dipy has a problem calling fury

[zp1008611]

Description

When I use dipy, I found that the radial_scale parameter of actor.odf_slicer has some issues.

In the attached code, the last line uses actor.odf_slicer. When radial_scale is set to True, it doesn't raise an error, but when set to False, it does result in an error. And the member of dipy said This is a FURY issue.

Way to reproduce

Code example：

# %%
import numpy as np 
from dipy.sims.voxel import multi_tensor, multi_tensor_odf 
from dipy.data import get_sphere 
from dipy.core.sphere import disperse_charges, Sphere, HemiSphere 
from dipy.core.gradients import gradient_table 
from fury import window, actor 
from IPython.core.display import Image 
from PIL import Image as PILImage 

import os

# %%
# helper functions for visualization 
WINDOW_SIZE = (400,400)
SAVEIM_FOLDER = "images"
if not os.path.exists(SAVEIM_FOLDER): 
    os.mkdir(SAVEIM_FOLDER)
def screenshot_animated_sf(sf, sphere, rot=True, norm=True, scale=True, title='Modeling', theta_step=30):

    """
        Render a spherical function to file. Returns path to image.
    """
    scene = window.Scene() 
    scene.background(window.colors.white)
    sf_actor = actor.odf_slicer(sf[None, None, None,:], 
        sphere=sphere, colormap='jet', 
        norm=norm, radial_scale=scale)
    if rot: 
        scene.add(sf_actor)
        sf_actor.Rotatex(90)
    n_frames = 360//theta_step 
    images=[] 
    for i in np.arange(n_frames): 
        sf_actor.Rotatex(theta_step)
        scene.reset_clipping_range() 
        images.append(PILImage.fromarray(window.snapshot(scene, size=WINDOW_SIZE)))

    frame_duration = 15000 // theta_step
    filename = os.path.join(SAVEIM_FOLDER, '{0}.gif'.format(title))
    images[0].save(filename, save_all=True, append_images=images[1:], duration=frame_duration, optimize=False, loop=0)
    scene.clear()
    return filename

def screenshot_gradients(sph_gtab, title='Modeling'):
    scene = window.Scene()
    scene.background(window.colors.white)
    scene.add(actor.point(sph_gtab.vertices, window.colors.green, point_radius=0.05))
    outfile = os.path.join(SAVEIM_FOLDER, '{0}.png'.format(title))
    window.snapshot(scene, size=WINDOW_SIZE, fname=outfile)
    scene.clear()
    return outfile

# %% [markdown]
# ### Part 1 - Apparent diffusion coefficient and spherical harmonics Generating a gradient table

# %%
n_pts = 64
bvalue = 1000
theta = np.pi * np.random.rand(n_pts)
phi = 2 * np.pi * np.random.rand(n_pts)
hsph_initial = HemiSphere(theta=theta, phi=phi)
hsph_updated, potential = disperse_charges(hsph_initial, 5000)

vertices = hsph_updated.vertices
values = np.ones(vertices.shape[0])
bvecs = np.vstack((vertices))
bvals = np.hstack((bvalue * values)) 
#add some b=0 bvals/bvecs
bvecs = np.insert(bvecs, (0, bvecs.shape[0]), np.array([0, 0, 0]), axis=0)
bvals = np.insert(bvals, (0, bvals.shape[0]), 0)

gtab = gradient_table(bvals, bvecs)
sph_gtab = Sphere(xyz=np.vstack((vertices, -vertices)))
print('bvecs:\n', bvecs)
print('bvals:\n', bvals)

# %%
image = screenshot_gradients(sph_gtab, title='Example directions')
Image(filename=image)

# %% [markdown]
# #### Playing with different single and multi-tensor signal generation
# 

# %%
S0 = 100
SNR = 100
N = 2 # change this value to try other number of fibers
if N == 1:
    mevals = np.array([[0.0015, 0.0004, 0.0004]])
    angles = [(0, 0)]
    fractions = [100]
elif N == 2:
    separation_angle = 90 # play with this parameter to change the angle between fibers
    mevals = np.array([[0.0015, 0.0004, 0.0004],
                        [0.0015, 0.0004, 0.0004]])
    angles = [(0, 0), (separation_angle, 0)]
    fractions = [50, 50]
elif N == 3:
    mevals = np.array([[0.0015, 0.0004, 0.0004],
                        [0.0004, 0.0015, 0.0004], 
                        [0.0004, 0.0004, 0.0015]])
    angles = [(0, 0), (90, 0), (0, 90)]
    fractions = [33, 33, 34]
else:
    raise ValueError('Invalid number of fibers.')
signal, sticks = multi_tensor(gtab, mevals, S0 = S0, angles = angles,
                               fractions = fractions, snr = SNR)
print(signal)

# %%
# we generate an antipodally symmetric spherical function from our signal
signal_sph = np.zeros(vertices.shape[0]*2)
signal_sph[0:vertices.shape[0]] = signal[1:-1]
signal_sph[vertices.shape[0]:] = signal[1:-1]

actor.odf_slicer(signal_sph[None, None, None,:], sphere=sph_gtab, colormap='jet', norm=False, radial_scale=False,)

error png

python version

python 3.9.10

dipy version

1.9.0

fury version

0.11.0

[skoudoro]

Hi @zp1008611,

Thank you for this. This is due to the new VTK.

to fix this issue, downgrade your VTK version and make sure that vtk<=9.3.1

We will release FURY to make sure this is the correct vtk version

Thank for your feedback