iblviewer.application

Classes

CameraModel

UIModel

Viewer

This class is the container and context for having an interactive VTK viewer with a controllable scene and objects.

ViewerModel

class CameraModel(camera: vtkmodules.vtkRenderingCore.vtkCamera = None, autofocus: bool = True, target: Any = None, distance_factor: int = 3, orthographic_scale_factor: int = 1)[source]

Bases: object

camera: vtkmodules.vtkRenderingCore.vtkCamera = None
autofocus: bool = True
target: Any = None
distance_factor: int = 3
orthographic_scale_factor: int = 1
class UIModel(visible: bool = True, embed: bool = False, embed_menu_x: int = 40, embed_menu_y: int = 50, embed_submenu_x: int = 200, embed_submenu_y: int = 50, embed_slider_width: int = 250, color: Any = '#000000', background_color: Any = '#ffffff', context: str = 'default', context_changed: bool = False, last_context: str = None, main_context: str = None, dark_mode: bool = False)[source]

Bases: object

DEFAULT = 'default'
CAMERA = 'camera'
SCENE = 'scene'
OBJECT = 'object'
DATA = 'data'
EXPORT = 'export'
visible: bool = True
embed: bool = False
embed_menu_x: int = 40
embed_menu_y: int = 50
embed_submenu_x: int = 200
embed_submenu_y: int = 50
embed_slider_width: int = 250
color: Any = '#000000'
background_color: Any = '#ffffff'
contexts = {'camera': {}, 'data': {}, 'default': {}, 'export': {}, 'object': {}, 'scene': {}}
font_path = 'C:\\Users\\Mayo\\anaconda3\\envs\\iblenv\\lib\\site-packages\\iblviewer_assets\\fonts'
font = 'SourceSansPro-Regular'
font_size = 15
toggle_config = {'bc': ['#dddddd', '#ffffff'], 'bold': False, 'c': ['black', '#bbbbbb'], 'font': 'SourceSansPro-Regular', 'italic': False, 'size': 15}
button_config = {'bc': ['#dddddd', '#dddddd'], 'bold': False, 'c': ['black', 'black'], 'font': 'SourceSansPro-Regular', 'italic': False, 'size': 15}
slider_config = {'c': 'black', 'font': 'SourceSansPro-Regular'}
context: str = 'default'
context_changed: bool = False
last_context: str = None
main_context: str = None
dark_mode: bool = False
set_dark_mode(on=True)[source]
all_elements()[source]
get_elements(context=None)[source]
get_element(name, context=None)[source]
is_camera_context()[source]
is_scene_context()[source]
is_object_context()[source]
is_data_context()[source]
is_export_context()[source]
is_valid_context(context)[source]
toggle_context(context=None)[source]

Toggles between current context and given one

Parameters

context – A context string

set_context(context)[source]

Set the context

Parameters

context – A context from CONTEXTS

Returns

True if context was changed

register(element, context=None)[source]

Register UI components (or anything else really) to the given context

class ViewerModel(title: str = 'VTK Viewer', window_size: numpy.ndarray = array([1280, 720]), web_window_size: numpy.ndarray = array([960, 600]), web_ui: bool = False, offscreen: bool = False, ui: iblviewer.application.UIModel = <factory>, origin: numpy.ndarray = array([0., 0., 0.]), cameras: iblviewer.collection.Collection = <factory>, volumes: iblviewer.collection.Collection = <factory>, slicers: iblviewer.collection.Collection = <factory>, points: iblviewer.collection.Collection = <factory>, lines: iblviewer.collection.Collection = <factory>, surfaces: iblviewer.collection.Collection = <factory>, probes: iblviewer.collection.Collection = <factory>, luts: iblviewer.collection.Collection = <factory>, interactive_volume_subsampling: bool = False, runtime: datetime.datetime = datetime.datetime(2022, 6, 6, 12, 20, 2, 269830), timer_id: Any = None, playback_speed: int = 20, animation_playing: bool = False, animation_function: Any = None, time: float = 0.0, selection_changed: bool = False, selection_point_changed: bool = False, selection: Any = None, selection_type: Any = None, selection_point: Any = None, selection_relative_point: Any = None, selection_controller: Any = None, selection_value: float = None, selection_related_value: float = None, selection_related_name: str = None, selection_camera_position: Any = None, selection_marker_visible: bool = True, selection_text_visible: bool = True, selection_outline_visible: bool = True, selection_color_bar_visible: bool = True, probe_initial_point1: Any = None, probe_initial_point2: Any = None, outline_opacity: float = 1.0, outline_color: list = <factory>, outline_width: int = 3, pickings: list = <factory>, first_picked_position: numpy.ndarray = None, last_picked_position: numpy.ndarray = None, video_start_angle: float = 0.0, video_end_angle: float = 360.0, video_duration: float = 8.0, global_slicer: vtkmodules.vtkCommonDataModel.vtkPlaneCollection = None)[source]

Bases: object

POINT = 'point'
LINE = 'line'
SURFACE = 'surface'
VOLUME = 'volume'
UI = 'ui'
OBJECTS_TYPE = {'line': 1, 'point': 0, 'surface': 2, 'ui': 4, 'volume': 3}
X_UP = array([1., 0., 0.])
Y_UP = array([0., 1., 0.])
Z_UP = array([0., 0., 1.])
X_DOWN = array([-1.,  0.,  0.])
Y_DOWN = array([ 0., -1.,  0.])
Z_DOWN = array([ 0.,  0., -1.])
title: str = 'VTK Viewer'
window_size: numpy.ndarray = array([1280,  720])
web_window_size: numpy.ndarray = array([960, 600])
web_ui: bool = False
offscreen: bool = False
ui: iblviewer.application.UIModel
origin: numpy.ndarray = array([0., 0., 0.])
cameras: iblviewer.collection.Collection
volumes: iblviewer.collection.Collection
slicers: iblviewer.collection.Collection
points: iblviewer.collection.Collection
lines: iblviewer.collection.Collection
surfaces: iblviewer.collection.Collection
probes: iblviewer.collection.Collection
luts: iblviewer.collection.Collection
interactive_volume_subsampling: bool = False
runtime: datetime.datetime = datetime.datetime(2022, 6, 6, 12, 20, 2, 269830)
timer_id: Any = None
playback_speed: int = 20
animation_playing: bool = False
animation_function: Any = None
time: float = 0.0
selection_changed: bool = False
selection_point_changed: bool = False
selection: Any = None
selection_type: Any = None
selection_point: Any = None
selection_relative_point: Any = None
selection_controller: Any = None
selection_value: float = None
selection_camera_position: Any = None
selection_marker_visible: bool = True
selection_text_visible: bool = True
selection_outline_visible: bool = True
selection_color_bar_visible: bool = True
probe_initial_point1: Any = None
probe_initial_point2: Any = None
outline_opacity: float = 1.0
outline_color: list
outline_width: int = 3
pickings: list
first_picked_position: numpy.ndarray = None
last_picked_position: numpy.ndarray = None
video_start_angle: float = 0.0
video_end_angle: float = 360.0
video_duration: float = 8.0
global_slicer: vtkmodules.vtkCommonDataModel.vtkPlaneCollection = None
initialize()[source]

Initialize the model

get_actor_type(actor)[source]

Get the type of the given actor Vedo does a similar thing for some of its events: “isPoints”: isinstance(actor, vedo.Points), “isMesh”: isinstance(actor, vedo.Mesh), “isAssembly”: isinstance(actor, vedo.Assembly), “isVolume”: isinstance(actor, vedo.Volume), “isPicture”: isinstance(actor, vedo.Picture), “isActor2D”: isinstance(actor, vtk.vtkActor2D),

Parameters

actor – vtkActor

Returns

String

got_selection()[source]

Whether a selection is set :return: Boolean

got_new_selection()[source]

Whether a the selection target changed :return: Boolean

is_selection_point()[source]

Whether the type of selection is a point cloud :return: Boolean

is_selection_line()[source]

Whether the type of selection is a set of lines :return: Boolean

is_selection_surface()[source]

Whether the type of selection is a surface mesh :return: Boolean

is_selection_volume()[source]

Whether the type of selection is a volume :return: Boolean

define_view_axis(normal)[source]
class Viewer[source]

Bases: object

This class is the container and context for having an interactive VTK viewer with a controllable scene and objects.

initialize(offscreen=False, jupyter=False, embed_ui=False, embed_font_size=15, plot=None, plot_window_id=0, num_windows=1, dark_mode=False, silent=False)[source]

Initialize the controller, main entry point to the viewer

Parameters
  • context – Context of the visualization

  • embed_ui – Whether the UI is embed within the VTK window

  • embed_font_size – Embed font size. Defaults to 16 points. You might need larger values in case you have a small screen with high dpi (but VTK methods fail to detect that).

  • jupyter – Whether we’re running from a jupyter notebook or not

  • offscreen – Whether the rendering is done offscreen (headless) or not

  • plot – A vedo Plotter instance. You can either create it by yourself before hand, in case you want to have multiple windows with other stats or let the controller create a new one

  • plot_window_id – Sub-window id where the 3D visualization will be displayed

  • num_windows – Number of subwindows, in case you want to display your own stuff later

  • render – Whether rendering occurs at the end of the initialization or not. Defaults to False

  • dark_mode – Whether the viewer is in dark mode

  • auto_select_first_object – Auto select the first object displayed

  • silent – Whether printing to console is disabled or not

initialize_window_interactions()[source]

Initialize window interactions on the VTK window

initialize_selection_ui()[source]

Initialize selection marker and text

handle_key_press(iren, event)[source]

Handle key press events

Parameters
  • iren – vtk iren

  • event – vtk event

exit_interactive_mode()[source]

Exit/leave interactive mode

toggle_dark_mode()[source]

Toggle dark/light mode

set_dark_mode(on=True, update_ui=True)[source]

Set dark mode on or off

set_renderer()[source]

Set VTK renderer, attempts to use OSPRay, if available OSPRay is not supported (2021) by default and there is no pip wheel for it with vtk, or paraview or any vtk-based tool. So you can only rely on OSPRay if you compile it alongside VTK.

register_object(vtk_object, name=None, selectable=True)[source]

Register an object as selectable by the user in the UI

Parameters
  • vtk_object – VTK object

  • name – Name or given id. IF None, the name of the

object is used

get_unique_object_name(name, spacer='_')[source]

Get a unique key/name for selectable objects with similar names

Parameters
  • name – Name (for instance ‘Points’)

  • spacer – Spacer char

Returns

New name, for instance ‘Points_4’

unregister_object(name)[source]

Unregister an object from the selectable objects list

Parameters

name – Object name or given id or int or the object itself

update_selection_slider(max_value=None)[source]

Update the selection slider max value

Parameters

max_value – Max value. If None, the maximum value

is the length of the self.objects

register_controller(controller, vtk_objects)[source]

Register/map VTK objects to a view

Parameters
  • controller – A controller instance (like VolumeController)

  • vtk_objects – All objects directly related to this view

get_view_objects()[source]

Get all view objects registered in this model :return: List

get_view_objects_names()[source]

Get view objects names :return: Dict

get_window()[source]

Get the plot window object. This is useful for displaying this window in Jupyter notebooks for instance :return: iren window object

render(save_to_file=None, width=None, height=None, scale=1)[source]

Render the current state of the viewer, optionally to a file. Supported formats are jpg, png, pdf, svg, eps

Parameters
  • save_to_file – File path

  • width – Width of the rendered image

  • height – Height of the rendered image

  • scale – Rendering scale factor. Defaults to 1

show(interactive=True, actors=None, at=0, **kwargs)[source]

Render the plot and let the user interact with it

Parameters
  • interactive – Whether we render and make the window interactive

  • actors – List of actors to show. Use this parameter only if you know what you’re doing.

  • at – Which VTK window to use. Defaults to 0

close()[source]

Close the current plot

add_callback(event_name, func, priority=0.0)[source]

Add an event listener (aka callback method)

Parameters
  • event_name – A VTK event name

  • func – Listener function

  • priority – Priority in event queue

Returns

Callback id

remove_callback(callback_id)[source]

Add an event listener (aka callback method)

Parameters

callback_id_or_event_name – A VTK event name

handle_timer(iren, event, **kwargs)[source]

Handle vtk timer event

Parameters
  • iren – Render window

  • event – TimerEvent

handle_left_mouse_press(event)[source]

Handle left mouse down event. The event is triggered for any “pickable” object

Parameters

mesh – Selected object

clear_depth_picking(return_element=None)[source]

Clear depth picking, making all objects put in depth queue pickable again

Parameters

return_element – An element to be returned by its index of insertion

Returns

object and picked 3d coordinates (only if return_element is valid)

get_actor_type(actor)[source]

Get what type is the given actor

Parameters

actor – vtkActor

Returns

String

handle_left_mouse_release(event)[source]

Handle left mouse up event.

Parameters

event – vtkEvent

Returns

Int value. 0 for invalid click, 1 for actor click,

2 for double click on actor

handle_actor2d_click(state, actor, event)[source]

Handle click on a 2D actor

handle_void_click(state=None, event=None)[source]

Handle click and drag

handle_drag_release(state, actor, event)[source]

Handle click and drag

handle_object_click(actor, state=1, event=None)[source]

Handle valid object selection

Parameters
  • actor – Selected actor

  • state – Number of mouse clicks

  • event – Event given by vedo

objects_changed()[source]

Function called when a new object is registered

initialized()[source]

Function called the viewer is initialized

selection_changed()[source]

Function called when another object is selected.

sub_selection_changed()[source]

Function called when for the same object, a new data point is selected

get_object_names()[source]
get_selectable_key_by_id(value=0)[source]

Get an object by the id of the key (not by the key/name itself) This is useful for sliders :return: String

select(target=None, allow_none=False)[source]

Select an object, either by its name (or subname) or by reference to the vtk object.

Parameters
  • target – Either the vtk actor or its name or its index (an int from object.keys())

  • allow_none – Whether an invalid target is accepted as clicking on nothing (to cancel the current selection)

get_selection_info()[source]

Get information about the current selection :return: Preformatted multiline text and a dictionary of extra data

update_selection_info()[source]

Update text and point information for the current selection

draw_axes()[source]

Draw axes around selection

draw_outline(auto_hide_if_no_selection=True)[source]

Draw the bounding box of the current selection.

Parameters

auto_hide_if_no_selection – Whether we hide the outline when there is no selection

add_segments(points, end_points=None, line_width=2, values=None, color_map='Accent', name='Segments', use_origin=True, add_to_scene=True, relative_end_points=False, spherical_angles=None, radians=True)[source]

Add a set of segments (lines made of two points). The difference with add_lines() is that you have more options like giving spherical angles and setting relative end points.

Parameters
  • points – 3D numpy array of points of length n

  • end_points – 3D numpy array of points of length n

  • line_width – Line width, defaults to 2px

  • values – 1D list of length n, for one scalar value per line

  • color_map – A color map, it can be a color map built by IBLViewer or a color map name (see vedo documentation), or a list of values, etc.

  • name – Name to give to the object

  • use_origin – Whether the current origin (not necessarily absolute 0) is used as offset

  • add_to_scene – Whether the new lines are added to scene/plot and rendered

  • relative_end_points – Whether the given end point is relative to the start point. False by default, except is spherical coordinates are given

  • spherical_angles – 3D numpy array of spherical angle data of length n In case end_points is None, this replaces end_points by finding the relative coordinate to each start point with the given radius/depth, theta and phi

  • radians – Whether the given spherical angle data is in radians or in degrees

Returns

Lines

add_lines(points, line_width=2, values=None, color_map='Accent', name='Lines', use_origin=True, add_to_scene=True)[source]

Create a set of lines with given point sets

Parameters
  • points – List or 2D array of 3D coordinates

  • line_width – Line width, defaults to 2px

  • values – 1D list of length n, for one scalar value per line

  • color_map – A color map, it can be a color map built by IBLViewer or a color map name (see vedo documentation), or a list of values, etc.

  • name – Name to give to the object

  • use_origin – Whether the current origin (not necessarily absolute 0) is used as offset

  • add_to_scene – Whether the new lines are added to scene/plot and rendered

Returns

objects.Lines

add_spheres(positions, radius=10, values=None, color_map='Accent', name='Points', use_origin=True, add_to_scene=True, **kwargs)[source]

Add new spheres. This is a shortcut for add_points(screen_space=False)

Parameters
  • positions – 3D array of coordinates

  • radius – List same length as positions of radii. The default size is 5um, or 5 pixels in case as_spheres is False.

  • values – 1D array of values, one per neuron or a time series of such 1D arrays (numpy format)

  • color_map – A color map, it can be a color map built by IBLViewer or a color map name (see vedo documentation), or a list of values, etc.

  • name – All point neurons are grouped into one object, you can give it a custom name

  • use_origin – Whether the current origin (not necessarily absolute 0) is used as offset

  • add_to_scene – Whether the new lines are added to scene/plot and rendered

Returns

objects.Points

add_points(positions, radius=10, values=None, color_map='Accent', name='Points', screen_space=True, use_origin=True, add_to_scene=True, **kwargs)[source]

Add new points, either as screen-space dots or as 3D spheres (see screen_space param)

Parameters
  • positions – 3D array of coordinates

  • radius – List same length as positions of radii. The default size is 5um, or 5 pixels in case as_spheres is False.

  • values – 1D array of values, one per neuron or a time series of such 1D arrays (numpy format)

  • color_map – A color map, it can be a color map built by IBLViewer or a color map name (see vedo documentation), or a list of values, etc.

  • name – All point neurons are grouped into one object, you can give it a custom name

  • screen_space – Type of point, Defaults to True. If True then the points always occupy the same amount of pixels defined by the radius, this is the fastest method to display large amount of points. If False, then points are 3D spheres and you see them larger when you zoom closer to them with the camera.

  • use_origin – Whether the current origin (not necessarily absolute 0) is used as offset

  • add_to_scene – Whether the new lines are added to scene/plot and rendered

Returns

objects.Points

add_mesh(file_path, mesh_name=None, use_origin=True, add_to_scene=True)[source]

Add a surface mesh to the scene

Parameters
  • file_path – Mesh file path (any kind of file supported by vedo)

  • mesh_name – Name of the mesh. If None, the file name will be used.

  • use_origin – Whether the origin is used in positioning the mesh

  • add_to_scene – Whether the new lines are added to scene/plot and rendered

Returns

Mesh

add_surface_mesh(file_path, mesh_name=None, use_origin=True, add_to_scene=True)[source]

Add a surface mesh to the scene

Parameters
  • file_path – Mesh file path (any kind of file supported by vedo)

  • mesh_name – Name of the mesh. If None, the file name will be used.

  • use_origin – Whether the origin is used in positioning the mesh

  • add_to_scene – Whether the new lines are added to scene/plot and rendered

Returns

Mesh

add_volume(data=None, resolution=None, file_path=None, color_map='viridis', alpha_map=None, select=False, add_to_scene=True, transpose=None)[source]

Add a volume to the viewer with box clipping and slicing enabled by default

Parameters
  • data – Volume image data or a file_path

  • resolution – Resoluton of the volume

  • file_path – File path of the volume. If you don’t provide an image volume data, then the file_path will be used to load the volume data

  • color_map – Color map for the volume

  • alpha_map – Alpha map for the volume. If None, it will assume that 0 values are transparent and maximum values are opaque

  • select – Whether the volume is selected

  • add_to_scene – Whether the volume is added to scene

  • transpose – Transposition parameter. If None. nothing happens. If True, then the default IBL transposition is applied. You can provide your own, that is, a list of 3 elements to reorder the volume as desired.

Returns

VolumeController

remove_object(target=None, unregister=False)[source]

Remove an object from the plot

Parameters
  • target – Target object

  • unregister – Whether the object is also unregistered, which means that it’s not in the list of objects anymore and cannot be recovered using select(object_name)

toggle_menu(name=None, context=None)[source]

Toggle menu and activate only one button in the set

set_menu_context(button_name, context)[source]

Set the context from the main menu buttons

Parameters
  • button_name – Which button is clicked

  • context – What context to activate

camera_context()[source]

Set camera context

scene_context()[source]

Set scene context

data_context()[source]

Set data context

object_context()[source]

Set object context

time_series_context()[source]

Set time series context

export_context()[source]

Set export context

toggle_marker_type()[source]

Toggle marker type (between cross and sphere)

set_selection_marker(marker_type='cross', size=500, cross_thickness=3)[source]

Set the selection marker type. Accepted values currently are ‘cross’ or ‘sphere’

Parameters

marker_type – Marker type

initialize_vtk_ui(x=40, y=50, sx=None, sy=None, sw=None)[source]

Initialize a per-context VTK UI.

Parameters
  • x – Base screen-space x coordinate

  • y – Base screen-space y coordinate (starts from the bottom in VTK)

add_camera_embed_ui(x, y, sw, nc=150)[source]

Add camera-context UI

Parameters
  • x – Base X position

  • y – Base Y position (0 is at the bottom of the screen)

  • sw – Slider width

add_scene_embed_ui(x, y, sw)[source]

Add scene-context UI

Parameters
  • x – Base X position

  • y – Base Y position (0 is at the bottom of the screen)

  • sw – Slider width

add_object_embed_ui(x, y, sw)[source]

Add object-context UI

Parameters
  • x – Base X position

  • y – Base Y position (0 is at the bottom of the screen)

  • sw – Slider width

add_data_embed_ui(x, y, sw)[source]

Add data-context UI

Parameters
  • x – Base X position

  • y – Base Y position (0 is at the bottom of the screen)

  • sw – Slider width

add_export_embed_ui(x, y, sw)[source]

Add export-context UI

Parameters
  • x – Base X position

  • y – Base Y position (0 is at the bottom of the screen)

  • sw – Slider width

update_scene_ui(context_elements)[source]

Update the scene-related UI

Parameters

context_elements – Current UI context elements

is_volume(target=None)[source]

Get whether the target object is a volume

Parameters

target – vtkActor. If None, the current selected object is used.

Returns

Boolean

get_selection_opacity()[source]

Get the opacity of the current selected object :return: Float or None

get_selection_slices_opacity()[source]

Get the opacity of the current volume slices :return: Float or None

update_object_ui(context_elements)[source]

Update the object mode UI

Parameters

context_elements – Current UI context elements

update_data_ui(context_elements)[source]

Update data UI

Parameters

context_elements – Current UI context elements

get_time_series_info(target=None)[source]

Get the number of time series and id of the current one for a target. If None, then the current selection is used

Parameters

target – a vtk object

Returns

Int, Int

update_ui()[source]

Update the UI

set_color_bar_visibility(on=None)[source]

Show or hide the color bar

Parameters

on – Visibility boolean

draw_color_bar()[source]

Draw a color bar for the current selection

clear_color_bar()[source]

Clear the color bar

set_button_state(element, state)[source]

Set the state of a button. For a toggle, True or False.

get_button_state(element)[source]

Get the state of a button

set_element_visibility(element, visible=True)[source]

Set a UI element’s visibility

Parameters
  • element – a vtk2DActor or something like that (changes for sliders, texts, etc.)

  • visible – Visible or not

update_element_color(element)[source]

Set a UI element’s color

Parameters

element – a vtk2DActor or something like that (changes for sliders, texts, etc.)

set_ui_visibility(visible, exceptions=None, ui_button_visible=True)[source]

Set the UI visibility

Parameters
  • visible – Whether the UI is visible or not

  • exceptions – Dictionary of objects that have to be the inverse of the given state

  • ui_button_visible – Whether the UI button is still visible or not, so that the user can restore the UI by clicking on it. This is not necessary in case of Jupyter NB

add_text(name, text, pos, color=None, justify='top-left', context=None, **kwargs)[source]

Add a 2D text on scene

Parameters
  • name – Name of the object

  • text – Text string

  • pos – Position on screen

  • color – Color of the font

  • justify – Type of justification

  • context – Context to register this object to

Returns

Text2D

add_button(name, event_handler, pos, label=None, toggle=False, state=0, context=None)[source]

Add a left-aligned button

Parameters
  • name – Button name

  • event_handler – Event handler function

  • pos – Screen-space position

  • label – Button text label

  • toggle – Whether it’s a toggle button or not

Returns

Button

get_slider_bounds(x, y, length, horizontal=True)[source]

Get slider coordinates, releative to lower left corner of the window

Parameters
  • x – X position

  • y – Y position

  • length – Length of the slider

  • horizontal – Whether the length is horizontal or vertical

Returns

np 2d array with min and max coordinates

add_slider(name, event_handler, min_value, max_value, value, pos, title=None, oid=None, precision=0, context=None, **kwargs)[source]

Add a slider to the UI

Parameters
  • event_handler – Event handler function called when the slider is updated

  • min_value – Min slider value

  • max_value – Max slider value

  • value – Default value

  • size – Font size

  • pos – Position in the UI as a tuple or list, see get_slider_bounds for details

  • kwargs – Dictionary of kwargs, see vedo.addons.addSlider2D() for details

Returns

2D Slider

slider_value(element_id, value=None, widget=None)[source]

Abstract method to get or set a value on a VTK slider element

Parameters
  • element_id – Element id (found in self.model.ui.get_elements().keys())

  • value – Value of Z slice, defaults to 0.0

  • widget – Widget instance (given by the event caller)

Returns

Float value

clip_to_bounds(bounds_obj, target=None)[source]

Clip a target object with the bounding box of another object

Parameters
  • bounds_obj – a vtkActor

  • target – Target object. If None, the current selection is used

isosurface(value=None, volume_controller=None, split_meshes=False, remove_existing=True)[source]

Generate mesh(es) for a given value in a volume

Parameters
  • value – Value/label for which we want to generate an isosurface mesh

  • volume_controller – Volume controller. If None, the current one is used.

If the current one is None, then nothing happens. :param split_meshes: Whether manifold meshes are split if there are multiple ones :param remove_existing: Whether existing meshes are removed from the plot :return: List of meshes computed

set_probe_position(pt1=None, pt2=None)[source]

Set the position of the current probe

add_probe()[source]

Add a new probe widget

is_probe(probe=None)[source]

Check if an object is (the result of) a probe

Parameters

probe – Probe object

Returns

Boolean

update_current_probe(widget=None, event=None, point1=None, point2=None)[source]

Update the current probe

Parameters
  • widget – vtkLineWidget

  • event – vtkEvent

  • point1 – Point 1, this will override the widget’s point 1

  • point2 – Point 2, this will override the widget’s point 2

edit_probe(probe=None)[source]

Edit/move an existing probe

clear_line_widget()[source]

Clear the active line widget

toggle_box_widget()[source]

Toggle box widget

add_box_widget()[source]

Add a box widget for clipping the selected object

clear_box_widget()[source]

Clear the active box widget

update_px_slicer(widget=None, event=None, value=0.0)[source]

Event handler for Slicer on +X axis

Parameters
  • widget – Widget instance (given by the event caller)

  • event – Event (given by the event caller)

  • value – Value of X slice, defaults to 0.0

update_nx_slicer(widget=None, event=None, value=0.0)[source]

Event handler for Slicer on -X axis

Parameters
  • widget – Widget instance (given by the event caller)

  • event – Event (given by the event caller)

  • value – Value of X slice, defaults to 0.0

update_py_slicer(widget=None, event=None, value=0.0)[source]

Event handler for Slicer on +Y axis

Parameters
  • widget – Widget instance (given by the event caller)

  • event – Event (given by the event caller)

  • value – Value of Y slice, defaults to 0.0

update_ny_slicer(widget=None, event=None, value=0.0)[source]

Event handler for Slicer on -Y axis

Parameters
  • widget – Widget instance (given by the event caller)

  • event – Event (given by the event caller)

  • value – Value of Y slice, defaults to 0.0

update_pz_slicer(widget=None, event=None, value=0.0)[source]

Event handler for Slicer on +Z axis

Parameters
  • widget – Widget instance (given by the event caller)

  • event – Event (given by the event caller)

  • value – Value of Z slice, defaults to 0.0

update_nz_slicer(widget=None, event=None, value=0.0)[source]

Event handler for Slicer on -Z axis

Parameters
  • widget – Widget instance (given by the event caller)

  • event – Event (given by the event caller)

  • value – Value of Z slice, defaults to 0.0

toggle_slices(event=None)[source]

Toggle slicers visibility

Parameters
  • widget – Widget instance (given by the event caller)

  • event – Event (given by the event caller)

toggle_global_slicer(event=None)[source]

Toggle global slicer mode

Parameters
  • widget – Widget instance (given by the event caller)

  • event – Event (given by the event caller)

set_camera(quat, camera_distance=10000)[source]

TODO: make it possible to store and assign a camera transformation matrix

update_camera(normal=None, view_up=None, scale_factor=1.5, min_distance=10000)[source]

Update the camera frustrum

Parameters
  • normal – View normal

  • view_up – Up axis normal

  • scale_factor – Scale factor to make the camera closer to the target

Smaller values than 1 make the target closer to the camera.

toggle_orthographic_view()[source]

Toggle orthographic/perspective views

set_left_view()[source]

Set left sagittal view

set_right_view()[source]

Set right sagittal view

set_anterior_view()[source]

Set anterior coronal view

set_posterior_view()[source]

Set posterior coronal view

set_dorsal_view()[source]

Set dorsal axial view

set_ventral_view()[source]

Set ventral axial view

toggle_autofocus()[source]

Reset the camera target to the selected object

view_selected()[source]

Reset the camera target to the selected object

move_camera_pivot(point=None)[source]

Focus the camera on the current selection point

Parameters

point – Point to focus on

toggle_ui()[source]

Toggle user interface

toggle_hollow_mode()[source]

Toggle hollow volume visualization

toggle_info()[source]

Toggle visibility of information about current selection

toggle_outline(event=None)[source]

Toggle outline visibility

Parameters

event – Event (given by the event caller)

set_outline_visibility(on=None)[source]

Set outline visibility

Parameters

on – Visibility boolean

toggle_marker()[source]

Toggle visibility of the marker

set_marker_visibility(on=True)[source]

Set marker visibility

Parameters

on – Visibility boolean

toggle_info_text()[source]

Toggle visibility of the marker

set_info_text_visibility(on=True)[source]

Set info text visibility

Parameters

on – Visibility boolean

toggle_color_bar()[source]

Togggle the color bar visibility

set_info_visibility(visible=True, actors=None, update_color_bar=True)[source]

Set the visibility of info data

Parameters
  • visible – Whether info data is visible or not

  • actors – Any desired actors to be made visible/invisible

  • update_color_bar – Whether this method also affects the color bar

select_object_by_name(name)[source]
select_previous_object()[source]

Select the next object in the list of selectable objects

select_object_by_id(widget=None, event=None, value=1.0)[source]

Select object by id (order in which objects were registered in this app)

Parameters
  • widget – Widget instance (given by the event caller)

  • event – Event (given by the event caller)

  • value – Object id

select_next_object()[source]

Select the next object in the list of selectable objects

toggle_pickable(widget=None, event=None, value=1.0)[source]

Toggle the clickable state of an object

Parameters
  • widget – Widget instance (given by the event caller)

  • event – Event (given by the event caller)

  • value – 0 for disabled, 1 for enabled

update_opacity(widget=None, event=None, value=1.0)[source]

Update the alpha unit of the current volume, making it more or less transparent

Parameters
  • widget – Widget instance (given by the event caller)

  • event – Event (given by the event caller)

  • value – alpha unit value. If none given by the event, the value defaults to 1.0

update_slices_opacity(widget=None, event=None, value=1.0)[source]

Update the opacity of the current volume slices

Parameters
  • widget – Widget instance (given by the event caller)

  • event – Event (given by the event caller)

  • value – alpha unit value. If none given by the event, the value defaults to 1.0

play_time_series(widget=None, event=None)[source]

Play/pause time series

Parameters
  • widget – Widget instance (given by the event caller)

  • event – Event (given by the event caller)

previous_time_series(offset=1, loop=True)[source]

Previous time series

Parameters
  • offset – Offset integer. If negative, then it’s like using next_time_series()

  • loop – Whether next() goes to 0 when it reached the end of the time series or not

Returns

Returns whether the next time series is valid (within range of the time series)

next_time_series(offset=1, loop=True)[source]

Next time series

Parameters
  • offset – Offset integer, can be negative to go backwards

  • loop – Whether next() goes to 0 when it reached the end of the time series or not

Returns

Returns whether the next time series is valid (within range of the time series)

update_time_series(widget=None, event=None, value=None)[source]

Update the time series

Parameters
  • widget – The slider widget (optional)

  • event – The slider event (optional)

  • value – The value to set. If None, then the slider value is used, if it’s given as widget param

set_time_series(value, force_update=False)[source]

Set the time series for the current selected object

Parameters
  • value – The given time step

  • force_update – Whether an update is forced even if the given value is the same as the existing time step

assign_scalars(scalar_map=None, scalar_range=None, color_map='viridis', make_active=True)[source]

Assign a new data set and a color map to a target min_value=None, max_value=None

handle_lut_update()[source]

Update the view with the given or current transfer function

Parameters

lut_model – A LUTModel (whose table property is a vtkLookupTable) to set on the current volume. If None, the current one will be used.

animation_callback(progress)[source]

You may override this function according to your needs

Parameters

progress – ratio of total animation (from 0.0 to 1.0)

update_video_duration(widget=None, event=None, value=None)[source]

Update the video duration

Parameters
  • widget – The slider widget (optional)

  • event – The slider event (optional)

  • value – The value to set. If None, then the slider value is used, if it’s given as widget param

update_video_start_angle(widget=None, event=None, value=None)[source]

Update the video start angle

Parameters
  • widget – The slider widget (optional)

  • event – The slider event (optional)

  • value – The value to set. If None, then the slider value

is used, if it’s given as widget param

update_video_end_angle(widget=None, event=None, value=None)[source]

Update the video end angle

Parameters
  • widget – The slider widget (optional)

  • event – The slider event (optional)

  • value – The value to set. If None, then the slider value is used, if it’s given as widget param

toggle_volumetric_lod()[source]

Toggle volumetric LOD (subsampling)

volumetric_lod(on=False)[source]

Enable or disable volumetric LOD subsampling. Turn this on when you want faster interactive visualizations

Parameters

on – Whether volumetric subsampling is activated

export_image(file_name='iblviewer.png', width=None, height=None, scale=2)[source]

Export the current image to a file

Parameters
  • file_name – File name with extension. PNG by default

  • width – Width in pixels. If None, the width of the window is used.

  • height – Height in pixels. If None, the height of the window is used.

  • scale – Scale factor to make the image larger. Defaults to 2.

export_turntable_video(file_name='iblviewer.mp4', start_angle=0, end_angle=360, duration=None, fps=25)[source]

Export a sagittal turntable video of the viewer.

Parameters
  • file_name – File name

  • start_angle – Start angle

  • end_angle – End angle. If it’s the same value as start angle, then 360 is added

  • duration – Duration of the video

  • fps – Frames per second, defaults to 25