Visualize surfacesΒΆ

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 fury import window, utils
from fury.io import save_polydata, load_polydata
from fury.utils import 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

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

Save the vtkPolyData

file_name = "my_cube.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 = load_polydata(file_name)

add color based on vertices position

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

print("new surface colors")
print(utils.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 = utils.get_actor_from_polydata(cube_polydata)

# Create a scene
scene = window.Scene()
scene.add(cube_actor)
scene.set_camera(position=(10, 5, 7), focal_point=(0.5, 0.5, 0.5))
scene.zoom(3)

# display
# window.show(scene, size=(600, 600), reset_camera=False)
window.record(scene, out_path='cube.png', size=(600, 600))
../_images/sphx_glr_viz_surfaces_001.png

Total running time of the script: ( 0 minutes 0.489 seconds)

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