Visualize surfaces

Visualize surfaces

Here is a simple tutorial that shows how to visualize surfaces using DIPY. It also shows how to load/save, get/set and update vtkPolyData and show surfaces.

vtkPolyData is a structure used by VTK to represent surfaces and other data structures. Here we show how to visualize a simple cube but the same idea should apply for any surface.

import numpy as np

Import useful functions from dipy.viz.utils

import dipy.io.vtk as io_vtk
from dipy.viz import window, utils as ut_vtk

# Conditional import machinery for vtk
# Allow import, but disable doctests if we don't have vtk
from dipy.utils.optpkg import optional_package
vtk, have_vtk, setup_module = optional_package('vtk')

Create an empty vtkPolyData

my_polydata = vtk.vtkPolyData()

Create a cube with vertices and triangles as numpy arrays

my_vertices = np.array([[0.0,  0.0,  0.0],
                       [0.0,  0.0,  1.0],
                       [0.0,  1.0,  0.0],
                       [0.0,  1.0,  1.0],
                       [1.0,  0.0,  0.0],
                       [1.0,  0.0,  1.0],
                       [1.0,  1.0,  0.0],
                       [1.0,  1.0,  1.0]])
# the data type for vtk is needed to mention here, numpy.int64
my_triangles = np.array([[0,  6,  4],
                         [0,  2,  6],
                         [0,  3,  2],
                         [0,  1,  3],
                         [2,  7,  6],
                         [2,  3,  7],
                         [4,  6,  7],
                         [4,  7,  5],
                         [0,  4,  5],
                         [0,  5,  1],
                         [1,  5,  7],
                         [1,  7,  3]], dtype='i8')

Set vertices and triangles in the vtkPolyData

ut_vtk.set_polydata_vertices(my_polydata, my_vertices)
ut_vtk.set_polydata_triangles(my_polydata, my_triangles)

Save the vtkPolyData

file_name = "my_cube.vtk"
io_vtk.save_polydata(my_polydata, file_name)
print("Surface saved in " + file_name)

Load the vtkPolyData

cube_polydata = io_vtk.load_polydata(file_name)

add color based on vertices position

cube_vertices = ut_vtk.get_polydata_vertices(cube_polydata)
colors = cube_vertices * 255
ut_vtk.set_polydata_colors(cube_polydata, colors)

print("new surface colors")
print(ut_vtk.get_polydata_colors(cube_polydata))

Visualize surfaces

# get vtkActor
cube_actor = ut_vtk.get_actor_from_polydata(cube_polydata)

# renderer and scene
renderer = window.Renderer()
renderer.add(cube_actor)
renderer.set_camera(position=(10, 5, 7), focal_point=(0.5, 0.5, 0.5))
renderer.zoom(3)

# display
# window.show(renderer, size=(600, 600), reset_camera=False)
window.record(renderer, out_path='cube.png', size=(600, 600))
../../_images/cube.png

An example of a simple surface visualized with DIPY.

Example source code

You can download the full source code of this example. This same script is also included in the dipy source distribution under the doc/examples/ directory.