Simple VTK Visualization

This module contains utilities for working with VTK visualizations.

Simple VTK Viewer

The simple vtk viewer is a limited viewer class that wraps most of the vtk boilerplate code. It is meant to do simple tests or to use interactively from the python console.

class SimpleVtkViewer[source]

A very simple windows with vtk renderers and interactors.

This class is intended for interactive work and fast prototyping. As such it is very simple and limited. For full interactive applications consider using subject_viewer

addImg(img)[source]

Use this method to show an image inside an image plane widget.

Parameters:img (vtkImageData) – Image
Returns:The created imagePlaneWidget
addPolyData(polyData, LUT=None)[source]

Adds a poly data to the viewer, a LUT can be set.

Parameters:
Returns:

The vtkActor instance created, it may be used to change the visual properties
clear_poly_data()[source]

Removes all polydata from the viewer

start(reset=True)[source]

Call this method to start the interaction, interaction can be stopped by pressing ‘q’ on the main window

Parameters:reset (bool) – If True the camera will be reset

VTK Widgets

Warning

Sphinx bug, methods are not static

class persistentImagePlane(orientation=0)[source]

A vtkImagePlaneWidget which can keep its state between calls to SetInputData.

It adds a second text message showing the mm coordinates of the cursors This message can be further enhanced by using a label image and a label dictionary Additionally the values displayed in the first message can be replaced by values taken from another image, this is useful when the displayed image contains colors or other contexts that are not the main value (ex, fmri) Finally, this class generates custom events when moving the cursor and when changing the slice.

On()[source]

Turn the widget on

SetInputData(img)[source]

Changes the input data por the plane widget

Parameters:img (vtkImageData) – New image data
SetInteractor(iact)[source]

Links the widget to an interactor

Parameters:iact (vtkRenderWindowInteractor) – Render window interactor
addLabels(label_img)[source]

A second image can be used to get labels for image coordinates (ex. aparc)

Parameters:label_img (vtkImageData) – Image to use as reference for labels
get_label(x, y, z)[source]

Auxiliary function to get the label in a given coordinate (in mm)

Parameters:
  • x (float) – x coordinate
  • y (float) – y coordinate
  • z (float) – z coordinate
Returns:

If a lookuptable is set returns the text label, otherwise the numeric label
setLabelsLut(lut)[source]

A lookup table can be used to translate numeric labels into text labels

Parameters:lut (vtkLookupTable) – Lookup table
set_orientation(orientation)[source]

Sets image plane orientation

Parameters:orientation (int) – x:0 , y:1, z:2
text1_to_std()[source]

Turn text1 behaviour back to standard, reverts the effects of text1_value_from_img

text1_value_from_img(img2)[source]

Text 1 value can be read from a different image than the one been shown, useful for composed images

Parameters:img2 (vtkImageData) – Image to get values for lower left corner text
class OutlineActor[source]

A simple shortcut for displaying the outline of an object

Encapsulates an outline filter, a mapper and an actor

SetInputData(input_data)[source]

For better compatibility with vtk methods style

Parameters:input_data (vtkDataObject) – Object whose outline we want
set_input_data(input_data)[source]

Sets the input data for the outline

Parameters:input_data (vtkDataObject) – Object whose outline we want
class OrientationAxes[source]

An orientation cube with faces labeled for Right, Left, Anterior, Posterior, Superior and Inferior

initialize(render_window_interactor)[source]

Link the orientation cube with an interactor

render_window_interactor (vtkRenderWindowInteractor) : vtk interactor

class cursors(axis=0)[source]

Emulates the cursors in vtkImagePlaneWidget

There will be two copies of the cursors polydata, one in front and one at the back of the image plane, the separation between them is controlled by the set_delta() method

change_axis(axis)[source]

Change the axis perpendicular to the image plane

Parameters:axis (int) – x:0 , y:1, z:2
set_cursor(x, y, z)[source]

Set the position of the cursor

Parameters:
  • x (float) – x position
  • y (float) – y position
  • z (float) – z position
set_delta(delta)[source]

Sets separation between front and back cursors.

Parameters:delta (float) – Separation
set_dimensions(nx, ny, nz)[source]

Sets the dimensions of the underlying image

Parameters:
  • nx (float) – x dimension
  • ny (float) – y dimension
  • nz (float) – z dimension
set_origin(x, y, z)[source]

Sets the origin of the underlying image

Parameters:
set_spacing(dx, dy, dz)[source]

Sets the spacing of the underlying image

Parameters:
  • dx (float) – x spacing
  • dy (float) – y spacing
  • dz (float) – z spacing

Other Utilities

save_ren_win_picture(ren_win, file_name, magnification=1)[source]

Saves an screenshot of a render window

Parameters:
build_grid(orig_img, img_slice, sampling_rate=5)[source]

Creates an homogenous grid, useful for showing the effects of transformations

The grid dimensions are based on the orig_img, img_slice is used to position the grid along the x axis, For the moment only grids perpendicular to the x axis are available

Parameters:
  • orig_img (vtkImageData) – Image to base grid on
  • img_slice (int) – Slice of the image where the grid will be located (along the x asis)
  • sampling_rate (int) – Density of the grid, there will be a line each sampling_rate voxels
remove_nan_from_grid(grid)[source]

Remove missing values from a grid, it is necessary in some version of vtk to avoid crash

Parameters:grid (vtkPolyData) – Should only contain lines
get_arrow(head, tail)[source]

create a polydata arrow, consider using vtkArrowSource

Parameters:
  • head (tuple) – coordinates for arrow head
  • tail (tuple) – coordinates for arrow tail
get_window_level(img)[source]

Automatically gets appropriate window and level values for displaying an image

Parameters:img (vtkImageData) – Image
Returns
(window,level), proposed values