ibl_alignment_gui.plugins.datoviz_3d

Functions

`callback`	Open the 3D viewer.
`create_random_color`	Create a random hex color code.
`data_to_colors`	Convert data values to RGBA color codes.
`get_regions`	Get unique brain regions that the shank passes through.
`get_xyz_picks`	Get the xyz coordinates of the picks for the shank.
`setup`	Set up the 3D Features plugin.
`update_channels`	Get the channel data for the chosen plot.
`update_clusters`	Get the cluster data for the chosen plot.

Classes

`Features3D`	A class to manage viewing features in a 3D Urchin viewer.
`Viewer3D`	Popup window hosting the datoviz 3D scene and its display controls.

class ibl_alignment_gui.plugins.datoviz_3d.Features3D(controller)[source] 

Bases: object

A class to manage viewing features in a 3D Urchin viewer.

Parameters:

controller (AlignmentGUIController) – The main application controller.

Variables:

controller (AlignmentGUIController) – The main application controller.
particles (oursin.particles.ParticleSystem or None) – The particle system for displaying points.
markers (oursin.particles.ParticleSystem or None) – The particle system for displaying markers.
regions (list or np.ndarray) – The list of brain regions displayed.
texts (list) – The list of text objects displayed.
point_size (float) – The size of the points displayed.
plot (str) – The type of plot currently displayed (‘channels’ or ‘clusters’).
plot_type (str or None) – The specific plot name currently displayed.
side (oursin.utils.Side) – The hemisphere side for displaying regions.
region_toggle (QtWidgets.QAction or None) – The action to toggle region visibility.
ba (AllenAtlas) – A brain atlas instance.

add_regions(regions, hemisphere=-1)[source] 

Add a list of brain regions to the 3D view.

Parameters:

regions (list or np.ndarray) – A list of region names to add.
hemisphere (int, optional) – The hemisphere to display the regions in (-1 for left, 1 for right). Default is -1.

Return type:

None

data_button_pressed()[source] 

Add regions and plots to the 3D view for the chosen probe.

Called when the data button is pressed in the main application.

Return type:: None

on_close()[source] 

Triggered when the plugin window is closed.

Deactivate the plugin and callbacks.

Return type:: None

on_point_size_changed(slider)[source] 

Update the size of the points in the 3D view based on the slider value.

Parameters:: slider (QtWidgets.QSlider) – A slider widget with values from 1 to 10 representing point size.
Return type:: None

plot_channels(plot_key, *args)[source] 

Plot channel data in the 3D view.

Parameters:: plot_key (str) – The name of channel plot to display.
Return type:: None

plot_clusters(plot_key, *args)[source] 

Plot cluster data in the 3D view.

Parameters:: plot_key (str) – The name of the cluster plot to display.
Return type:: None

plot_picks()[source] 

Plot channel data in the 3D view.

Parameters:: plot_key (str) – The name of channel plot to display.
Return type:: None

remove_markers()[source] 

Remove all markers from the 3D view.

Return type:: None

remove_regions()[source] : Remove all brain regions from the 3D view.

set_markers(markers)[source] 

Add markers and text to indicate shank positions in the 3D view.

Parameters:: markers (dict) – A list of marker positions, colors, and names.
Return type:: None

set_picks(points)[source] 

Add a set of pick points to the 3D view.

Parameters:: points (dict) – The position and color of the pick points to add.
Return type:: None

set_point_size(point_size)[source] 

Set the size of the points in the 3D view.

Parameters:: point_size (float) – The size of the points to set.
Return type:: None

set_points(points)[source] 

Add a set of points to the 3D view.

Parameters:: points (dict) – The position and color of the points to add.
Return type:: None

setup()[source] : Launch the 3D Urchin viewer and display the initial probe channels.

toggle_picks(display)[source] 

Show or hide the pick points in the 3D view.

Parameters:: display (bool) – Whether to display the pick points.
Return type:: None

toggle_regions(display)[source] 

Show or hide the brain regions in the 3D view.

Parameters:: display (bool) – Whether to display the brain regions.
Return type:: None

update_plots()[source] 

Update the plots in the 3D view based on the current selection.

Return type:: None

class ibl_alignment_gui.plugins.datoviz_3d.Viewer3D(title, controller)[source] 

Bases: PopupWindow

Popup window hosting the datoviz 3D scene and its display controls.

Parameters:

title (str) – Title shown in the popup’s title bar.
controller (AlignmentGUIController) – The main application controller.

setup()[source] : Create the datoviz server and figure, and add the display controls.

ibl_alignment_gui.plugins.datoviz_3d.callback(controller)[source] 

Open the 3D viewer.

Return type:: None

ibl_alignment_gui.plugins.datoviz_3d.create_random_color()[source] 

Create a random hex color code.

Returns:: A hex color code.
Return type:: str

ibl_alignment_gui.plugins.datoviz_3d.data_to_colors(data, cmap, vmin, vmax)[source] 

Convert data values to RGBA color codes.

Parameters:

data (list or np.ndarray) – The data values to convert to colors.
cmap (str) – The name of the matplotlib colormap to use.
vmin (float) – The minimum value for the colormap.
vmax (float) – The maximum value for the colormap.

Returns:

chex – A list of RGBA color codes corresponding to each data value.

Return type:

list

ibl_alignment_gui.plugins.datoviz_3d.get_regions(_, items, **kwargs)[source] 

Get unique brain regions that the shank passes through.

Parameters:: items (ShankController) – A ShankController instance containing model data.
Returns:: An array of unique region names.
Return type:: np.ndarray

ibl_alignment_gui.plugins.datoviz_3d.get_xyz_picks(_, items, **kwargs)[source] 

Get the xyz coordinates of the picks for the shank.

Parameters:: items (ShankController) – A ShankController instance containing model data.
Returns:: An array of xyz coordinates of the picks.
Return type:: np.ndarray

ibl_alignment_gui.plugins.datoviz_3d.setup(controller)[source] 

Set up the 3D Features plugin.

Adds a submenu to the main menu with options to show/hide regions and adjust point size. Also attaches necessary callbacks to the controller.

Parameters:: controller (AlignmentGUIController) – The main application controller.
Return type:: None

ibl_alignment_gui.plugins.datoviz_3d.update_channels(_, items, plot_key, **kwargs)[source] 

Get the channel data for the chosen plot.

Parameters:

items (ShankController) – A ShankController instance containing model data.
plot_key (str) – The name of the plot to display data for.

Returns:

A dictionary containing data for 3D plotting.

Return type:

dict

ibl_alignment_gui.plugins.datoviz_3d.update_clusters(_, items, plot_key, **kwargs)[source] 

Get the cluster data for the chosen plot.

Parameters:

items (ShankController) – A ShankController instance containing model data.
plot_key (str) – The name of the plot to display data for.

Returns:

A dictionary containing data for 3D plotting.

Return type:

dict