Python API

class morphio.AccessMode

Members:

MODE_READ

MODE_WRITE

MODE_OVERWRITE

MODE_READWRITE

MODE_READOVERWRITE

property name

handle) -> str

Type

(self

class morphio.Annotation

Container class for information about anomalies detected while parsing the file (no soma, section with a single child…)

property details

Returns the details

property diameters

Returns the list of diameters of annotated points

property line_number

Returns the lineNumber

property perimeters

Returns the list of perimeters of annotated points

property points

Returns the list of coordinates of annotated points

property section_id

Returns the sectionId

property type

Returns the type

class morphio.AnnotationType

Members:

single_child : Indicates that a section has only one child

property name

handle) -> str

Type

(self

class morphio.CellFamily

Members:

NEURON

GLIA

property name

handle) -> str

Type

(self

class morphio.CellLevel

Container class for information available at the cell level (cell type, file version, soma type)

property cell_family

Returns the cell family (neuron or glia)

property soma_type

Returns the soma type

property version

Returns the version

class morphio.EndoplasmicReticulum

The entry-point class to access endoplasmic reticulum data Spec https://bbpteam.epfl.ch/documentation/projects/Morphology%20Documentation/latest/h5v1.html

property filament_counts

Returns the number of filaments for each neuronal section

property section_indices

Returns the list of neuronal section indices

property surface_areas

Returns the surface areas for each neuronal section

property volumes

Returns the list of neuronal section indices

exception morphio.IDSequenceError
class morphio.IterType

Members:

depth_first

breadth_first

upstream

property name

handle) -> str

Type

(self

class morphio.LogLevel

Members:

error

warning

info

debug

property name

handle) -> str

Type

(self

exception morphio.MissingParentError
class morphio.Mitochondria

The entry-point class to access mitochondrial data By design, it is the equivalent of the Morphology class but at the mitochondrial level As the Morphology class, it implements a section accessor and a root section accessor returning views on the Properties object for the queried mitochondrial section

property root_sections

Returns a list of all root sections (section whose parent ID is -1)

section(section_id: int) morphio::MitoSection

Returns the mithochondrial section with the given ID

property sections

Returns a list of all mitochondrial sections

class morphio.MitochondriaPointLevel

Container class for the information available at the mitochondrial point level (enclosing neuronal section, relative distance to start of neuronal section, diameter)

exception morphio.MorphioError
exception morphio.MultipleTrees
class morphio.Option

Members:

no_modifier

two_points_sections

soma_sphere

no_duplicates

nrn_order

property name

handle) -> str

Type

(self

class morphio.PointLevel

Container class for information available at the point level (point coordinate, diameter, perimeter)

property diameters

Returns the list of diameters

property perimeters

Returns the list of perimeters

property points

Returns the list of point coordinates

class morphio.Properties

The higher level container structure is Property::Properties

property cell_level

Returns the structure that stores information at the cell level

property point_level

Returns the structure that stores information at the point level

property section_level

Returns the structure that stores information at the section level

exception morphio.RawDataError
exception morphio.SectionBuilderError
class morphio.SectionLevel

Container class for information available at the section level (section type, parent section)

property children

Returns a dictionary where key is a section ID and value is the list of children section IDs

property section_types

Returns the list of section types

property sections

Returns a list of [offset, parent section ID]

class morphio.SectionType

Members:

undefined

soma

axon

basal_dendrite

apical_dendrite

property name

handle) -> str

Type

(self

exception morphio.SomaError
class morphio.SomaType

Members:

SOMA_UNDEFINED

SOMA_SINGLE_POINT

SOMA_NEUROMORPHO_THREE_POINT_CYLINDERS

SOMA_CYLINDERS

SOMA_SIMPLE_CONTOUR

property name

handle) -> str

Type

(self

exception morphio.UnknownFileType
class morphio.VasculatureSectionType

Members:

undefined

vein

artery

venule

arteriole

venous_capillary

arterial_capillary

transitional

property name

handle) -> str

Type

(self

class morphio.Warning

Members:

undefined

mitochondria_write_not_supported

write_no_soma

write_empty_morphology

soma_non_conform

no_soma_found

disconnected_neurite

wrong_duplicate

appending_empty_section

wrong_root_point

only_child

property name

handle) -> str

Type

(self

exception morphio.WriterError
morphio.set_ignored_warning(*args, **kwargs)

Overloaded function.

  1. set_ignored_warning(warning: morphio::enums::Warning, ignore: bool = True) → None

    Ignore/Unignore a specific warning message

  2. set_ignored_warning(warning: List[morphio::enums::Warning], ignore: bool = True) → None

    Ignore/Unignore a list of warnings

morphio.set_maximum_warnings(arg0: int) None

Set the maximum number of warnings to be printed on screen 0 will print no warning -1 will print them all