Backend Sessions¶

These modules are useful when you are subclassing a live backend or adjusting the default scene-building behavior.

NEURON Backend¶

neuron ¶

Public NEURON backend entrypoints for live session authoring.

Classes:

Name	Description
`NeuronSceneBuilder`	Build default morphology geometry and Scene objects for NEURON sessions.
`NeuronSession`	Base class for live NEURON-backed CompNeuroVis sessions.

NeuronSceneBuilder ¶

Build default morphology geometry and Scene objects for NEURON sessions.

Methods:

Name	Description
`build_morphology_geometry`	Convert NEURON sections with pt3d data into MorphologyGeometry.
`build_scene`	Build the default morphology-plus-trace Scene for a NEURON session.

Attributes:

Name	Type	Description
`DISPLAY_FIELD_ID`
`HISTORY_FIELD_ID`
`TRACE_FIELD_ID`

DISPLAY_FIELD_ID `class-attribute` `instance-attribute` ¶

DISPLAY_FIELD_ID = 'segment_display'

HISTORY_FIELD_ID `class-attribute` `instance-attribute` ¶

HISTORY_FIELD_ID = 'segment_history'

TRACE_FIELD_ID `class-attribute` `instance-attribute` ¶

TRACE_FIELD_ID = HISTORY_FIELD_ID

build_morphology_geometry `staticmethod` ¶

build_morphology_geometry(sections)

Convert NEURON sections with pt3d data into MorphologyGeometry.

build_scene `staticmethod` ¶

build_scene(
    *,
    geometry: MorphologyGeometry,
    display_values: ndarray,
    trace_values: ndarray,
    trace_segment_ids: ndarray,
    trace_times: ndarray,
    display_field_id: str | None = None,
    history_field_id: str | None = None,
    display_unit: str | None = None,
    history_unit: str | None = None,
    morphology_color_map: str = "scalar",
    morphology_color_limits: tuple[float, float]
    | None = None,
    morphology_color_norm: str = "auto",
    trace_title: str = "Trace",
    trace_y_label: str = "Value",
    trace_y_unit: str | None = None,
    controls=None,
    actions=None,
    title: str = "CompNeuroVis",
    control_ids: tuple[str, ...] | None = None,
    action_ids: tuple[str, ...] | None = None,
) -> Scene

Build the default morphology-plus-trace Scene for a NEURON session.

NeuronSession ¶

NeuronSession(
    *,
    dt: float = 0.1,
    v_init: float = -65.0,
    max_samples: int = 1000,
    display_dt: float | None = 0.1,
    history_capture_mode: HistoryCaptureMode
    | str = HistoryCaptureMode.ON_DEMAND,
    title: str = "CompNeuroVis",
)

Bases: BufferedSession, ABC

Base class for live NEURON-backed CompNeuroVis sessions.

Methods:

Name	Description
`startup_scene`
`read_updates`
`is_live`
`shutdown`
`emit`
`build_sections`	Return the NEURON sections that define the model morphology.
`setup_model`	Insert mechanisms, stimuli, or recorders after sections are created.
`control_specs`
`action_specs`
`control_order`
`action_order`
`trace_view_updates`
`display_field_id`
`history_field_id`
`display_unit`
`history_unit`
`morphology_color_map`
`morphology_color_limits`
`morphology_color_norm`
`trace_title`
`trace_y_label`
`trace_y_unit`
`apply_control`
`apply_action`
`on_action`
`on_key_press`
`on_entity_clicked`
`should_capture_trace_on_click`
`record`	Register one NEURON variable ref for batched PtrVector sampling.
`record_many`	Register NEURON variable refs for sampling once per fadvance step.
`on_recorded_samples`	Handle one batched set of values registered with record()/record_many().
`build_scene`	Build the initial Scene from sampled values and morphology geometry.
`initialize`	Initialize the NEURON model, sample it once, and return the first Scene.
`recorded_values`
`steps_per_update`
`idle_sleep`
`advance`	Advance the simulation and emit incremental frontend updates.
`handle`

Attributes:

Name	Type	Description
`HISTORY_CAPTURE_ON_DEMAND`
`HISTORY_CAPTURE_FULL`
`dt`
`v_init`
`max_samples`
`display_dt`
`history_capture_mode`
`title`
`sections`
`geometry`

HISTORY_CAPTURE_ON_DEMAND `class-attribute` `instance-attribute` ¶

HISTORY_CAPTURE_ON_DEMAND = ON_DEMAND

HISTORY_CAPTURE_FULL `class-attribute` `instance-attribute` ¶

HISTORY_CAPTURE_FULL = FULL

dt `instance-attribute` ¶

dt = dt

v_init `instance-attribute` ¶

v_init = v_init

max_samples `instance-attribute` ¶

max_samples = max_samples

display_dt `instance-attribute` ¶

display_dt = display_dt

history_capture_mode `instance-attribute` ¶

history_capture_mode = HistoryCaptureMode(
    history_capture_mode
)

title `instance-attribute` ¶

title = title

sections `instance-attribute` ¶

sections = None

geometry `instance-attribute` ¶

geometry = None

startup_scene `classmethod` ¶

startup_scene() -> Scene | None

read_updates ¶

read_updates() -> list[SessionUpdate]

is_live ¶

is_live() -> bool

shutdown ¶

shutdown() -> None

emit ¶

emit(update: SessionUpdate) -> None

build_sections `abstractmethod` ¶

build_sections()

Return the NEURON sections that define the model morphology.

setup_model ¶

setup_model(sections)

Insert mechanisms, stimuli, or recorders after sections are created.

control_specs ¶

control_specs() -> dict[str, ControlSpec]

action_specs ¶

action_specs() -> dict[str, ActionSpec]

control_order ¶

control_order() -> tuple[str, ...] | None

action_order ¶

action_order() -> tuple[str, ...] | None

trace_view_updates ¶

trace_view_updates() -> dict[str, Any]

display_field_id ¶

display_field_id() -> str

history_field_id ¶

history_field_id() -> str

display_unit ¶

display_unit() -> str | None

history_unit ¶

history_unit() -> str | None

morphology_color_map ¶

morphology_color_map() -> str

morphology_color_limits ¶

morphology_color_limits() -> tuple[float, float] | None

morphology_color_norm ¶

morphology_color_norm() -> str

trace_title ¶

trace_title() -> str

trace_y_label ¶

trace_y_label() -> str

trace_y_unit ¶

trace_y_unit() -> str

apply_control ¶

apply_control(control_id: str, value) -> bool

apply_action ¶

apply_action(
    action_id: str, payload: dict[str, object]
) -> bool

on_action ¶

on_action(
    action_id: str, payload: dict[str, Any], context
) -> bool

on_key_press ¶

on_key_press(key: str, context) -> bool

on_entity_clicked ¶

on_entity_clicked(entity_id: str, context) -> bool

should_capture_trace_on_click ¶

should_capture_trace_on_click(
    entity_id: str, context
) -> bool

record ¶

record(name: str, ref: Any) -> None

Register one NEURON variable ref for batched PtrVector sampling.

record_many ¶

record_many(
    names: Sequence[str], refs: Sequence[Any]
) -> None

Register NEURON variable refs for sampling once per fadvance step.

on_recorded_samples ¶

on_recorded_samples(
    times: ndarray, values: dict[str, ndarray]
) -> None

Handle one batched set of values registered with record()/record_many().

build_scene ¶

build_scene(
    *, geometry, display_values: ndarray, time_value: float
) -> Scene

Build the initial Scene from sampled values and morphology geometry.

initialize ¶

initialize()

Initialize the NEURON model, sample it once, and return the first Scene.

recorded_values ¶

recorded_values() -> dict[str, float]

steps_per_update ¶

steps_per_update() -> int

idle_sleep ¶

idle_sleep() -> float

advance ¶

advance() -> None

Advance the simulation and emit incremental frontend updates.

handle ¶

handle(command) -> None

Jaxley Backend¶

jaxley ¶

Public Jaxley backend entrypoints for live session authoring.

Classes:

Name	Description
`JaxleySceneBuilder`	Build default morphology geometry and Scene objects for Jaxley sessions.
`JaxleySession`	Base class for live Jaxley-backed CompNeuroVis sessions.

JaxleySceneBuilder ¶

Build default morphology geometry and Scene objects for Jaxley sessions.

Methods:

Name	Description
`build_morphology_geometry`	Convert Jaxley morphology/network data into MorphologyGeometry.
`build_scene`	Build the default morphology-plus-trace Scene for a Jaxley session.

Attributes:

Name	Type	Description
`DISPLAY_FIELD_ID`
`HISTORY_FIELD_ID`
`TRACE_FIELD_ID`

DISPLAY_FIELD_ID `class-attribute` `instance-attribute` ¶

DISPLAY_FIELD_ID = 'segment_display'

HISTORY_FIELD_ID `class-attribute` `instance-attribute` ¶

HISTORY_FIELD_ID = 'segment_history'

TRACE_FIELD_ID `class-attribute` `instance-attribute` ¶

TRACE_FIELD_ID = HISTORY_FIELD_ID

build_morphology_geometry `staticmethod` ¶

build_morphology_geometry(
    nodes,
    *,
    xyzr: list[ndarray] | tuple[ndarray, ...] | None = None,
    cell_names: list[str] | tuple[str, ...] | None = None,
) -> MorphologyGeometry

Convert Jaxley morphology/network data into MorphologyGeometry.

build_scene `staticmethod` ¶

build_scene(
    *,
    geometry: MorphologyGeometry,
    display_values: ndarray,
    trace_values: ndarray,
    trace_segment_ids: ndarray,
    trace_times: ndarray,
    display_field_id: str | None = None,
    history_field_id: str | None = None,
    display_unit: str | None = None,
    history_unit: str | None = None,
    morphology_color_map: str = "scalar",
    morphology_color_limits: tuple[float, float]
    | None = None,
    morphology_color_norm: str = "auto",
    trace_title: str = "Trace",
    trace_y_label: str = "Value",
    trace_y_unit: str | None = None,
    controls=None,
    actions=None,
    title: str = "CompNeuroVis",
    control_ids: tuple[str, ...] | None = None,
    action_ids: tuple[str, ...] | None = None,
) -> Scene

Build the default morphology-plus-trace Scene for a Jaxley session.

JaxleySession ¶

JaxleySession(
    *,
    dt: float = 0.1,
    v_init: float = -70.0,
    max_samples: int = 1000,
    display_dt: float | None = 0.1,
    history_capture_mode: HistoryCaptureMode
    | str = HistoryCaptureMode.ON_DEMAND,
    title: str = "CompNeuroVis",
)

Bases: BufferedSession, ABC

Base class for live Jaxley-backed CompNeuroVis sessions.

Methods:

Name	Description
`startup_scene`
`read_updates`
`is_live`
`shutdown`
`emit`
`build_cells`	Return one Jaxley cell or an iterable of cells for the session.
`build_network`	Build the Jaxley network from the returned cells.
`setup_model`	Configure channels, stimuli, recordings, or other runtime setup.
`cell_names`
`control_specs`
`action_specs`
`control_order`
`action_order`
`trace_view_updates`
`display_field_id`
`history_field_id`
`display_unit`
`history_unit`
`morphology_color_map`
`morphology_color_limits`
`morphology_color_norm`
`trace_title`
`trace_y_label`
`trace_y_unit`
`apply_control`
`apply_action`
`on_action`
`on_key_press`
`on_entity_clicked`
`should_capture_trace_on_click`
`build_scene`	Build the initial Scene from sampled values and morphology geometry.
`initialize`	Initialize the Jaxley model, sample it once, and return the first Scene.
`steps_per_update`
`idle_sleep`
`refresh_runtime_parameters`
`refresh_runtime_externals`
`advance`	Advance the simulation and emit incremental frontend updates.
`handle`

Attributes:

Name	Type	Description
`HISTORY_CAPTURE_ON_DEMAND`
`HISTORY_CAPTURE_FULL`
`dt`
`v_init`
`max_samples`
`display_dt`
`history_capture_mode`
`title`
`cells`
`network`
`geometry`

HISTORY_CAPTURE_ON_DEMAND `class-attribute` `instance-attribute` ¶

HISTORY_CAPTURE_ON_DEMAND = ON_DEMAND

HISTORY_CAPTURE_FULL `class-attribute` `instance-attribute` ¶

HISTORY_CAPTURE_FULL = FULL

dt `instance-attribute` ¶

dt = dt

v_init `instance-attribute` ¶

v_init = v_init

max_samples `instance-attribute` ¶

max_samples = max_samples

display_dt `instance-attribute` ¶

display_dt = display_dt

history_capture_mode `instance-attribute` ¶

history_capture_mode = HistoryCaptureMode(
    history_capture_mode
)

title `instance-attribute` ¶

title = title

cells `instance-attribute` ¶

cells = None

network `instance-attribute` ¶

network = None

geometry `instance-attribute` ¶

geometry = None

startup_scene `classmethod` ¶

startup_scene() -> Scene | None

read_updates ¶

read_updates() -> list[SessionUpdate]

is_live ¶

is_live() -> bool

shutdown ¶

shutdown() -> None

emit ¶

emit(update: SessionUpdate) -> None

build_cells `abstractmethod` ¶

build_cells() -> Iterable['jx.Cell'] | 'jx.Cell'

Return one Jaxley cell or an iterable of cells for the session.

build_network ¶

build_network(cells: list['jx.Cell'])

Build the Jaxley network from the returned cells.

setup_model ¶

setup_model(network, cells)

Configure channels, stimuli, recordings, or other runtime setup.

cell_names ¶

cell_names(cells: list['jx.Cell']) -> list[str]

control_specs ¶

control_specs() -> dict[str, ControlSpec]

action_specs ¶

action_specs() -> dict[str, ActionSpec]

control_order ¶

control_order() -> tuple[str, ...] | None

action_order ¶

action_order() -> tuple[str, ...] | None

trace_view_updates ¶

trace_view_updates() -> dict[str, Any]

display_field_id ¶

display_field_id() -> str

history_field_id ¶

history_field_id() -> str

display_unit ¶

display_unit() -> str | None

history_unit ¶

history_unit() -> str | None

morphology_color_map ¶

morphology_color_map() -> str

morphology_color_limits ¶

morphology_color_limits() -> tuple[float, float] | None

morphology_color_norm ¶

morphology_color_norm() -> str

trace_title ¶

trace_title() -> str

trace_y_label ¶

trace_y_label() -> str

trace_y_unit ¶

trace_y_unit() -> str

apply_control ¶

apply_control(control_id: str, value) -> bool

apply_action ¶

apply_action(
    action_id: str, payload: dict[str, object]
) -> bool

on_action ¶

on_action(
    action_id: str, payload: dict[str, Any], context
) -> bool

on_key_press ¶

on_key_press(key: str, context) -> bool

on_entity_clicked ¶

on_entity_clicked(entity_id: str, context) -> bool

should_capture_trace_on_click ¶

should_capture_trace_on_click(
    entity_id: str, context
) -> bool

build_scene ¶

build_scene(
    *, geometry, display_values: ndarray, time_value: float
) -> Scene

Build the initial Scene from sampled values and morphology geometry.

initialize ¶

initialize()

Initialize the Jaxley model, sample it once, and return the first Scene.

steps_per_update ¶

steps_per_update() -> int

idle_sleep ¶

idle_sleep() -> float

refresh_runtime_parameters ¶

refresh_runtime_parameters(
    *, preserve_state: bool = True
) -> None

refresh_runtime_externals ¶

refresh_runtime_externals() -> None

advance ¶

advance() -> None

Advance the simulation and emit incremental frontend updates.

handle ¶

handle(command) -> None

Backend Sessions¶

NEURON Backend¶

neuron ¶

NeuronSceneBuilder ¶

DISPLAY_FIELD_ID class-attribute instance-attribute ¶

HISTORY_FIELD_ID class-attribute instance-attribute ¶

TRACE_FIELD_ID class-attribute instance-attribute ¶

build_morphology_geometry staticmethod ¶

build_scene staticmethod ¶

NeuronSession ¶

HISTORY_CAPTURE_ON_DEMAND class-attribute instance-attribute ¶

HISTORY_CAPTURE_FULL class-attribute instance-attribute ¶

dt instance-attribute ¶

v_init instance-attribute ¶

max_samples instance-attribute ¶

display_dt instance-attribute ¶

history_capture_mode instance-attribute ¶

title instance-attribute ¶

sections instance-attribute ¶

geometry instance-attribute ¶

startup_scene classmethod ¶

read_updates ¶

is_live ¶

shutdown ¶

emit ¶

build_sections abstractmethod ¶

setup_model ¶

control_specs ¶

action_specs ¶

control_order ¶

action_order ¶

trace_view_updates ¶

display_field_id ¶

history_field_id ¶

display_unit ¶

history_unit ¶

morphology_color_map ¶

morphology_color_limits ¶

morphology_color_norm ¶

trace_title ¶

trace_y_label ¶

trace_y_unit ¶

apply_control ¶

apply_action ¶

on_action ¶

on_key_press ¶

on_entity_clicked ¶

should_capture_trace_on_click ¶

record ¶

record_many ¶

on_recorded_samples ¶

build_scene ¶

initialize ¶

recorded_values ¶

steps_per_update ¶

idle_sleep ¶

advance ¶

handle ¶

Jaxley Backend¶

jaxley ¶

JaxleySceneBuilder ¶

DISPLAY_FIELD_ID class-attribute instance-attribute ¶

HISTORY_FIELD_ID class-attribute instance-attribute ¶

TRACE_FIELD_ID class-attribute instance-attribute ¶

build_morphology_geometry staticmethod ¶

build_scene staticmethod ¶

JaxleySession ¶

HISTORY_CAPTURE_ON_DEMAND class-attribute instance-attribute ¶

HISTORY_CAPTURE_FULL class-attribute instance-attribute ¶

dt instance-attribute ¶

v_init instance-attribute ¶

max_samples instance-attribute ¶

display_dt instance-attribute ¶

history_capture_mode instance-attribute ¶

title instance-attribute ¶

cells instance-attribute ¶

network instance-attribute ¶

geometry instance-attribute ¶

startup_scene classmethod ¶

read_updates ¶

DISPLAY_FIELD_ID `class-attribute` `instance-attribute` ¶

HISTORY_FIELD_ID `class-attribute` `instance-attribute` ¶

TRACE_FIELD_ID `class-attribute` `instance-attribute` ¶

build_morphology_geometry `staticmethod` ¶

build_scene `staticmethod` ¶

HISTORY_CAPTURE_ON_DEMAND `class-attribute` `instance-attribute` ¶

HISTORY_CAPTURE_FULL `class-attribute` `instance-attribute` ¶

dt `instance-attribute` ¶

v_init `instance-attribute` ¶

max_samples `instance-attribute` ¶

display_dt `instance-attribute` ¶

history_capture_mode `instance-attribute` ¶

title `instance-attribute` ¶

sections `instance-attribute` ¶

geometry `instance-attribute` ¶

startup_scene `classmethod` ¶

build_sections `abstractmethod` ¶

DISPLAY_FIELD_ID `class-attribute` `instance-attribute` ¶

HISTORY_FIELD_ID `class-attribute` `instance-attribute` ¶

TRACE_FIELD_ID `class-attribute` `instance-attribute` ¶

build_morphology_geometry `staticmethod` ¶

build_scene `staticmethod` ¶

HISTORY_CAPTURE_ON_DEMAND `class-attribute` `instance-attribute` ¶

HISTORY_CAPTURE_FULL `class-attribute` `instance-attribute` ¶

dt `instance-attribute` ¶

v_init `instance-attribute` ¶

max_samples `instance-attribute` ¶

display_dt `instance-attribute` ¶

history_capture_mode `instance-attribute` ¶

title `instance-attribute` ¶

cells `instance-attribute` ¶

network `instance-attribute` ¶

geometry `instance-attribute` ¶

startup_scene `classmethod` ¶

build_cells `abstractmethod` ¶