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| """ | |
| 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) |
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