Python API

Immutable objects

class morphio.Annotation

Class that holds service information about a warning.

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

Service information that is available at the Morphology level (morphology version, morphology family, soma type, etc.)

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 to represent morphologies of dendritic spines

property cell_family

Return 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

Return a vector with all diameters from all sections (soma points are not included)

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

Return a vector with all points from all sections (soma points are not included)

property root_sections

Return a vector of all root sections (sections whose parent ID are -1)

section(section_id: int) → morphio.Section

Return the Section with the given id.

Raises:

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 Morphology::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

Return a vector with the section type of every section

property sections

Return a vector containing all section objects

Notes: Soma is not included

property version

Return 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%20Docum entation/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 volumes for each neuronal section

class morphio.GlialCell

Class to represent morphologies of glial cells

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

Return a list of children sections

property diameters

Returns list of section’s point diameters

has_same_shape(arg0: morphio.MitoSection) → bool

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

property id

Return the ID of this section.

property is_root

Return 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

property parent

Return the parent section of this section

Raises:

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 sectionn 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

Return a vector of all root sections

section(section_id: int) → morphio::MitoSection

Return the Section with the given id.

property sections

Return a vector containing all section objects

Notes: Soma is not included

class morphio.MitochondriaPointLevel

Information that is available at the mitochondrial point level (enclosing neuronal section, relative distance to start of neuronal section, diameter)

exception morphio.MorphioError

class morphio.Morphology

Class that gives read access to a Morphology file.

Following RAII, this class is ready to use after the creation and will ensure release of resources upon destruction.

property annotations

Return the annotation object

as_mutable() → morphio::mut::Morphology

property cell_family

Return 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

Return a vector with all diameters from all sections (soma points are not included)

property endoplasmic_reticulum

Return 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

Return the markers

property mitochondria

Return the mitochondria object

property n_points

Returns the number of points from all sections (soma points are not included)

property perimeters

Return a vector with all perimeters from all sections

property points

Return a vector with all points from all sections (soma points are not included)

property root_sections

Return a vector of all root sections (sections whose parent ID are -1)

section(section_id: int) → morphio::Section

Return the Section with the given id.

Raises:

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 Morphology::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

Return a vector with the section type of every section

property sections

Return the Section with the given id.

Raises:

RawDataError if the id is out of range

property soma

Return the soma object

property soma_type

Return the soma type

property version

Return 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

Information that is 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

class morphio.Section

Class representing a Section

property children

Return a list of children sections

property diameters

Return a view (https://github.com/isocpp/CppCoreGuidelines/blob/master/docs/gsl- intro.md#gslspan-what-is-gslspan-and-what-is-it-for) to this section’s point diameters

has_same_shape(arg0: morphio.Section) → bool

Return true if the both sections have the same points, diameters and perimeters

property id

Return the ID of this section.

is_heterogeneous(downstream: bool = True) → bool

Return true if the sections of the tree downstream (downstream = true) or upstream (donwstream = false) have the same section type as the current section.

property is_root

Return 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

Return the parent section of this section

Raises:

MissingParentError is the section doesn’t have a parent.

property perimeters

Return a view (https://github.com/isocpp/CppCoreGuidelines/blob/master/docs/gsl- intro.md#gslspan-what-is-gslspan-and-what-is-it-for) to this section’s point perimeters

property points

Return a view (https://github.com/isocpp/CppCoreGuidelines/blob/master/docs/gsl- intro.md#gslspan-what-is-gslspan-and-what-is-it-for) to this section’s point coordinates

property type

Return the morphological type of this section (dendrite, axon, …)

exception morphio.SectionBuilderError

class morphio.SectionLevel

Information that is 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

custom11

custom12

custom13

custom14

custom15

custom16

custom17

custom18

custom19

glia_perivascular_process

glia_process

spine_head

spine_neck

all

property name

class morphio.Soma

A class to represent a neuron soma.

This class provides functions to query information about the soma of a neuron.

Typically the soma is described as the poly-line of the projection of the soma onto a plane, where the plane normal points in the vertical direction in the local coordinate system of the morphology. In other cases the poly-line is not projected onto a plane, but is an approximation of the countour of the soma as seen in an orhogonal projection down the vertical axis (this is basically the same as before, but the vertical coordinate is not 0 for all the points). This class can also be used for both descriptions as well as somas simply approximated as spheres.

The coordinates system used by a soma will be in the same as the brain::Morphology from where it comes.

@version unstable

property center

Return the center of gravity of the soma points

property diameters

Return 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

Return the coordinates (x,y,z) of all soma points

property surface

the soma surface computation depends on the soma type

Type:

Return the soma surfacen” Note

property type

Return 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

soma_non_conform

no_soma_found

disconnected_neurite

wrong_duplicate

appending_empty_section

wrong_root_point

only_child

write_empty_morphology

zero_diameter

soma_non_contour

soma_non_cylinder_or_point

property name

exception morphio.WriterError

morphio.set_ignored_warning(*args, **kwargs)

Overloaded function.

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

   Set a warning to ignore

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

   Set a warning to ignore

morphio.set_maximum_warnings(arg0: int) → None

Set the maximum number of warnings to be printed on screen

morphio.set_raise_warnings(arg0: bool) → None

Set whether to interpet warning as errors

Mutable objects

class morphio.mut.DendriticSpine

Mutable(editable) morphio::DendriticSpine

append_root_section(*args, **kwargs)

Overloaded function.

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

   Append the existing morphio::Section as a root section

   If recursive == true, all descendent will be appended as well

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

   Append an existing Section as a root section

   If recursive == true, all descendent will be appended as well

property cell_family

The cell family represented by morphio::Morphology.

property post_synaptic_density

Returns the post synaptic density values

property root_sections

Returns all section ids at the tree root

property sections

Returns the dictionary id -> Section for this tree

write(filename: object) → None

class morphio.mut.EndoplasmicReticulum

Mutable(editable) morphio::EndoplasmicReticulum

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

Mutable(editable) morphio::GlialCell

class morphio.mut.MitoSection

Mutable(editable) morphio::MitoSection

append_section(*args, **kwargs)

Overloaded function.

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

   Append a MitoSection

2. append_section(section: morphio.mut.MitoSection, recursive: bool = False) → morphio.mut.MitoSection

   Append a MitoSection

   If recursive == true, all descendent mito sections will be appended as well

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

   Append a MitoSection

   If recursive == true, all descendent mito sections will be appended as well

property diameters

Returns the diameters of all points of this section

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

Return true if the both sections have the same neuriteSectionIds, diameters and pathLengths

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

Mutable(editable) morphio::Mitochondria

append_root_section(*args, **kwargs)

Overloaded function.

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

   Append a new root MitoSection

2. append_root_section(immutable_section: morphio.MitoSection, recursive: bool = True) → morphio::mut::MitoSection

   Append a root MitoSection

   If recursive == true, all descendent mito sections will be appended as well

3. append_root_section(section: morphio::mut::MitoSection, recursive: bool = True) → morphio::mut::MitoSection

   Append a root MitoSection

   If recursive == true, all descendent mito sections will be appended as well

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

Breadth first iterator

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

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

Get the Section children

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

Depth first iterator starting at a given section id

If id == -1, the iteration will start at each root section, successively

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

Return the parent mithochondrial section ID

property root_sections

Return the list of IDs of all mitochondrial root sections (sections whose parent ID are -1)

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

Get the shared pointer for the given section

Note: multiple morphologies can share the same Section instances.

property sections

Returns the dictionary id -> Section for this tree

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

Upstream first iterator

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

Return the annotation objects

append_root_section(*args, **kwargs)

Overloaded function.

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

   Append the existing morphio::Section as a root section

   If recursive == true, all descendent will be appended as well

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

   Append the existing morphio::Section as a root section

   If recursive == true, all descendent will be appended as well

3. append_root_section(mutable_section: morphio::mut::Section, recursive: bool = False) → morphio::mut::Section

   Append the existing morphio::Section as a root section

   If recursive == true, all descendent will be appended as well

as_immutable() → morphio.Morphology

build_read_only() → morphio.Properties

Return the data structure used to create read-only morphologies

property cell_family

Return 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

Return 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

Return the markers from the ASC file

property mitochondria

Return the mitochondria container class

remove_unifurcations() → None

Fixes the morphology single child sections and issues warnings if the section starts and ends are inconsistent

property root_sections

Returns all section ids at the tree root

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

Get the shared pointer for the given section

Note: multiple morphologies can share the same Section instances.

property sections

Returns the dictionary id -> Section for this tree

property soma

Returns a shared pointer on the Soma

Note: multiple morphologies can share the same Soma instance

property soma_type

Return the soma type

property version

Return 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.

1. append_section(point_level_properties: morphio.PointLevel, section_type: morphio.SectionType = <SectionType.undefined: 0>) → morphio.mut.Section

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

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

property children

Return a vector of children IDs

property diameters

@{ Return the diameters of all points of this section

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

Return true if the both sections have the same points, diameters and perimeters

property id

Return the section ID

is_heterogeneous(downstream: bool = True) → bool

Return true if the sections of the tree downstream (downstream = true) or upstream (donwstream = false) have the same section 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

@{ Return the perimeters of all points of this section

property points

@{ Return the coordinates (x,y,z) of all points of this section

property type

@{ Return the morphological type of this section (dendrite, axon, …)

class morphio.mut.Soma

Mutable(editable) morphio::Soma

property center

Return the center of gravity of the soma points

property diameters

Return 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

Return the coordinates (x,y,z) of all soma points

property surface

the soma surface computation depends on the soma type

Type:

Return the soma surface Note

property type

Return the soma type