Enumerations | Functions
morphio::enums Namespace Reference

Enumerations

enum  LogLevel { ERROR, WARNING, INFO, DEBUG }
 
enum  Option {
  NO_MODIFIER = 0x00, TWO_POINTS_SECTIONS = 0x01, SOMA_SPHERE = 0x02, NO_DUPLICATES = 0x04,
  NRN_ORDER = 0x08
}
 
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
}
 
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

The cell family represented by morphio::Morphology.

Enumerator
NEURON 

Neuron.

GLIA 

Glia.

SPINE 

Spine.

◆ 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.

◆ 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

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

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

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.