morphio Namespace Reference

Classes
class	breadth_iterator_t
class	depth_iterator_t
class	EndoplasmicReticulum
class	GlialCell
class	IDSequenceError
class	MissingParentError
class	Mitochondria
class	MitoSection
class	MorphioError
class	Morphology
class	MultipleTrees
class	NotImplementedError
class	RawDataError
class	Section
class	SectionBase
class	SectionBuilderError
class	Soma
class	SomaError
class	UnknownFileType
class	upstream_iterator_t
class	WriterError

Typedefs
using	mito_upstream_iterator = upstream_iterator_t< MitoSection >
using	mito_breadth_iterator = morphio::breadth_iterator_t< MitoSection, Mitochondria >
using	mito_depth_iterator = morphio::depth_iterator_t< MitoSection, Mitochondria >
using	breadth_iterator = breadth_iterator_t< Section, Morphology >
using	depth_iterator = depth_iterator_t< Section, Morphology >
using	upstream_iterator = upstream_iterator_t< Section >
using	SectionRange = std::pair< size_t, size_t >
using	MorphologyVersion = std::tuple< std::string, uint32_t, uint32_t >
template<typename T >
using	range = gsl::span< T >
using	floatType = float
using	Point = std::array< morphio::floatType, 3 >
using	Points = std::vector< Point >

Enumerations
enum	SomaClasses { SOMA_CONTOUR, SOMA_CYLINDER }

Functions
void	set_maximum_warnings (int n_warnings)
void	set_raise_warnings (bool is_raise)
void	set_ignored_warning (Warning warning, bool ignore=true)
void	set_ignored_warning (const std::vector< Warning > &warning, bool ignore=true)
void	printError (Warning warning, const std::string &msg)
bool	diff (const Morphology &left, const Morphology &right, morphio::enums::LogLevel verbose=morphio::enums::LogLevel::INFO)
bool	diff (const Section &left, const Section &right, morphio::enums::LogLevel verbose=morphio::enums::LogLevel::INFO)
Point	operator+ (const Point &left, const Point &right)
Point	operator- (const Point &left, const Point &right)
Point	operator+= (Point &left, const Point &right)
Point	operator-= (Point &left, const Point &right)
Point	operator/= (Point &left, const floatType factor)
Points	operator+ (const Points &points, const Point &right)
Points	operator- (const Points &points, const Point &right)
Points	operator+= (Points &points, const Point &right)
Points	operator-= (Points &points, const Point &right)
template<typename T >
Point	operator* (const Point &from, T factor)
template<typename T >
Point	operator* (T factor, const Point &from)
template<typename T >
Point	operator/ (const Point &from, T factor)
template<typename T >
Point	centerOfGravity (const T &points)
template<typename T >
floatType	maxDistanceToCenterOfGravity (const T &points)
template Point	centerOfGravity (const Points &)
template floatType	maxDistanceToCenterOfGravity (const Points &)
std::string	dumpPoint (const Point &point)
std::string	dumpPoints (const Points &point)
char	my_tolower (char ch)
floatType	distance (const Point &left, const Point &right)
std::ostream &	operator<< (std::ostream &os, const morphio::Point &point)
std::ostream &	operator<< (std::ostream &os, const Points &points)
std::string	getVersionString ()
int	getMajor ()
int	getMinor ()
int	getPatch ()

Variables
constexpr floatType	epsilon = 1e-6f
constexpr floatType	PI = static_cast<floatType>(M_PI)

Detailed Description

The property namespace is the core of MorphIO as it is where all the internal data are stored.

The higher level container structure is Property::Properties.

It contains low-lever structure that stores information at various levels:

• PointLevel: information that is available at the point level (point coordinate, diameter, perimeter)
• SectionLevel: information that is available at the section level (section type, parent section)
• CellLevel: information that is available at the cell level (cell type, file version, soma type)
• MitochondriaPointLevel: information that is available at the mitochondrial point level (enclosing neuronal section, relative distance to start of neuronal section, diameter)
• MitochondriaSectionLevel: information that is available at the mitochondrial section level (parent section)

Blue Brain File IO classes

Typedef Documentation

upstream_iterator

using morphio::upstream_iterator = typedef upstream_iterator_t<Section>

A class to represent a morphological section.

A Section is an unbranched piece of a morphological skeleton. This class provides functions to query information about the sample points that compose the section and functions to obtain the parent and children sections.

The cell soma is also considered a section, but some functions have special meaning for it.

Sections cannot be directly created, but are returned by several morphio::Morphology and morphio::Section methods.

This is a lightweight object with STL container style thread safety. It is also safe to use a section after the morphology from where it comes has been deallocated. The morphological data will be kept as long as there is a Section referring to it.

Function Documentation

diff() [1/2]

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

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

diff() [2/2]

bool morphio::diff	(	const Section &	left,
		const Section &	right,
		morphio::enums::LogLevel	verbose = morphio::enums::LogLevel::INFO
	)

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

distance()

floatType morphio::distance	(	const Point &	left,
		const Point &	right
	)

Euclidian distance between two points

set_maximum_warnings()

void morphio::set_maximum_warnings

(

int

n_warnings

)

Set the maximum number of warnings to be printed on screen