#include <morphology.h>

Inheritance diagram for morphio::mut::Morphology:

Public Member Functions
	Morphology (const std::string &uri, unsigned int options=NO_MODIFIER)

	Morphology (const morphio::mut::Morphology &morphology, unsigned int options=NO_MODIFIER)

	Morphology (const morphio::Morphology &morphology, unsigned int options=NO_MODIFIER)

const std::vector< std::shared_ptr< Section > > &	rootSections () const noexcept

const std::map< uint32_t, std::shared_ptr< Section > > &	sections () const noexcept

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

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

Mitochondria &	mitochondria () noexcept

const Mitochondria &	mitochondria () const noexcept

EndoplasmicReticulum &	endoplasmicReticulum () noexcept

const EndoplasmicReticulum &	endoplasmicReticulum () const noexcept

const std::vector< Property::Annotation > &	annotations () const noexcept

const std::vector< Property::Marker > &	markers () const noexcept

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)

void	applyModifiers (unsigned int modifierFlags)

SomaType	somaType () const noexcept

CellFamily	cellFamily () const noexcept

MorphologyVersion	version () const noexcept

void	write (const std::string &filename)

void	addAnnotation (const morphio::Property::Annotation &annotation)

void	addMarker (const morphio::Property::Marker &marker)

Property::Properties	buildReadOnly () const

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

void	removeUnifurcations ()

void	removeUnifurcations (const morphio::readers::DebugInfo &debugInfo)

void	_raiseIfUnifurcations ()

uint32_t	_register (const std::shared_ptr< Section > &)

Public Attributes
morphio::readers::ErrorMessages	_err

uint32_t	_counter

std::shared_ptr< Soma >	_soma

std::shared_ptr< morphio::Property::CellLevel >	_cellProperties

std::vector< std::shared_ptr< Section > >	_rootSections

std::map< uint32_t, std::shared_ptr< Section > >	_sections

Mitochondria	_mitochondria

EndoplasmicReticulum	_endoplasmicReticulum

morphio::Property::DendriticSpine::Level	_dendriticSpineLevel

std::map< uint32_t, uint32_t >	_parent

std::map< uint32_t, std::vector< std::shared_ptr< Section > > >	_children

Friends
class	Section

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

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

Detailed Description

Mutable(editable) morphio::Morphology

Constructor & Destructor Documentation

◆ Morphology() [1/3]

morphio::mut::Morphology::Morphology	(	const std::string &	uri,
		unsigned int	options = `NO_MODIFIER`
	)

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);

◆ Morphology() [2/3]

morphio::mut::Morphology::Morphology	(	const morphio::mut::Morphology &	morphology,
		unsigned int	options = `NO_MODIFIER`
	)

Build a mutable Morphology from a mutable morphology

◆ Morphology() [3/3]

morphio::mut::Morphology::Morphology	(	const morphio::Morphology &	morphology,
		unsigned int	options = `NO_MODIFIER`
	)

Build a mutable Morphology from a read-only morphology

Member Function Documentation

◆ _raiseIfUnifurcations()

void morphio::mut::Morphology::_raiseIfUnifurcations ( )

Used before writing to SWC to check that there is no unifurcation

◆ annotations()

const std::vector< Property::Annotation > & morphio::mut::Morphology::annotations ( ) const

inlinenoexcept

Return the annotation object

◆ appendRootSection() [1/3]

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() [2/3]

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

◆ appendRootSection() [3/3]

std::shared_ptr<Section> morphio::mut::Morphology::appendRootSection	(	const Property::PointLevel &	,
		SectionType	sectionType
	)

Append a root Section

◆ 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

◆ buildReadOnly()

Property::Properties morphio::mut::Morphology::buildReadOnly ( ) const

Return the data structure used to create read-only morphologies

◆ cellFamily()

CellFamily morphio::mut::Morphology::cellFamily ( ) const

inlinenoexcept

Return the cell family (neuron or glia)

◆ 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

◆ endoplasmicReticulum() [1/2]

EndoplasmicReticulum & morphio::mut::Morphology::endoplasmicReticulum ( )

inlinenoexcept

Return the endoplasmic reticulum container class

◆ endoplasmicReticulum() [2/2]

const EndoplasmicReticulum & morphio::mut::Morphology::endoplasmicReticulum ( ) const

inlinenoexcept

Return the endoplasmic reticulum container class

◆ markers()

const std::vector< Property::Marker > & morphio::mut::Morphology::markers ( ) const

inlinenoexcept

Return the markers from the ASC file

◆ mitochondria() [1/2]

Mitochondria & morphio::mut::Morphology::mitochondria ( )

inlinenoexcept

Return the mitochondria container class

◆ mitochondria() [2/2]

const Mitochondria & morphio::mut::Morphology::mitochondria ( ) const

inlinenoexcept

Return the mitochondria container class

◆ removeUnifurcations()

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

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

◆ rootSections()

const std::vector< std::shared_ptr< Section > > & morphio::mut::Morphology::rootSections ( ) const

inlinenoexcept

Returns all section ids at the tree root

◆ 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.

◆ sections()

const std::map< uint32_t, std::shared_ptr< Section > > & morphio::mut::Morphology::sections ( ) const

inlinenoexcept

Returns the dictionary id -> Section for this tree

◆ soma() [1/2]

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

inlinenoexcept

Returns a shared pointer on the Soma

Note: multiple morphologies can share the same Soma instance

◆ soma() [2/2]

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

◆ somaType()

SomaType morphio::mut::Morphology::somaType ( ) const

inlinenoexcept

Return the soma type

◆ version()

MorphologyVersion morphio::mut::Morphology::version ( ) const

inlinenoexcept

Return the version

◆ write()

void morphio::mut::Morphology::write ( const std::string & filename )

Write file to H5, SWC, ASC format depending on filename extension

Friends And Related Function Documentation

◆ diff

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

friend

Perform a diff on 2 morphologies, returns True if items differ

Public Member Functions

Public Attributes

Friends

Detailed Description

Constructor & Destructor Documentation

◆ Morphology() [1/3]

◆ Morphology() [2/3]

◆ Morphology() [3/3]

Member Function Documentation

◆ _raiseIfUnifurcations()

◆ annotations()

◆ appendRootSection() [1/3]

◆ appendRootSection() [2/3]

◆ appendRootSection() [3/3]

◆ breadth_begin()

◆ buildReadOnly()

◆ cellFamily()

◆ connectivity()

◆ deleteSection()

◆ depth_begin()

◆ endoplasmicReticulum() [1/2]

◆ endoplasmicReticulum() [2/2]

◆ markers()

◆ mitochondria() [1/2]

◆ mitochondria() [2/2]

◆ removeUnifurcations()

◆ rootSections()

◆ section()

◆ sections()

◆ soma() [1/2]

◆ soma() [2/2]

◆ somaType()

◆ version()

◆ write()

Friends And Related Function Documentation

◆ diff