build a mutable Morphology from a mutable morphology.

	Morphology (const morphio::Morphology &morphology, unsigned int options=NO_MODIFIER, std::shared_ptr< WarningHandler > warning_handler=nullptr)
	Build a mutable Morphology from a read-only morphology.

const std::vector< std::shared_ptr< Section > > &	rootSections () const noexcept
	Returns all section ids at the tree root.

const std::map< uint32_t, std::shared_ptr< Section > > &	sections () const noexcept
	Returns the dictionary id -> Section for this tree.

std::shared_ptr< Soma > &	soma () noexcept

const std::shared_ptr< Soma > &	soma () const noexcept

Mitochondria &	mitochondria () noexcept
	Return the mitochondria container class.

const Mitochondria &	mitochondria () const noexcept
	Return the mitochondria container class.

EndoplasmicReticulum &	endoplasmicReticulum () noexcept
	Return the endoplasmic reticulum container class.

const EndoplasmicReticulum &	endoplasmicReticulum () const noexcept
	Return the endoplasmic reticulum container class.

const std::vector< Property::Annotation > &	annotations () const noexcept
	Return the annotation objects.

const std::vector< Property::Marker > &	markers () const noexcept
	Return the markers from the ASC file.

const std::shared_ptr< Section > &	section (uint32_t id) const

depth_iterator	depth_begin () const

depth_iterator	depth_end () const

breadth_iterator	breadth_begin () const

breadth_iterator	breadth_end () const

void	deleteSection (std::shared_ptr< Section > section, bool recursive=true)

std::shared_ptr< Section >	appendRootSection (const morphio::Section &, bool recursive=false)

std::shared_ptr< Section >	appendRootSection (const std::shared_ptr< Section > &section, bool recursive=false)

std::shared_ptr< Section >	appendRootSection (const Property::PointLevel &, SectionType sectionType)
	Append a root Section.

void	applyModifiers (unsigned int modifierFlags)

SomaType	somaType () const noexcept
	Return the soma type.

CellFamily	cellFamily () const noexcept
	Return the cell family (neuron or glia)

MorphologyVersion	version () const noexcept
	Return the version.

void	write (const std::string &filename) const
	Write file to H5, SWC, ASC format depending on filename extension.

void	addAnnotation (const Property::Annotation &annotation)

void	addMarker (const Property::Marker &marker)

Property::Properties	buildReadOnly () const
	Return the data structure used to create read-only morphologies.

std::unordered_map< int, std::vector< unsigned int > >	connectivity ()

void	removeUnifurcations ()

std::shared_ptr< WarningHandler >	getWarningHandler () const

Public Attributes
std::shared_ptr< Soma >	_soma

std::shared_ptr< Property::CellLevel >	_cellProperties

EndoplasmicReticulum	_endoplasmicReticulum

Property::DendriticSpine::Level	_dendriticSpineLevel

Friends
class	Section

void	modifiers::nrn_order (mut::Morphology &morpho)

bool	diff (const Morphology &left, const Morphology &right, enums::LogLevel verbose)

Detailed Description

Mutable(editable) morphio::Morphology

Constructor & Destructor Documentation

◆ Morphology()

morphio::mut::Morphology::Morphology	(	const std::string &	uri,
		unsigned int	options = `NO_MODIFIER`,
		std::shared_ptr< WarningHandler >	warning_handler = `nullptr`
	)

explicit

Build a mutable Morphology from an on-disk morphology

options is the modifier flags to be applied. All flags are defined in their enum: morphio::enum::Option and can be composed.

Example: Morphology("neuron.asc", TWO_POINTS_SECTIONS | SOMA_SPHERE);

Member Function Documentation

◆ appendRootSection() [1/2]

std::shared_ptr<Section> morphio::mut::Morphology::appendRootSection	(	const morphio::Section &	,
		bool	recursive = `false`
	)

Append the existing morphio::Section as a root section

If recursive == true, all descendent will be appended as well

◆ appendRootSection() [2/2]

std::shared_ptr<Section> morphio::mut::Morphology::appendRootSection	(	const std::shared_ptr< Section > &	section,
		bool	recursive = `false`
	)

Append an existing Section as a root section

If recursive == true, all descendent will be appended as well

◆ breadth_begin()

breadth_iterator morphio::mut::Morphology::breadth_begin ( ) const

Breadth first iterator

If id == -1, the iteration will be successively performed starting at each root section

◆ connectivity()

std::unordered_map<int, std::vector<unsigned int> > morphio::mut::Morphology::connectivity ( )

Return the graph connectivity of the morphology where each section is seen as a node Note: -1 is the soma node

◆ deleteSection()

void morphio::mut::Morphology::deleteSection	(	std::shared_ptr< Section >	section,
		bool	recursive = `true`
	)

Delete the given section

Will silently fail if the section is not part of the tree

If recursive == true, all descendent sections will be deleted as well Else, children will be re-attached to their grand-parent

◆ depth_begin()

depth_iterator morphio::mut::Morphology::depth_begin ( ) const

Depth first iterator starting at a given section id

If id == -1, the iteration will start at each root section, successively

◆ removeUnifurcations()

void morphio::mut::Morphology::removeUnifurcations ( )

Fixes the morphology single child sections and issues warnings if the section starts and ends are inconsistent

◆ section()

const std::shared_ptr<Section>& morphio::mut::Morphology::section ( uint32_t id ) const

inline

Get the shared pointer for the given section

Note: multiple morphologies can share the same Section instances.

◆ soma() [1/2]

const std::shared_ptr<Soma>& morphio::mut::Morphology::soma ( ) const

inlinenoexcept

Returns a shared pointer on the Soma

Note: multiple morphologies can share the same Soma instance

◆ soma() [2/2]

std::shared_ptr<Soma>& morphio::mut::Morphology::soma ( )