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 PolyData and show surfaces.

PolyData 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 fury

Import useful functions

Create an empty PolyData

my_polydata = fury.lib.PolyData()

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 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 PolyData

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

<vtkmodules.vtkCommonDataModel.vtkPolyData(0x14c0f8210) at 0x15f770040>

Save the PolyData

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

Surface saved in my_cube.vtk

Load the PolyData

cube_polydata = fury.io.load_polydata(file_name)

add color based on vertices position

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

print("new surface colors")
print(fury.utils.get_polydata_colors(cube_polydata))

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 Actor
cube_actor = fury.utils.get_actor_from_polydata(cube_polydata)

# Create a scene
scene = fury.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
# fury.window.show(scene, size=(600, 600), reset_camera=False)
fury.window.record(scene, out_path="cube.png", size=(600, 600))

/opt/homebrew/Caskroom/miniforge/base/envs/py39/lib/python3.9/site-packages/sphinx_gallery/gen_rst.py:722: UserWarning: We'll no longer accept the way you call the record function in future versions of FURY.

Here's how to call the Function record: record(scene='value', cam_pos='value', cam_focal='value', cam_view='value', out_path='value', path_numbering='value', n_frames='value', az_ang='value', magnification='value', size='value', reset_camera='value', screen_clip='value', stereo='value', verbose='value')

  exec(self.code, self.fake_main.__dict__)