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 pressL
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 whenbackend='vispy'
. Instead ofnavis.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()
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 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.
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.
Set to
True
to allow picking.pinned
List IDs of currently pinned neurons.
Return IDs of or set selected neurons.
show_bounds
Set to
True
to show bounding box.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