garyfallidis / dipy Goto Github PK

Memory consumption is easily > 500Mbytes. Why? Datasets are much less than that. We need to think of that.

T = [downsample(t, 18) - np.array(data.shape[:3]) / 2. for t in T]
axis = np.array([1, 0, 0])
theta = - 90.
T = np.dot(T,rotation_matrix(axis, theta))
axis = np.array([0, 1, 0])
theta = 180.
T = np.dot(T, rotation_matrix(axis, theta))

qb=QuickBundles(T, 10., None)
#save_pickle(fpkl,qb)
#qb=load_pickle(fpkl)

#create the interaction system for tracks 
tl = StreamlineLabeler('Bundle Picker', qb, qb.downsampled_tracks(), vol_shape=None, tracks_alpha=1)   

--> 59 tl = StreamlineLabeler('Bundle Picker', qb, qb.downsampled_tracks(), vol_shape=None, tracks_alpha=1)
60
61 title = 'Streamline Interaction and Segmentation'

/home/bao/dipy/dipy/viz/fos/streamshow.pyc in init(self, name, qb, tracks, reps, colors, vol_shape, virtuals_line_width, tracks_line_width, virtuals_alpha, tracks_alpha, affine, verbose)

/home/bao/dipy/dipy/viz/fos/streamshow.pyc in compute_buffers(self, tracks, alpha)

/home/bao/dipy/dipy/viz/fos/streamshow.pyc in compute_colors(self, tracks, alpha)

AssertionError:

Greetings, all.

It looks like from some discussions here, the API is currently being revamped a bit. I'm running into some issues getting the imports right between the online examples and the ones provided in /doc/examples. My knowledge of DIPY is limited, but trying to rectify the issues myself for the most past.

What version of Mayavi is supported? Using 5.x, I get the exception that Mayavi is not installed. Using 4.2.0, I get the following error in nii_2_tracks.py:

Traceback (most recent call last):
File "doc/examples/nii_2_tracks.py", line 174, in
from dipy.viz import fvtk
File "/usr/local/lib/python2.7/dist-packages/dipy/viz/init.py", line 30, in
from .mayavi.spheres import show_odfs
ImportError: No module named mayavi.spheres

Am I using an incompatible version of Mayavi? Thank you.

Whoops - too many tabs open. Posted this in a fork. Please disregard.

Appears to be a known issue already open in main branch: dipy#125