Enumerations
enum	LogLevel { ERROR, WARNING }

enum	Option { NO_MODIFIER = 0x00, TWO_POINTS_SECTIONS = 0x01, SOMA_SPHERE = 0x02, NO_DUPLICATES = 0x04, NRN_ORDER = 0x08, ALLOW_UNIFURCATED_SECTION_CHANGE = 0x10 }

enum	Warning { UNDEFINED, MITOCHONDRIA_WRITE_NOT_SUPPORTED, WRITE_NO_SOMA, SOMA_NON_CONFORM, NO_SOMA_FOUND, DISCONNECTED_NEURITE, WRONG_DUPLICATE, WRITE_UNDEFINED_SOMA, APPENDING_EMPTY_SECTION, WRONG_ROOT_POINT, ONLY_CHILD, WRITE_EMPTY_MORPHOLOGY, ZERO_DIAMETER, SOMA_NON_CONTOUR, SOMA_NON_CYLINDER_OR_POINT, SECTION_TYPE_CHANGED }

enum	AnnotationType { SINGLE_CHILD }

enum	CellFamily { NEURON = 0, GLIA = 1, SPINE = 2 }

enum	SomaType { SOMA_UNDEFINED = 0, SOMA_SINGLE_POINT, SOMA_NEUROMORPHO_THREE_POINT_CYLINDERS, SOMA_CYLINDERS, SOMA_SIMPLE_CONTOUR }

enum	SectionType { SECTION_UNDEFINED = 0, SECTION_SOMA = 1, SECTION_AXON = 2, SECTION_DENDRITE = 3, SECTION_APICAL_DENDRITE = 4, SECTION_GLIA_PERIVASCULAR_PROCESS = 2, SECTION_GLIA_PROCESS = 3, SECTION_SPINE_NECK = 2, SECTION_SPINE_HEAD = 3, SECTION_CUSTOM_5 = 5, SECTION_CUSTOM_6 = 6, SECTION_CUSTOM_7 = 7, SECTION_CUSTOM_8 = 8, SECTION_CUSTOM_9 = 9, SECTION_CUSTOM_10 = 10, SECTION_CUSTOM_11 = 11, SECTION_CUSTOM_12 = 12, SECTION_CUSTOM_13 = 13, SECTION_CUSTOM_14 = 14, SECTION_CUSTOM_15 = 15, SECTION_CUSTOM_16 = 16, SECTION_CUSTOM_17 = 17, SECTION_CUSTOM_18 = 18, SECTION_CUSTOM_19 = 19, SECTION_OUT_OF_RANGE_START = 20, SWC_SECTION_FORK_POINT = 5, SWC_SECTION_END_POINT = 6, SECTION_CNIC_CUSTOM_START = 7, SECTION_ALL = 32 }

enum	VascularSectionType { SECTION_NOT_DEFINED = 0, SECTION_VEIN = 1, SECTION_ARTERY = 2, SECTION_VENULE = 3, SECTION_ARTERIOLE = 4, SECTION_VENOUS_CAPILLARY = 5, SECTION_ARTERIAL_CAPILLARY = 6, SECTION_TRANSITIONAL = 7, SECTION_CUSTOM = 8 }

Functions
std::ostream &	operator<< (std::ostream &os, SomaType v)

Detailed Description

A collection of enums for different util purposes

Enumeration Type Documentation

◆ CellFamily

enum morphio::enums::CellFamily

The cell family represented by morphio::Morphology.

Enumerator
NEURON	Neuron.
GLIA	Glia.
SPINE	Spine.

◆ Option

enum morphio::enums::Option

The list of modifier flags that can be passed when loading a morphology See morphio::mut::modifiers for more information

Enumerator
NO_MODIFIER	Read morphology as is without any modification.
TWO_POINTS_SECTIONS	Read sections only with 2 or more points.
SOMA_SPHERE	Interpret morphology soma as a sphere.
NO_DUPLICATES	Skip duplicating points.
NRN_ORDER	Order of neurites will be the same as in NEURON simulator.
ALLOW_UNIFURCATED_SECTION_CHANGE	Allow section type to change without bifurcation.

◆ SectionType

enum morphio::enums::SectionType

Classification of neuron substructures.

Enumerator
SECTION_UNDEFINED	Undefined section.
SECTION_SOMA	Neuron cell body.
SECTION_AXON	Axon section.
SECTION_DENDRITE	General or basal dendrite (near to soma)
SECTION_APICAL_DENDRITE	Apical dendrite (far from soma)
SECTION_CUSTOM_5	Custom section type 5.
SECTION_CUSTOM_6	Custom section type 6.
SECTION_CUSTOM_7	Custom section type 7.
SECTION_CUSTOM_8	Custom section type 8.
SECTION_CUSTOM_9	Custom section type 9.
SECTION_CUSTOM_10	Custom section type 10.
SECTION_CUSTOM_11	Custom section type 11.
SECTION_CUSTOM_12	Custom section type 12.
SECTION_CUSTOM_13	Custom section type 13.
SECTION_CUSTOM_14	Custom section type 14.
SECTION_CUSTOM_15	Custom section type 15.
SECTION_CUSTOM_16	Custom section type 16.
SECTION_CUSTOM_17	Custom section type 17.
SECTION_CUSTOM_18	Custom section type 18.
SECTION_CUSTOM_19	Custom section type 19.
SECTION_ALL	Any section type.

◆ SomaType

enum morphio::enums::SomaType

Soma type.

Enumerator
SOMA_UNDEFINED	Undefined soma.
SOMA_SINGLE_POINT	Single point soma.
SOMA_NEUROMORPHO_THREE_POINT_CYLINDERS	Soma made of three cylinders.
SOMA_CYLINDERS	Soma made of cylinders.
SOMA_SIMPLE_CONTOUR	Contour soma. Assumed that contour is in XY plane.

◆ VascularSectionType

enum morphio::enums::VascularSectionType

Classification of vasculature section types.

Enumerator
SECTION_NOT_DEFINED	Undefined.
SECTION_VEIN	Vein.
SECTION_ARTERY	Artery.
SECTION_VENULE	Venule.
SECTION_ARTERIOLE	Arteriole.
SECTION_VENOUS_CAPILLARY	Venous capillary.
SECTION_ARTERIAL_CAPILLARY	Arterial capillary.
SECTION_TRANSITIONAL	Transitional.
SECTION_CUSTOM	Custom section type.

◆ Warning

enum morphio::enums::Warning

All possible warnings that can be ignored by user. This enum should be kept in sync with the warnings defined in morphio::ErrorMessages and with binds/python/bind_misc.cpp

Enumerator
UNDEFINED	undefined value
MITOCHONDRIA_WRITE_NOT_SUPPORTED	Mitochondria can be saved in H5 format only.
WRITE_NO_SOMA	Writing without a soma.
SOMA_NON_CONFORM	Soma does not conform the three point soma spec from NeuroMorpho.org.
NO_SOMA_FOUND	No soma found in a file.
DISCONNECTED_NEURITE	Found a disconnected neurite in a morphology.
WRONG_DUPLICATE	A wrong duplicate point in a section.
WRITE_UNDEFINED_SOMA	Soma is UNDEFINED.
APPENDING_EMPTY_SECTION	Appending of an empty section.
WRONG_ROOT_POINT	A wrong root point of a neurite in the case of 3 points soma.
ONLY_CHILD	Single child sections are not allowed in SWC format.
WRITE_EMPTY_MORPHOLOGY	Writing empty morphology.
ZERO_DIAMETER	Zero section diameter.
SOMA_NON_CONTOUR	Soma must be a contour for ASC and H5.
SOMA_NON_CYLINDER_OR_POINT	Soma must be stacked cylinders or a point.
SECTION_TYPE_CHANGED	In SWC, the type changed within a section, not post bifurcation.

Enumerations

Functions