Python API¶

Immutable objects¶

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¶

class morphio.CellFamily¶

Members:

NEURON

GLIA

SPINE

property name¶

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.Collection¶

A collection of morphologies

argsort(morphology_names: List[str]) → List[int]¶

Argsort morphology_names by optimal access order.

Note: This API is ‘experimental’, meaning it might change in the future.

close() → None¶

load(morph_name: str, options: int = <Option.no_modifier: 0>, mutable: bool = False) → object¶: Load the morphology named ‘morph_name’ form the collection.

load_unordered(morphology_names: List[str], options: int = <Option.no_modifier: 0>, mutable: bool = False) → object¶

Create an iterable of loop index and morphology.

When reading from containers, the order in which morphologies are read can have a large impact on the overall time to load those morphologies.

This iterator provides means of reordering loops to optimize the access pattern. Loops such as the following

for k, morph_name in enumerate(morphology_names):
morph = collection.load(morphology_names[k]) f(k, morph)

can be replaced with

for k, morph in collection.load_unordered(morphology_names):
assert collection.load(morphology_names[k]) == morph f(k, morph)

The order in which the morphologies are returned in unspecified, but the loop index k can be used to retrieve the correct state corresponding to iteration k of the original loop.

The iterable returned by Collection.load_unordered should only be used while collection is valid, e.g. within its context or before calling Collection.close.

Note: This API is ‘experimental’, meaning it might change in the future.

class morphio.DendriticSpine¶

Class representing a Dendritic Spine

property cell_family¶: Returns the cell family (neuron or glia)

property connectivity¶: Return the graph connectivity of the DendriticSpine where each section is seen as a node Note: -1 is the soma node

property diameters¶: Returns a list with all diameters from all sections Note: diameters belonging to the n’th section are located at indices: [DendriticSpine.sectionOffsets(n), DendriticSpine.sectionOffsets(n+1)[

iter(iter_type: morphio.IterType = <IterType.depth_first: 0>) → Iterator¶

Section iterator that runs successively on every neurite

iter_type controls the order of iteration on sections of a given neurite. 2 values can be passed:

morphio.IterType.depth_first (default)
morphio.IterType.breadth_first

property points¶: Returns a list with all points from all sections Note: points belonging to the n’th section are located at indices: [DendriticSpine.sectionOffsets(n), DendriticSpine.sectionOffsets(n+1)[

property post_synaptic_density¶: Returns the post synaptic density values

property root_sections¶: Returns a list of all root sections (sections whose parent ID are -1)

section(section_id: int) → morphio.Section¶: Returns the Section with the given id throw RawDataError if the id is out of range

property section_offsets¶

Returns a list with offsets to access data of a specific section in the points and diameters arrays.

Example: accessing diameters of n’th section will be located in the DIAMETERS array from DIAMETERS[sectionOffsets(n)] to DIAMETERS[sectionOffsets(n+1)-1]

Note: for convenience, the last point of this array is the points array size so that the above example works also for the last section.

property section_types¶: Returns a vector with the section type of every section

property sections¶

Returns a vector containing all sections objects

Notes: - Soma is not included - First section ID is 1 (0 is reserved for the soma) - To select sections by ID use: DendriticSpine::section(id)

property version¶: Returns the version

write(filename: object) → None¶

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

class morphio.GlialCell¶: Class representing a Glial Cell

exception morphio.IDSequenceError¶

class morphio.IterType¶

Members:

depth_first

breadth_first

upstream

property name¶

class morphio.LogLevel¶

Members:

error

warning

info

debug

property name¶

exception morphio.MissingParentError¶

class morphio.MitoSection¶

Class representing a Mitochondrial Section

property children¶: Returns a list of children mitochondrial sections

property diameters¶: Returns list of section’s point diameters

has_same_shape(arg0: morphio.MitoSection) → bool¶

property id¶: Returns the section ID The section ID can be used to query sections via Mitochondria::section(uint32_t id)

property is_root¶: Returns true if this section is a root section (parent ID == -1)

iter(iter_type: morphio.IterType = <IterType.depth_first: 0>) → Iterator¶

Depth first iterator starting at a given section id

If id == -1, the iteration will be successively performed starting at each root section

property neurite_section_ids¶: Returns list of neuronal section IDs associated to each point of this mitochondrial section

property parent¶: Returns the parent mitochondrial section of this section throw MissingParentError is the section doesn’t have a parent

property relative_path_lengths¶

Returns list of relative distances between the start of the neuronal section and each point of the mitochondrial section

Note: - a relative distance of 0 means the mitochondrial point is at the beginning of the neuronal section

a relative distance of 1 means the mitochondrial point is at the end of the neuronal section

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¶

class morphio.Morphology¶

Class representing a complete morphology

property annotations¶: Returns a list of annotations

as_mutable() → morphio.mut.Morphology¶

property cell_family¶: Returns the cell family (neuron or glia)

property connectivity¶: Return the graph connectivity of the morphology where each section is seen as a node Note: -1 is the soma node

property diameters¶: Returns a list with all diameters from all sections (soma points are not included) Note: diameters belonging to the n’th section are located at indices: [Morphology.sectionOffsets(n), Morphology.sectionOffsets(n+1)[

property endoplasmic_reticulum¶: Returns the endoplasmic reticulum object

iter(iter_type: morphio.IterType = <IterType.depth_first: 0>) → Iterator¶

Section iterator that runs successively on every neurite

iter_type controls the order of iteration on sections of a given neurite. 2 values can be passed:

morphio.IterType.depth_first (default)
morphio.IterType.breadth_first

property markers¶: Returns the list of NeuroLucida markers

property mitochondria¶: Returns the soma object

property n_points¶: Returns the number of points from all sections (soma points are not included)

property perimeters¶: Returns a list with all perimeters from all sections (soma points are not included) Note: perimeters belonging to the n’th section are located at indices: [Morphology.sectionOffsets(n), Morphology.sectionOffsets(n+1)[

property points¶: Returns a list with all points from all sections (soma points are not included) Note: points belonging to the n’th section are located at indices: [Morphology.sectionOffsets(n), Morphology.sectionOffsets(n+1)[

property root_sections¶: Returns a list of all root sections (sections whose parent ID are -1)

section(section_id: int) → morphio.Section¶: Returns the Section with the given id throw RawDataError if the id is out of range

property section_offsets¶

Returns a list with N+1 offsets to access data of a specific section in the points and diameters arrays (size N).

Example: accessing diameters of n’th section will be located in the diameters array: diameters[section_offsets[n]: section_offsets[n + 1]]

Note: for convenience, the last element of this array is equal to the length of the points/diameters arrays so that the above example works also for the last section.

property section_types¶: Returns a vector with the section type of every section

property sections¶

Returns a vector containing all sections objects

Notes: - Soma is not included - First section ID is 1 (0 is reserved for the soma) - To select sections by ID use: Morphology::section(id)

property soma¶: Returns the soma object

property soma_type¶: Returns the soma type

property version¶: Returns the version

exception morphio.MultipleTrees¶

class morphio.Option¶

Members:

no_modifier

two_points_sections

soma_sphere

no_duplicates

nrn_order

property name¶

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.PostSynapticDensity¶

DendriticSpine post-synaptic density

property offset¶: Returns offset of post-synaptic density

property section_id¶: Returns sectionId of post-synaptic density

property segment_id¶: Returns segmentId of post-synaptic density

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¶

class morphio.Section¶

Class representing a Section

property children¶: Returns a list of children sections

property diameters¶: Returns list of section’s point diameters

has_same_shape(arg0: morphio.Section) → bool¶

property id¶: Returns the section ID The section ID can be used to query sections via Morphology::section(uint32_t id)

is_heterogeneous(downstream: bool = True) → bool¶: Returns true if the tree downtream (downstream = true) or upstream (downstream = false) has the same type as the current section.

property is_root¶: Returns true if this section is a root section (parent ID == -1)

iter(iter_type: morphio.IterType = <IterType.depth_first: 0>) → Iterator¶

Section iterator

iter_type controls the iteration order. 3 values can be passed:

morphio.IterType.depth_first (default)
morphio.IterType.breadth_first
morphio.IterType.upstream

property n_points¶: Returns the number of points in section

property parent¶: Returns the parent section of this section throw MissingParentError is the section doesn’t have a parent

property perimeters¶: Returns list of section’s point perimeters

property points¶: Returns list of section’s point coordinates

property type¶: Returns the morphological type of this section (dendrite, axon, …)

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

custom5

custom6

custom7

custom8

custom9

custom10

glia_perivascular_process

glia_process

spine_head

spine_neck

all

property name¶

class morphio.Soma¶

Class representing a Soma

property center¶: Returns the center of gravity of the soma points

property diameters¶: Returns the diameters of all soma points

property max_distance¶: Return the maximum distance between the center of gravity and any of the soma points

property points¶: Returns the coordinates (x,y,z) of all soma point

property surface¶

Returns the soma surface

Note: the soma surface computation depends on the soma type

property type¶: Returns the soma type

exception morphio.SomaError¶

class morphio.SomaType¶

Members:

SOMA_UNDEFINED

SOMA_SINGLE_POINT

SOMA_NEUROMORPHO_THREE_POINT_CYLINDERS

SOMA_CYLINDERS

SOMA_SIMPLE_CONTOUR

property name¶

exception morphio.UnknownFileType¶

class morphio.VasculatureSectionType¶

Members:

undefined

vein

artery

venule

arteriole

venous_capillary

arterial_capillary

transitional

property name¶

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

zero_diameter

property name¶

exception morphio.WriterError¶

morphio.set_ignored_warning(*args, **kwargs)¶

Overloaded function.

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

Ignore/Unignore a specific warning message
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

morphio.set_raise_warnings(arg0: bool) → None¶: Whether to raise warning as errors

Mutable objects¶

class morphio.mut.DendriticSpine¶

Class representing a mutable Dendritic Spine

append_root_section(*args, **kwargs)¶

Overloaded function.

append_root_section(point_level_properties: morphio.PointLevel, section_type: morphio.SectionType) → morphio.mut.Section

Append a root Section
append_root_section(immutable_section: morphio.Section, recursive: bool = False) → morphio.mut.Section

Append the existing immutable Section as a root section If recursive == true, all descendent will be appended as well

property cell_family¶: Returns the cell family

property post_synaptic_density¶: Returns the post synaptic density values

property root_sections¶: Returns a list of all root sections IDs (sections whose parent ID are -1)

property sections¶: Returns a list containing IDs of all sections.

write(filename: object) → None¶

class morphio.mut.EndoplasmicReticulum¶

Class representing a mutable Endoplasmic Reticulum

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 volumes for each neuronal section

class morphio.mut.GlialCell¶: Class representing a mutable Glial Cell

class morphio.mut.MitoSection¶

Class representing a mutable Mitochondrial Section

append_section(*args, **kwargs)¶

Overloaded function.

append_section(point_level_properties: morphio.MitochondriaPointLevel) → morphio.mut.MitoSection

Append a new MitoSection to this mito section
append_section(section: morphio.mut.MitoSection, recursive: bool = False) → morphio.mut.MitoSection

Append a copy of the section to this section If recursive == true, all descendent will be appended as well
append_section(immutable_section: morphio.MitoSection, recursive: bool = False) → morphio.mut.MitoSection

Append the existing immutable MitoSection to this section If recursive == true, all descendent will be appended as well

property diameters¶: Returns the diameters of all points of this section

has_same_shape(arg0: morphio.mut.MitoSection) → bool¶

property id¶: Return the section ID

property neurite_section_ids¶: Returns the neurite section Ids of all points of this section

property relative_path_lengths¶: Returns the relative distance (between 0 and 1) between the start of the neuronal section and each point of this mitochondrial section

class morphio.mut.Mitochondria¶

Class representing a mutable Mitochondria

append_root_section(*args, **kwargs)¶

Overloaded function.

append_root_section(point_level_properties: morphio.MitochondriaPointLevel) → morphio.mut.MitoSection

Append a new root MitoSection
append_root_section(immutable_section: morphio.MitoSection, recursive: bool = True) → morphio.mut.MitoSection

Append a new root MitoSection (if recursive == true, all descendent will be appended as well)
append_root_section(section: morphio.mut.MitoSection, recursive: bool = True) → morphio.mut.MitoSection

Append a new root MitoSection (if recursive == true, all descendent will be appended as well)

breadth_begin(section_id: morphio.mut.MitoSection = -1) → Iterator¶

Breadth first iterator starting at a given section id

If id == -1, the iteration will be successively performed starting at each root section

children(section_id: morphio.mut.MitoSection) → List[morphio.mut.MitoSection]¶

depth_begin(section_id: morphio.mut.MitoSection = -1) → Iterator¶

Depth first iterator starting at a given section id

If id == -1, the iteration will be successively performed starting at each root section

is_root(section_id: morphio.mut.MitoSection) → bool¶: Return True if section is a root section

parent(section_id: morphio.mut.MitoSection) → morphio.mut.MitoSection¶: Returns the parent mithochondrial section ID

property root_sections¶: Returns a list of all root sections IDs (sections whose parent ID are -1)

section(section_id: int) → morphio.mut.MitoSection¶

Get a reference to the given mithochondrial section

Note: multiple mitochondria can shared the same references

property sections¶: Return a dict where key is the mitochondrial section ID and value is the mithochondrial section

upstream_begin(section_id: morphio.mut.MitoSection = -1) → Iterator¶

Upstream iterator starting at a given section id

If id == -1, the iteration will be successively performed starting at each root section

class morphio.mut.Morphology¶

Class representing a mutable Morphology

property annotations¶: Returns a list of annotations

append_root_section(*args, **kwargs)¶

Overloaded function.

append_root_section(point_level_properties: morphio.PointLevel, section_type: morphio.SectionType) → morphio.mut.Section

Append a root Section
append_root_section(immutable_section: morphio.Section, recursive: bool = False) → morphio.mut.Section

Append the existing immutable Section as a root section If recursive == true, all descendent will be appended as well
append_root_section(mutable_section: morphio.mut.Section, recursive: bool = False) → morphio.mut.Section

Append the existing mutable Section as a root section If recursive == true, all descendent will be appended as well

as_immutable() → morphio.Morphology¶

build_read_only() → morphio.Properties¶: Returns the data structure used to create read-only morphologies

property cell_family¶: Returns the cell family (neuron or glia)

property connectivity¶: Return the graph connectivity of the morphology where each section is seen as a node Note: -1 is the soma node

delete_section(section: morphio.mut.Section, recursive: bool = True) → None¶

Delete the given section

Will silently fail if the section is not part of the tree

If recursive == true, all descendent sections will be deleted as well Else, children will be re-attached to their grand-parent

property endoplasmic_reticulum¶: Returns a reference to the endoplasmic reticulum container class

iter(iter_type: morphio.IterType = <IterType.depth_first: 0>) → Iterator¶

Section iterator that runs successively on every neurite

iter_type controls the order of iteration on sections of a given neurite. 2 values can be passed:

morphio.IterType.depth_first (default)
morphio.IterType.breadth_first

property markers¶: Returns the list of NeuroLucida markers

property mitochondria¶: Returns a reference to the mitochondria container class

remove_unifurcations() → None¶: Fixes the morphology single child sections and issues warningsif the section starts and ends are inconsistent

property root_sections¶: Returns a list of all root sections IDs (sections whose parent ID are -1)

section(section_id: int) → morphio.mut.Section¶

Returns the section with the given id

Note: multiple morphologies can share the same Section instances

property sections¶: Returns a list containing IDs of all sections. The first section of the vector is the soma section

property soma¶

Returns a reference to the soma object

Note: multiple morphologies can share the same Soma instance

property soma_type¶: Returns the soma type

property version¶: Returns the version

write(filename: object) → None¶: Write file to H5, SWC, ASC format depending on filename extension

class morphio.mut.Section¶

Class representing a mutable Section

append_section(*args, **kwargs)¶

Overloaded function.

append_section(immutable_section: morphio.Section, recursive: bool = False) → morphio.mut.Section

Append the existing immutable Section to this sectionIf recursive == true, all descendent will be appended as well
append_section(mutable_section: morphio.mut.Section, recursive: bool = False) → morphio.mut.Section

Append the existing mutable Section to this section If recursive == true, all descendent will be appended as well
append_section(point_level_properties: morphio.PointLevel, section_type: morphio.SectionType = <SectionType.undefined: 0>) → morphio.mut.Section

Append a new Section to this section
If section_type is omitted or set to ‘undefined’ the type of the parent section will be used

property children¶: Returns a list of children IDs

property diameters¶: Returns the diameters of all points of this section

has_same_shape(arg0: morphio.mut.Section) → bool¶

property id¶: Return the section ID

is_heterogeneous(downstream: bool = True) → bool¶: Returns true if the tree downtream (downstream = true) or upstream (downstream = false) has the same type as the current section.

property is_root¶: Return True if section is a root section

iter(iter_type: morphio.IterType = <IterType.depth_first: 0>) → Iterator¶

Section iterator

iter_type controls the iteration order. 3 values can be passed:

morphio.IterType.depth_first (default)
morphio.IterType.breadth_first
morphio.IterType.upstream

property parent¶

Get the parent ID

Note: Root sections return -1

property perimeters¶: Returns the perimeters of all points of this section

property points¶: Returns the coordinates (x,y,z) of all points of this section

property type¶: Returns the morphological type of this section (dendrite, axon, …)

class morphio.mut.Soma¶

Class representing a mutable Soma

property center¶: Returns the center of gravity of the soma points

property diameters¶: Returns the diameters of all soma points

property max_distance¶: Return the maximum distance between the center of gravity and any of the soma points

property points¶: Returns the coordinates (x,y,z) of all soma point

property surface¶

Returns the soma surface

Note: the soma surface computation depends on the soma type

property type¶: Returns the soma type