sisl.viz.SitesPlot

class sisl.viz.SitesPlot(sites_obj: BrillouinZone, axes: Axes = ['x', 'y', 'z'], sites: AtomsIndex = None, sites_style: Sequence[AtomsStyleSpec] = [], sites_scale: float = 1.0, sites_name: str = 'Sites', sites_colorscale: Colorscale | None = None, drawing_mode: Literal['scatter', 'balls', 'line', None] = None, show_cell: Literal['box', 'axes', False] = False, cell_style: StyleSpec = {}, nsc: tuple[int, int, int] = (1, 1, 1), sites_ndim_scale: tuple[float, float, float] = (1, 1, 1), dataaxis_1d: np.ndarray | Callable | None = None, arrows: Sequence[AtomArrowSpec] = (), backend='plotly')[source]

Bases: Plot

Plots sites from an object that can be parsed into a geometry.

The only differences between this plot and a geometry plot is the naming of the inputs and the fact that there are no options to plot bonds.

Parameters:

  • sites_obj – The object to be converted to sites.

  • axes – The axes to project the sites to.

  • sites – The sites to plot. If None, all sites are plotted.

  • sites_style – List of style specifications for the sites. See the showcase notebooks for examples.

  • sites_scale – Scaling factor for the size of all sites.

  • sites_name – Name to give to the trace that draws the sites.

  • sites_colorscale – Colorscale to use for the sites in case the color attribute is an array of values. If None, the default colorscale is used for each backend.

  • drawing_mode – The method used to draw the sites.

  • show_cell – Mode to display the reciprocal cell. If False, the cell is not displayed.

  • cell_style – Style specification for the reciprocal cell. See the showcase notebooks for examples.

  • nsc – Number of unit cells to display in each direction.

  • sites_ndim_scale – Scaling factor for the size of the sites for different dimensionalities (1D, 2D, 3D).

  • dataaxis_1d – Only meaningful for 1D plots. The data to plot on the Y axis.

  • arrows – List of arrow specifications to display. See the showcase notebooks for examples.

  • backend – The backend to use to generate the figure.

Methods

evaluate_input_node(node)

final_node_key(*args)

Returns the key of the final (output) node of the workflow.

find_node_key(node, *args)

Returns the identifier key of a node in this workflow

from_func([func, context, module])

Builds a node from a function.

from_node_tree(output_node[, workflow_name])

Creates a workflow class from a node.

function(sites_obj[, axes, sites, ...])

Plots sites from an object that can be parsed into a geometry.

get()

Returns the up to date output of the workflow.

get_diagram_label()

Returns the label to be used in diagrams when displaying this node.

get_input(key)

get_tree()

is_output_outdated(evaluated_inputs)

Checks if the node needs to be ran

map_inputs(inputs, func[, only_nodes, exclude])

Maps all inputs of the node applying a given function.

merge(*others, **kwargs)

plot_class_key()

recursive_update_inputs([cls])

Updates the inputs of the node recursively.

setup(*args, **kwargs)

Sets up the node based on its initial inputs.

update_inputs(**inputs)

Updates the inputs of the workflow.

update_settings(*args, **kwargs)

Attributes

DELETE_KWARG

context

default_inputs

dryrun_nodes

get_syntax

inputs

last_log

Last time the logs of this node were updated

network

nodes

logs

__call__(*args, **kwargs)

Call self as a function.

static evaluate_input_node(node: Node)
classmethod final_node_key(*args) → str

Returns the key of the final (output) node of the workflow.

classmethod find_node_key(node, *args) → str

Returns the identifier key of a node in this workflow

classmethod from_func(func: Callable | None = None, context: dict | None = None, module: str | None = None)

Builds a node from a function.

Parameters:

  • func (function, optional) – The function to be converted to a node.

    If not provided, the return of this method is just a lambda function that expects the function. This is useful if you want to use this method as a decorator while also providing extra arguments (like the context argument).

  • context (dict, optional) – The context to be used as the default for the node class that will be created.

classmethod from_node_tree(output_node: Node, workflow_name: str | None = None)

Creates a workflow class from a node.

It does so by recursively traversing the tree in the inputs direction until it finds the leaves. All the nodes found are included in the workflow. For each node, inputs that are not nodes are connected to the inputs of the workflow.

Parameters:

  • output_node (Node) – The final node, that should be connected to the output of the workflow.

  • workflow_name (str, optional) – The name of the new workflow class. If None, the name of the output node will be used.

Returns:

Workflow – The newly created workflow class.

static function(sites_obj: BrillouinZone, axes: Sequence[Literal['x', 'y', 'z', '-x', '-y', '-z', 'a', 'b', 'c', '-a', '-b', '-c'] | Sequence[float]] = ['x', 'y', 'z'], sites: sisl.typing.AtomsIndex = None, sites_style: Sequence[AtomsStyleSpec] = [], sites_scale: float = 1.0, sites_name: str = 'Sites', sites_colorscale: str | Sequence[Color] | Sequence[tuple[float, Color]] | None = None, drawing_mode: Literal['scatter', 'balls', 'line', None] = None, show_cell: Literal['box', 'axes', False] = False, cell_style: StyleSpec = {}, nsc: tuple[int, int, int] = (1, 1, 1), sites_ndim_scale: tuple[float, float, float] = (1, 1, 1), dataaxis_1d: ndarray | Callable | None = None, arrows: Sequence[AtomArrowSpec] = (), backend='plotly') → Figure

Plots sites from an object that can be parsed into a geometry.

The only differences between this plot and a geometry plot is the naming of the inputs and the fact that there are no options to plot bonds.

Parameters:

  • sites_obj – The object to be converted to sites.

  • axes – The axes to project the sites to.

  • sites – The sites to plot. If None, all sites are plotted.

  • sites_style – List of style specifications for the sites. See the showcase notebooks for examples.

  • sites_scale – Scaling factor for the size of all sites.

  • sites_name – Name to give to the trace that draws the sites.

  • sites_colorscale – Colorscale to use for the sites in case the color attribute is an array of values. If None, the default colorscale is used for each backend.

  • drawing_mode – The method used to draw the sites.

  • show_cell – Mode to display the reciprocal cell. If False, the cell is not displayed.

  • cell_style – Style specification for the reciprocal cell. See the showcase notebooks for examples.

  • nsc – Number of unit cells to display in each direction.

  • sites_ndim_scale – Scaling factor for the size of the sites for different dimensionalities (1D, 2D, 3D).

  • dataaxis_1d – Only meaningful for 1D plots. The data to plot on the Y axis.

  • arrows – List of arrow specifications to display. See the showcase notebooks for examples.

  • backend – The backend to use to generate the figure.

get()

Returns the up to date output of the workflow.

It will recompute it if necessary.

get_diagram_label()

Returns the label to be used in diagrams when displaying this node.

get_input(key: str)
get_tree()
is_output_outdated(evaluated_inputs: Dict[str, Any])

Checks if the node needs to be ran

map_inputs(inputs: Dict[str, Any], func: Callable, only_nodes: bool = False, exclude: Sequence[str] = ()) → Dict[str, Any]

Maps all inputs of the node applying a given function.

It considers the args and kwargs keys.

Parameters:

  • inputs (Dict[str, Any]) – The inputs of the node.

  • func (Callable) – The function to apply to each value.

  • only_nodes (bool, optional) – Whether to apply the function only to nodes, by default False.

  • exclude (Sequence[str], optional) – The keys to exclude from the mapping. This means that these keys are returned as they are.

merge(*others, **kwargs)
classmethod plot_class_key() → str
recursive_update_inputs(cls: Type | Tuple[Type, ...] | None = None, **inputs)

Updates the inputs of the node recursively.

This method updates the inputs of get node and all its children.

Parameters:

  • cls (Optional[Union[Type, Tuple[Type, ]]], optional) – Only update nodes of this class. If None, update all nodes.

  • inputs (Dict[str, Any]) – The inputs to update.

setup(*args, **kwargs)

Sets up the node based on its initial inputs.

update_inputs(**inputs)

Updates the inputs of the workflow.

update_settings(*args, **kwargs)
DELETE_KWARG = <object object>
context: NodeContext = NodeContext({}, {}, {}, {}, {'lazy': True, 'lazy_init': None, 'log_level': 'INFO', 'raise_custom_errors': False, 'on_init': None, 'batch_iter': 'zip'})
property default_inputs
dryrun_nodes: WorkflowNodes = <nodify.workflow.WorkflowNodes object>
get_syntax: Callable[[Any], str] | None = None
property inputs
property last_log: float

Last time the logs of this node were updated

logs: str
network = <nodify.workflow.Network object>
nodes: WorkflowNodes