brain_mayavi.py

"""
Animation of a head slicing.

Based on a BSD-like licenced code by Gael Varoquaux
http://docs.enthought.com/mayavi/mayavi/auto/example_mri.html

Result:
http://i.imgur.com/EJZELfi.gif
"""

from urllib import urlretrieve # to download the data
import tarfile # to uncompress the data
import numpy as np # to load the data
from mayavi import mlab # to plot the data
import moviepy.editor as mpy # to animate the data

# DOWNLOAD THE DATA AND LOAD IT IN THE RAM

name = "MRbrain.tar.gz"
urlretrieve("http://graphics.stanford.edu/data/voldata/"+name, name)

with tarfile.open(name) as f:
    data = np.array([np.fromstring(f.extractfile('MRbrain.%d'%i).read(),
                     dtype='>u2') for i in range(1, 110)])
data.shape = (109, 256, 256)
data = data.T

# MAKE THE FIGURE

fig = mlab.figure(bgcolor=(0, 0, 0), size=(250, 250))
src = mlab.pipeline.scalar_field(data)
src.spacing = [1, 1, 1.5]
src.update_image_data = True

blur = mlab.pipeline.user_defined(src, filter='ImageGaussianSmooth')
voi = mlab.pipeline.extract_grid(blur)
voi.set(x_min=125, x_max=193, y_min=92, y_max=125, z_min=34, z_max=75)

mlab.pipeline.iso_surface(voi, contours=[1610, 2480], colormap='Spectral')

thr = mlab.pipeline.threshold(src, low=1120)
plane = mlab.pipeline.scalar_cut_plane(thr, vmin=1400, vmax=2600,
                    plane_orientation='y_axes', colormap='black-white')
plane.implicit_plane.widget.enabled = False

voi = mlab.pipeline.extract_grid(src)
outer = mlab.pipeline.iso_surface(voi, contours=[1776,],color=(.8,.7,.6))

mlab.view(-125, 54, 326, (145.5, 138, 66.5))
mlab.roll(-175)

# ANIMATE WITH MOVIEPY

def make_frame(t):
    fig.scene.disable_render = True
    new_y = 50+12.5*t
    plane.implicit_plane.origin = (136, new_y+0.5, 82)
    voi.set(y_min=new_y)
    fig.scene.disable_render = False
    return mlab.screenshot(antialiased=True)

clip = mpy.VideoClip(make_frame, duration=6)
clip.write_gif('brain.gif', fps=10)

I find that my jupyter notebook will die at this statement:

blur = mlab.pipeline.user_defined(src, filter='ImageGaussianSmooth')
voi = mlab.pipeline.extract_grid(blur)

When I run this script via terminal, I will get those ERRORs:

ERROR: In /home/travis/miniconda/conda-bld/work/VTK-7.0.0/Common/ExecutionModel/vtkStreamingDemandDrivenPipeline.cxx, line 857
vtkCompositeDataPipeline (0x3bd5a70): The update extent specified in the information for output port 0 on algorithm vtkImageGaussianSmooth(0x3bb1620) is 0 2147483647 0 2147483647 0 2147483647, which is outside the whole extent 0 255 0 255 0 108.

ERROR: In /home/travis/miniconda/conda-bld/work/VTK-7.0.0/Common/Core/vtkDataArrayTemplate.txx, line 142
vtkUnsignedShortArray (0x7fbf4c381d20): Unable to allocate 6917529022809243648 elements of size 2 bytes. 

terminate called after throwing an instance of 'std::bad_alloc'
  what():  std::bad_alloc
Aborted (core dumped)
``
Can you tell me how to fix those probelm.

I get those ERRORs too,Do you know how to fix those probelms now?

@577528249 @Thatfreesky
blur = mlab.pipeline.user_defined(src, filter='ImageGaussianSmooth')
voi = mlab.pipeline.extract_grid(blur)
just change it to this "voi = mlab.pipeline.extract_grid(src)"and then it will display, although it says the error "./Common/ExecutionModel/vtkStreamingDemandDrivenPipeline.cxx"

I tried it several times. It's ok.

I'm getting this:
ImportError: Could not import backend for traits

Im using ubuntu and virtualenv, any suggestions on how to fix this? I googled, but none of the suggestions worked?