morphio Namespace Reference

Namespaces
	enums
	mut
	Property
	readers
	vasculature

Classes
class	breadth_iterator_t
class	DendriticSpine
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 >

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

Blue Brain File IO classes

Typedef Documentation

breadth_iterator

typedef breadth_iterator_t< Section, Morphology > morphio::breadth_iterator

Morphology breadth iterator

depth_iterator

typedef depth_iterator_t< Section, Morphology > morphio::depth_iterator

Morphology depth iterator

floatType

using morphio::floatType = typedef float

Type of float to use. Can be double or float depending on MORPHIO_USE_DOUBLE

Point

using morphio::Point = typedef std::array<morphio::floatType, 3>

An array of size 3 for x,y,z coordinates

Points

using morphio::Points = typedef std::vector<Point>

An array of points

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

printError()

void morphio::printError	(	Warning	warning,
		const std::string &	msg
	)

Print a warning. Raises an error if set_raise_warnings was set to true.

set_ignored_warning() [1/2]

void morphio::set_ignored_warning	(	Warning	warning,
		bool	ignore = true
	)

Set a warning to ignore

set_ignored_warning() [2/2]

void morphio::set_ignored_warning	(	const std::vector< Warning > &	warning,
		bool	ignore = true
	)

Set an array of warnings to ignore

set_maximum_warnings()

void morphio::set_maximum_warnings

(

int

n_warnings

)

Set the maximum number of warnings to be printed on screen

set_raise_warnings()

void morphio::set_raise_warnings

(

bool

is_raise

)

Set whether to interpet warning as errors

Variable Documentation

epsilon

constexpr floatType morphio::epsilon = 1e-6f

A really small value that is used to measure how close are two values