plugins¶

Plugins subpackage.

It includes all science related features and optional components.

atlas¶

class AtlasColumnHighlight(position: ~brayns.plugins.atlas.ColumnPosition, color: ~brayns.utils.color.Color4, neighbors: list[~brayns.plugins.atlas.ColumnNeighbor] = <factory>)¶

Bases: AtlasUsecase

Place a column and (optionally) its neighbors.

Columns are always aligned on the Y axis so their position uses only XZ.

Parameters:

position (ColumnPosition) – Column coordinates.
color (Color4) – Color to apply to the column.
neighbors (list[ColumnNeighbor], optional) – Neighbors to color, defaults to empty.

color: Color4¶

get_properties() → dict[str, Any]¶: Low level API.

class property name: str¶: Low level API.

neighbors: list[ColumnNeighbor]¶

position: ColumnPosition¶

class AtlasDensity¶

Bases: AtlasUsecase

Display the volume density.

The relation between the density and the color can be changed using the color ramp of the model created.

get_properties() → dict[str, Any]¶: Low level API.

class property name: str¶: Low level API.

class AtlasDistanceType(value)¶

Bases: Enum

Type of distance displayed for an atlas layer.

Params LOWER:: Distance of the current layer from the one below.
Params UPPER:: Distance of the current layer from the one above.

LOWER = 'lower'¶

UPPER = 'upper'¶

class AtlasFlatmapAreas¶

Bases: AtlasUsecase

Display the volumne flatmap areas.

get_properties() → dict[str, Any]¶: Low level API.

class property name: str¶: Low level API.

class AtlasLayerDistance(distance_type: AtlasDistanceType)¶

Bases: AtlasUsecase

Display the volume as the distance of a layer from its neighbors.

distance_type: AtlasDistanceType¶

get_properties() → dict[str, Any]¶: Low level API.

class property name: str¶: Low level API.

class AtlasOrientationField¶

Bases: AtlasUsecase

Display the volume data as an orientation field.

get_properties() → dict[str, Any]¶: Low level API.

class property name: str¶: Low level API.

class AtlasShellOutline¶

Bases: AtlasUsecase

Display the volume using its shell outline.

This is the default atlas volume usecase and is always supported.

get_properties() → dict[str, Any]¶: Low level API.

class property name: str¶: Low level API.

class AtlasUsecase¶

Bases: ABC

Base class for all atlas visualization usecases.

abstract get_properties() → dict[str, Any]¶: Low level API.

abstract class property name: str¶: Low level API.

run(instance: Instance, model_id: int) → Model¶

Create a model to visualize the usecase on an atlas volume.

Parameters:

instance (Instance) – Instance.
model_id (int) – ID of the atlas volume model.

Returns:

Model created for the usecase.

Return type:

Model

class ColumnNeighbor(position: ColumnPosition, color: Color4)¶

Bases: object

Column neighbor position and color.

The position is relative to the main column coordinates.

color: Color4¶

position: ColumnPosition¶

class ColumnPosition(x: int = 0, z: int = 0)¶

Bases: Vector[int]

Column position XZ.

Parameters:

x (float) – X component.
z (float) – Z component.

property x: float¶

property z: float¶

get_atlas_usecases(instance: Instance, model_id: int) → list[tuple[str, JsonSchema]]¶

Return the list of visualization usecases supported by an atlas volume.

Parameters:

instance (Instance) – Instance.
model_id (int) – ID of the atlas volume model.

Returns:

Names of the supported usecase (see AtlasUsecase.name)

Return type:

list[str]

cell_placement¶

class CellPlacementLoader(morphologies_folder: str = '', density: float = 1.0, extension: str | None = None, ids: list[int] | None = None, morphology: Morphology = <factory>)¶

Bases: Loader

Partial circuit loader.

Loads the cells from the circuit builder intermediate files.

To load morphologies, a base folder must be specified as the H5 file only contains filenames.

Parameters:

morphologies_folder (str) – Path to the folder containing the morphologies.
density (float, optional) – Density of morphologies to load [0-1].
extension (str | None, optional) – Morphology file extension (will be guessed from folder if empty).
ids (list[str] | None, optional) – IDs of the nodes to load, overrides density if not None.
morphology (Morphology, optional) – Morphology settings.

density: float = 1.0¶

extension: str | None = None¶

get_properties() → dict[str, Any]¶: Low level API to serialize to JSON.

ids: list[int] | None = None¶

morphologies_folder: str = ''¶

morphology: Morphology¶

class property name: str¶

Get the loader name.

Can be compared with LoaderInfo.name.

Returns:: Loader name.
Return type:: str

circuit¶

class CircuitColorMethod¶

Bases: object

Available coloring methods for circuits.

ETYPE: ClassVar[str] = 'etype'¶

HEMISPHERE: ClassVar[str] = 'hemisphere'¶

ID: ClassVar[str] = 'id'¶

LAYER: ClassVar[str] = 'layer'¶

MORPHOLOGY: ClassVar[str] = 'morphology'¶

MORPHOLOGY_CLASS: ClassVar[str] = 'morphology class'¶

MORPHOLOGY_SECTION: ClassVar[str] = 'morphology section'¶

MTYPE: ClassVar[str] = 'mtype'¶

REGION: ClassVar[str] = 'region'¶

SUBREGION: ClassVar[str] = 'subregion'¶

SYNAPSE_CLASS: ClassVar[str] = 'synapse class'¶

get_circuit_ids(instance: Instance, model_id: int) → list[int]¶

Retreive the list of loaded neurons / astrocytes / vasculatures by ID.

Parameters:

instance (Instance) – Instance.
model_id (int) – ID of the circuit model.

Returns:

ID list of the element loaded in given circuit.

Return type:

list[int]

set_circuit_thickness(instance: Instance, model_id: int, radius_multiplier: float) → None¶

Multiply the radius of all primitives of a circuit by given factor.

Parameters:

instance (Instance) – Instance.
model_id (int) – Circuit model ID.
radius_multiplier (float) – Scaling factor for capsules and spheres.

morphology¶

class GeometryType(value)¶

Bases: Enum

Type of geometry to use when loading a morphology.

Parameters:

ORIGINAL – Use raw geometries dimensions.
SMOOTH – Smooth radius changes between geometries for better visual.
SECTION_SMOOTH – Smooth radius change between whole sections.
CONSTANT_RADII – Apply the same radius to all geometries.

CONSTANT_RADII = 'constant_radii'¶

ORIGINAL = 'original'¶

SECTION_SMOOTH = 'section_smooth'¶

SMOOTH = 'smooth'¶

SPHERES = 'spheres'¶

class Morphology(radius_multiplier: float = 1.0, load_soma: bool = False, load_axon: bool = False, load_dendrites: bool = False, geometry_type: GeometryType = GeometryType.SMOOTH, resampling: float = 2, subsampling: int = 1)¶

Bases: object

Describe how to load a morphology.

If no sections are selected (default), a sphere of radius_multiplier is used.

Parameters:

radius_multiplier (float, optional) – Radius scaling, defaults to 1.
load_soma (bool, optional) – Wether to load somas, defaults to False.
load_axon (bool, optional) – Wether to load axons, defaults to False.
load_dendrites (bool, optional) – Wether to load dendrites, defaults to False.
geometry_type (GeometryType, optional) – How to load geometries, defaults to smooth.
resampling (float, optional) – Min cos of angle between two segments to merge them (disabled if > 1).
subsampling (int, optional) – Step factor to skip morphology samples.

static full() → Morphology¶

Return settings to load all sections of a morphology.

Returns:: Morphology: Settings for full morphology loading.

geometry_type: GeometryType = 'smooth'¶

load_axon: bool = False¶

load_dendrites: bool = False¶

load_soma: bool = False¶

radius_multiplier: float = 1.0¶

resampling: float = 2¶

subsampling: int = 1¶

class MorphologyColorMethod¶

Bases: object

Available coloring methods for morphologies.

MORPHOLOGY_SECTION: ClassVar[str] = 'morphology section'¶

MORPHOLOGY_SECTION_GEOMETRY: ClassVar[str] = 'morphology section geometry'¶

class MorphologyLoader(morphology: ~brayns.plugins.morphology.Morphology = <factory>)¶

Bases: Loader

Loader for morphology files.

Parameters:: morphology (Morphology, optional) – How to load the morphologies, default constructed.

ASC: ClassVar[str] = 'asc'¶

H5: ClassVar[str] = 'h5'¶

SWC: ClassVar[str] = 'swc'¶

get_properties() → dict[str, Any]¶: Low level API to serialize to JSON.

morphology: Morphology¶

class property name: str¶

Get the loader name.

Can be compared with LoaderInfo.name.

Returns:: Loader name.
Return type:: str

nrrd¶

class NrrdLoader(voxel_type: VoxelType)¶

Bases: Loader

Loader for NRRD volumes.

Parameters:: voxel_type (VoxelType) – Defines the representation of the volume voxels.

NRRD: ClassVar[str] = 'nrrd'¶

get_properties() → dict[str, Any]¶: Low level API to serialize to JSON.

class property name: str¶

Get the loader name.

Can be compared with LoaderInfo.name.

Returns:: Loader name.
Return type:: str

voxel_type: VoxelType¶

class VoxelType(value)¶

Bases: Enum

Defines the representation of the voxels of an NRRD volume.

Parameters:

SCALAR – Each voxel holds a single scalar value.
ORIENTATION – Each voxel holds a quaternion (orientation field).
FLATMAP – Each voxel is a pair of integer.

FLATMAP = 'flatmap'¶

ORIENTATION = 'orientation'¶

SCALAR = 'scalar'¶

sonata¶

class SonataEdgePopulation(name: str, afferent: bool, density: float = 1.0, radius: float = 2.0, report: str | None = None)¶

Bases: object

SONATA edge population parameters.

Parameters:

name (str) – Population name.
afferent (bool) – If these edges are afferent or efferent ones.
afferent – If these edges are afferent ones.
density (float, optional) – Proportion of edges to load, defaults to 1.
radius (float, optional) – Edge radii, defaults to 2.
report (str | None, optional) – Report name, defaults to None.

afferent: bool¶

density: float = 1.0¶

name: str¶

radius: float = 2.0¶

report: str | None = None¶

class SonataLoader(node_populations: list[SonataNodePopulation])¶

Bases: Loader

Loader for SONATA circuit files.

Parameters:: node_populations (list[SonataNodePopulation]) – Nodes to load.

JSON: ClassVar[str] = 'json'¶

get_properties() → dict[str, Any]¶: Low level API to serialize to JSON.

class property name: str¶

Get the loader name.

Can be compared with LoaderInfo.name.

Returns:: Loader name.
Return type:: str

node_populations: list[SonataNodePopulation]¶

class SonataNodePopulation(name: str, nodes: SonataNodes = <factory>, report: SonataReport | None = None, edges: list[SonataEdgePopulation] | None = None, morphology: Morphology = <factory>, vasculature_radius_multiplier: float = 1.0)¶

Bases: object

SONATA node population parameters.

Parameters:

name (str) – Population name.
nodes (SonataNodes, optional) – Nodes to load, defaults to 0.01% of all nodes.
report (SonataReport | None, optional) – Report to load, defaults to None.
edges (list[SonataEdgePopulation] | None, optional) – Edges to load, defaults to None.
morphology (Morphology, optional) – How to load the morphologies, default constructed.
vasculature_radius_multiplier (float, optional) – Vasculature scale, defaults to 1.

edges: list[SonataEdgePopulation] | None = None¶

morphology: Morphology¶

name: str¶

nodes: SonataNodes¶

report: SonataReport | None = None¶

vasculature_radius_multiplier: float = 1.0¶

class SonataNodes(density: float | None = None, names: list[str] | None = None, ids: list[int] | None = None, node_count_limit: int | None = None)¶

Bases: object

Specify how to load SONATA nodes.

Use one of the factory methods to create this object.

static all() → SonataNodes¶: Load all nodes.

static default() → SonataNodes¶: Load a reasonable proportion of nodes.

density: float | None = None¶

static from_density(density: float) → SonataNodes¶: Load a proportion of all nodes (0 = none, 1 = all).

static from_ids(ids: list[int]) → SonataNodes¶: Load nodes with given IDs.

static from_names(names: list[str], density: float = 1.0) → SonataNodes¶: Load from node group names with optional density.

ids: list[int] | None = None¶

limit(node_count_limit: int) → SonataNodes¶: Limit the number nodes to be loaded.

names: list[str] | None = None¶

node_count_limit: int | None = None¶

class SonataReport(type: SonataReportType, name: str | None = None, spike_transition_time: float | None = None)¶

Bases: object

Describe a SONATA report to load.

Use one of the factory methods to create this object.

static bloodflow_pressure(name: str) → SonataReport¶: Bloodflow pressure report with given name.

static bloodflow_radii(name: str) → SonataReport¶: Bloodflow radii report with given name.

static bloodflow_speed(name: str) → SonataReport¶: Bloodflow speed report with given name.

static compartment(name: str) → SonataReport¶: Compartment report with given name.

name: str | None = None¶

static none() → SonataReport¶: No report to load.

spike_transition_time: float | None = None¶

static spikes(spike_transition_time: float = 1.0) → SonataReport¶: Spike report with transition time (units from report).

static summation(name: str) → SonataReport¶: Simulation report with given name.

static synapse(name: str) → SonataReport¶: Synapse report with given name.

type: SonataReportType¶

class SonataReportType(value)¶

Bases: Enum

All available SONATA report types.

BLOODFLOW_PRESSURE = 'bloodflow_pressure'¶

BLOODFLOW_RADII = 'bloodflow_radii'¶

BLOODFLOW_SPEED = 'bloodflow_speed'¶

COMPARTMENT = 'compartment'¶

NONE = 'none'¶

SPIKES = 'spikes'¶

SUMMATION = 'summation'¶

SYNAPSE = 'synapse'¶