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 fury.utils as ut_vtk
from fury 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)

Out:

Surface saved in my_cube.vtk

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))

Out:

new surface colors
[[  0   0   0]
 [  0   0 255]
 [  0 255   0]
 [  0 255 255]
 [255   0   0]
 [255   0 255]
 [255 255   0]
 [255 255 255]]

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))

Total running time of the script: ( 0 minutes 0.114 seconds)