spateo.plotting.static.three_d_plot.backbone_plots#

Module Contents#

Functions#

backbone(backbone_model[, backbone_key, ...])

Visualize constructed 3D backbone model.
spateo.plotting.static.three_d_plot.backbone_plots.backbone(backbone_model: pyvista.PolyData, backbone_key: str = 'backbone', backbone_model_size: float | int = 8, backbone_colormap: str | None = None, backbone_ambient: float | list = 0.2, backbone_opacity: float | numpy.ndarray | list = 1.0, nodes_key: str | None = 'nodes', nodes_label_size: float | int = 18, bg_model: pyvista.PolyData | pyvista.UnstructuredGrid | pyvista.MultiBlock | None = None, bg_key: str | list | None = None, bg_model_style: Literal[points, surface, wireframe] | list = 'points', bg_model_size: float | list = 10, bg_colormap: str | list | None = None, bg_ambient: float | list = 0.2, bg_opacity: float | numpy.ndarray | list = 0.6, show_axes: bool = True, show_legend: bool = True, legend_kwargs: dict | None = None, filename: str | None = None, jupyter: bool | Literal[none, static, trame] = False, off_screen: bool = False, window_size: tuple = (2048, 2048), background: str = 'white', cpo: str | list = 'iso', **kwargs)[source]#

Visualize constructed 3D backbone model.

Parameters:
backbone_model

The constructed backbone model.

backbone_key

Any point_data names or cell_data names to be used for coloring backbone_model.

backbone_model_size

The thickness of backbone.

backbone_colormap

Name of the Matplotlib colormap to use when mapping the scalars of backbone_model.

When the colormap is None, use {key}_rgba to map the scalars, otherwise use the colormap to map scalars.

backbone_ambient

When lighting is enabled, this is the amount of light in the range of 0 to 1 (default 0.0) that reaches the actor when not directed at the light source emitted from the viewer.

backbone_opacity

Opacity of the model.

If a single float value is given, it will be the global opacity of the model and uniformly applied everywhere, elif a numpy.ndarray with single float values is given, it will be the opacity of each point. - should be between 0 and 1.

A string can also be specified to map the scalars range to a predefined opacity transfer function (options include: ‘linear’, ‘linear_r’, ‘geom’, ‘geom_r’).

nodes_key

The key that corresponds to the coordinates of the nodes in the backbone.

nodes_label_size

Sets the size of the title font.

bg_model

The background model used to construct backbone model.

bg_key

Any point_data names or cell_data names to be used for coloring bg_model.

bg_model_style

Visualization style of bg_model. One of the following:

  • bg_model_style = 'surface',

  • bg_model_style = 'wireframe',

  • bg_model_style = 'points'.

bg_model_size

If bg_model_style = 'points', point size of any nodes in the dataset plotted.

If bg_model_style = 'wireframe', thickness of lines.

bg_colormap

Name of the Matplotlib colormap to use when mapping the scalars of bg_model.

When the colormap is None, use {key}_rgba to map the scalars, otherwise use the colormap to map scalars.

bg_ambient

When lighting is enabled, this is the amount of light in the range of 0 to 1 (default 0.0) that reaches the actor when not directed at the light source emitted from the viewer.

bg_opacity

Opacity of the model.

If a single float value is given, it will be the global opacity of the model and uniformly applied everywhere, elif a numpy.ndarray with single float values is given, it will be the opacity of each point. - should be between 0 and 1.

A string can also be specified to map the scalars range to a predefined opacity transfer function (options include: ‘linear’, ‘linear_r’, ‘geom’, ‘geom_r’).

show_axes

Whether to add a camera orientation widget to the active renderer.

show_legend

whether to add a legend of bg_model to the plotter.

legend_kwargs

A dictionary that will be pass to the add_legend function. By default, it is an empty dictionary and the add_legend function will use the {"legend_size": None, "legend_loc": None,  "legend_size": None, "legend_loc": None, "title_font_size": None, "label_font_size": None, "font_family": "arial", "fmt": "%.2e", "n_labels": 5, "vertical": True} as its parameters. Otherwise, you can provide a dictionary that properly modify those keys according to your needs.

filename

Filename of output file. Writer type is inferred from the extension of the filename.

  • Output an image file,please enter a filename ending with '.png', '.tif', '.tiff', '.bmp', '.jpeg', '.jpg', '.svg', '.eps', '.ps', '.pdf', '.tex'. When jupyter=False, if you want to save ‘.png’ file, please ensure off_screen=True.

jupyter

Whether to plot in jupyter notebook. Available jupyter are:

  • 'none' - Do not display in the notebook.

  • 'trame' - Show a trame widget

  • 'static' - Display a static figure.

off_screen

Renders off-screen when True. Useful for automated screenshots.

window_size

Window size in pixels. The default window_size is [512, 512].

background

The background color of the window.

cpo

Camera position of the active render window. Available cpo are:

  • Iterable containing position, focal_point, and view up.

    E.g.: [(2.0, 5.0, 13.0), (0.0, 0.0, 0.0), (-0.7, -0.5, 0.3)].

  • Iterable containing a view vector.

    E.g.: [-1.0, 2.0, -5.0].

  • A string containing the plane orthogonal to the view direction.

    E.g.: 'xy', 'xz', 'yz', 'yx', 'zx', 'zy', 'iso'.

**kwargs

Additional parameters that will be passed to .add_point_labels function.

Returns:

List of camera position, focal point, and view up.

Returned only if filename is None or filename ending with '.png', '.tif', '.tiff', '.bmp', '.jpeg', '.jpg', '.svg', '.eps', '.ps', '.pdf', '.tex'.

img: Numpy array of the last image.

Returned only if filename is None or filename ending with '.png', '.tif', '.tiff', '.bmp', '.jpeg', '.jpg', '.svg', '.eps', '.ps', '.pdf', '.tex'.

Return type:

cpo