# 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
import dipy.viz.utils as ut_vtk
from dipy.viz import window

# 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()

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.