navis.Viewer¶

class navis.Viewer(picking=False, **kwargs)[source]¶

Vispy 3D viewer.

Parameters:

picking (bool, default = False) – If True, allow selecting neurons by shift-clicking on neurons and placing a 3D cursor via control-click (for OSX: command-click).
**kwargs – Keyword arguments passed to vispy.scene.SceneCanvas.

picking¶

Set to True to allow picking via shift-clicking.

Type:: bool,

selected¶

List of currently selected neurons. Can also be used to set the selection.

Type:: np.array

show_legend¶

Set to True or press L to show legend. This may impact performance.

Type:: bool

legend_font_size¶

Font size for legend.

Type:: int

Examples

This viewer is what navis.plot3d() uses when backend='vispy'. Instead of navis.plot3d() we can interact with the viewer directly:

>>> # Open a 3D viewer
>>> import navis
>>> v = navis.Viewer()
>>> # Close the 3D viewer
>>> v.close()

You can change the background color from the start or on-the-go:

>>> # Set background to green
>>> v = navis.Viewer(bgcolor='green')
>>> # Set background back to white
>>> v.set_bgcolor((1, 1, 1))
>>> # Alternative to v.close():
>>> navis.close3d()

__init__(picking=False, **kwargs)[source]¶

Methods

`__init__`([picking])
`add`(x[, center, clear, combine])	Add objects to canvas.
`center_camera`()	Center camera on visuals.
`clear`()	Clear canvas.
`clear_legend`()	Clear legend.
`close`()	Close viewer.
`colorize`([palette, include_connectors])	Colorize neurons using a seaborn color palette.
`hide_neurons`(n)	Hide given neuron(s).
`hide_selected`()	Hide currently selected neuron(s).
`pin_neurons`(n)	Pin given neuron(s).
`pop`([N])	Remove the most recently added N visuals.
`remove`(to_remove)	Remove given neurons/visuals from canvas.
`remove_bounds`()	Remove bounding box visual.
`screenshot`([filename, pixel_scale, alpha, ...])	Save a screenshot of this viewer.
`set_alpha`(a[, include_connectors])	Set neuron color alphas.
`set_bgcolor`(c)	Set background color.
`set_colors`(c[, include_connectors])	Set neuron color.
`set_view`(view)	(Re-)set camera position.
`show`()	Show viewer.
`toggle_bounds`()	Toggle bounding box.
`toggle_neurons`(n)	Toggle neuron(s) visibility.
`toggle_overlay`()	Toggle legend on and off.
`toggle_picking`()	Toggle picking and overlay text.
`toggle_select`(n)	Toggle selected of given neuron.
`unhide_neurons`([n, check_alpha])	Unhide given neuron(s).
`unpin_neurons`([n])	Unpin given neuron(s).
`update_bounds`([color, width])	Update bounding box visual.
`update_legend`()	Update legend.
`visuals_at`(pos)	List visuals at given canvas position.

Attributes

`bounds`	Bounds of all currently visuals (visible and invisible).
`invisible`	List IDs of currently visible neurons.
`legend_font_size`	Change legend's font size.
`neurons`	Return visible and invisible neuron visuals currently on the canvas.
`objects`	Ordered dictionary {uuid->[visuals]} of all objects in order of addition.
`picking`	Set to `True` to allow picking.
`pinned`	List IDs of currently pinned neurons.
`selected`	Return IDs of or set selected neurons.
`show_bounds`	Set to `True` to show bounding box.
`show_legend`	Set to `True` to hide neuron legend.
`visible`	List IDs of currently visible neurons.
`visuals`	List of all 3D visuals on this canvas.
`canvas`	from PyQt5.QtWidgets import QPushButton